Starting phenix.real_space_refine (version: dev) on Sat May 14 19:15:01 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x9o_22106/05_2022/6x9o_22106.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x9o_22106/05_2022/6x9o_22106.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x9o_22106/05_2022/6x9o_22106.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x9o_22106/05_2022/6x9o_22106.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x9o_22106/05_2022/6x9o_22106.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x9o_22106/05_2022/6x9o_22106.pdb" } resolution = 2.6 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 ------------------------------------------------------------------------------- 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= 0.004 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 20899 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 19063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2425, 19063 Classifications: {'peptide': 2425} Link IDs: {'PTRANS': 109, 'TRANS': 2315} Chain breaks: 18 Chain: "B" Number of atoms: 1836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1836 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 15, 'TRANS': 228} Chain breaks: 2 Time building chain proxies: 11.91, per 1000 atoms: 0.57 Number of scatterers: 20899 At special positions: 0 Unit cell: (139.74, 151.248, 123.3, 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 130 16.00 O 3787 8.00 N 3603 7.00 C 13379 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 105 " - pdb=" SG CYS A 137 " distance=2.07 Simple disulfide: pdb=" SG CYS A 109 " - pdb=" SG CYS A 152 " distance=2.07 Simple disulfide: pdb=" SG CYS A 774 " - pdb=" SG CYS A 809 " distance=2.05 Simple disulfide: pdb=" SG CYS A1049 " - pdb=" SG CYS A1064 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.28 Conformation dependent library (CDL) restraints added in 3.0 seconds 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5108 Finding SS restraints... Secondary structure from input PDB file: 153 helices and 0 sheets defined 75.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.80 Creating SS restraints... Processing helix chain 'A' and resid 98 through 112 removed outlier: 4.910A pdb=" N CYS A 109 " --> pdb=" O CYS A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 135 removed outlier: 3.932A pdb=" N GLN A 124 " --> pdb=" O SER A 120 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LYS A 125 " --> pdb=" O PRO A 121 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N LEU A 126 " --> pdb=" O GLU A 122 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE A 129 " --> pdb=" O LYS A 125 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLU A 132 " --> pdb=" O GLY A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 140 removed outlier: 3.839A pdb=" N ASP A 140 " --> pdb=" O CYS A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 160 removed outlier: 4.094A pdb=" N ALA A 149 " --> pdb=" O VAL A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 178 Proline residue: A 166 - end of helix removed outlier: 3.558A pdb=" N GLU A 175 " --> pdb=" O GLU A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 194 Processing helix chain 'A' and resid 195 through 199 Processing helix chain 'A' and resid 203 through 220 Proline residue: A 213 - end of helix Processing helix chain 'A' and resid 223 through 242 Proline residue: A 235 - end of helix removed outlier: 3.641A pdb=" N SER A 240 " --> pdb=" O LYS A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 245 No H-bonds generated for 'chain 'A' and resid 243 through 245' Processing helix chain 'A' and resid 246 through 259 removed outlier: 3.649A pdb=" N ALA A 259 " --> pdb=" O LYS A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 263 Processing helix chain 'A' and resid 265 through 282 Processing helix chain 'A' and resid 285 through 300 Processing helix chain 'A' and resid 310 through 324 Processing helix chain 'A' and resid 325 through 327 No H-bonds generated for 'chain 'A' and resid 325 through 327' Processing helix chain 'A' and resid 352 through 367 Processing helix chain 'A' and resid 371 through 388 Processing helix chain 'A' and resid 390 through 399 removed outlier: 3.677A pdb=" N GLN A 395 " --> pdb=" O PRO A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 406 removed outlier: 3.615A pdb=" N GLY A 404 " --> pdb=" O GLY A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 695 removed outlier: 3.840A pdb=" N HIS A 685 " --> pdb=" O ALA A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 728 removed outlier: 3.747A pdb=" N LEU A 727 " --> pdb=" O ALA A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 734 Processing helix chain 'A' and resid 751 through 761 removed outlier: 3.685A pdb=" N ASP A 760 " --> pdb=" O ASN A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 785 Processing helix chain 'A' and resid 788 through 800 Processing helix chain 'A' and resid 805 through 808 Processing helix chain 'A' and resid 809 through 818 Processing helix chain 'A' and resid 821 through 841 removed outlier: 5.249A pdb=" N MET A 837 " --> pdb=" O ARG A 833 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N SER A 838 " --> pdb=" O ASN A 834 " (cutoff:3.500A) Processing helix chain 'A' and resid 844 through 856 removed outlier: 3.637A pdb=" N LEU A 856 " --> pdb=" O ILE A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 861 removed outlier: 3.615A pdb=" N ASN A 860 " --> pdb=" O THR A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 876 removed outlier: 3.607A pdb=" N GLU A 876 " --> pdb=" O GLU A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 889 Processing helix chain 'A' and resid 895 through 899 removed outlier: 4.197A pdb=" N HIS A 898 " --> pdb=" O GLY A 895 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N TYR A 899 " --> pdb=" O ALA A 896 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 895 through 899' Processing helix chain 'A' and resid 904 through 913 Processing helix chain 'A' and resid 915 through 920 Processing helix chain 'A' and resid 922 through 937 Processing helix chain 'A' and resid 938 through 940 No H-bonds generated for 'chain 'A' and resid 938 through 940' Processing helix chain 'A' and resid 950 through 964 removed outlier: 4.121A pdb=" N VAL A 962 " --> pdb=" O ASP A 958 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TYR A 963 " --> pdb=" O GLN A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1017 Processing helix chain 'A' and resid 1020 through 1038 Processing helix chain 'A' and resid 1066 through 1077 Processing helix chain 'A' and resid 1080 through 1083 Processing helix chain 'A' and resid 1084 through 1101 Processing helix chain 'A' and resid 1102 through 1106 removed outlier: 4.131A pdb=" N LYS A1105 " --> pdb=" O SER A1102 " (cutoff:3.500A) Processing helix chain 'A' and resid 1136 through 1159 Processing helix chain 'A' and resid 1235 through 1253 Processing helix chain 'A' and resid 1263 through 1280 Processing helix chain 'A' and resid 1281 through 1283 No H-bonds generated for 'chain 'A' and resid 1281 through 1283' Processing helix chain 'A' and resid 1284 through 1289 Processing helix chain 'A' and resid 1291 through 1303 removed outlier: 3.676A pdb=" N SER A1301 " --> pdb=" O GLY A1297 " (cutoff:3.500A) Processing helix chain 'A' and resid 1306 through 1322 Processing helix chain 'A' and resid 1361 through 1375 Processing helix chain 'A' and resid 1376 through 1377 No H-bonds generated for 'chain 'A' and resid 1376 through 1377' Processing helix chain 'A' and resid 1423 through 1426 Processing helix chain 'A' and resid 1427 through 1441 Processing helix chain 'A' and resid 1443 through 1460 Processing helix chain 'A' and resid 1463 through 1468 removed outlier: 3.891A pdb=" N LEU A1467 " --> pdb=" O ASN A1463 " (cutoff:3.500A) Processing helix chain 'A' and resid 1471 through 1487 removed outlier: 3.687A pdb=" N PHE A1481 " --> pdb=" O VAL A1477 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLU A1482 " --> pdb=" O LEU A1478 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N TYR A1483 " --> pdb=" O LYS A1479 " (cutoff:3.500A) Processing helix chain 'A' and resid 1495 through 1509 removed outlier: 3.680A pdb=" N TYR A1508 " --> pdb=" O VAL A1504 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU A1509 " --> pdb=" O LEU A1505 " (cutoff:3.500A) Processing helix chain 'A' and resid 1518 through 1532 Processing helix chain 'A' and resid 1539 through 1553 Proline residue: A1546 - end of helix Processing helix chain 'A' and resid 1564 through 1580 removed outlier: 3.668A pdb=" N THR A1568 " --> pdb=" O LYS A1564 " (cutoff:3.500A) Processing helix chain 'A' and resid 1583 through 1601 removed outlier: 3.874A pdb=" N LYS A1599 " --> pdb=" O GLN A1595 " (cutoff:3.500A) Processing helix chain 'A' and resid 1603 through 1623 removed outlier: 3.556A pdb=" N ILE A1615 " --> pdb=" O GLN A1611 " (cutoff:3.500A) Proline residue: A1618 - end of helix Processing helix chain 'A' and resid 1629 through 1643 Processing helix chain 'A' and resid 1644 through 1649 Processing helix chain 'A' and resid 1651 through 1659 Processing helix chain 'A' and resid 1667 through 1689 Processing helix chain 'A' and resid 1690 through 1701 Processing helix chain 'A' and resid 1704 through 1708 removed outlier: 3.998A pdb=" N ILE A1708 " --> pdb=" O PRO A1705 " (cutoff:3.500A) Processing helix chain 'A' and resid 1709 through 1718 removed outlier: 3.764A pdb=" N ASP A1718 " --> pdb=" O ASN A1714 " (cutoff:3.500A) Processing helix chain 'A' and resid 1737 through 1759 Processing helix chain 'A' and resid 1767 through 1791 Processing helix chain 'A' and resid 1794 through 1806 removed outlier: 3.544A pdb=" N ARG A1806 " --> pdb=" O THR A1802 " (cutoff:3.500A) Processing helix chain 'A' and resid 1816 through 1826 removed outlier: 3.638A pdb=" N SER A1826 " --> pdb=" O LEU A1822 " (cutoff:3.500A) Processing helix chain 'A' and resid 1831 through 1845 Processing helix chain 'A' and resid 1852 through 1857 Processing helix chain 'A' and resid 1890 through 1911 removed outlier: 3.615A pdb=" N GLN A1910 " --> pdb=" O ASP A1906 " (cutoff:3.500A) Processing helix chain 'A' and resid 1915 through 1932 removed outlier: 7.032A pdb=" N GLN A1927 " --> pdb=" O VAL A1923 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ASP A1928 " --> pdb=" O ASN A1924 " (cutoff:3.500A) Processing helix chain 'A' and resid 1935 through 1947 Processing helix chain 'A' and resid 1948 through 1961 Processing helix chain 'A' and resid 1968 through 1981 removed outlier: 4.632A pdb=" N GLY A1981 " --> pdb=" O GLN A1977 " (cutoff:3.500A) Processing helix chain 'A' and resid 1983 through 1987 Processing helix chain 'A' and resid 1988 through 1997 Processing helix chain 'A' and resid 2003 through 2024 Processing helix chain 'A' and resid 2025 through 2033 removed outlier: 3.873A pdb=" N ALA A2031 " --> pdb=" O GLN A2027 " (cutoff:3.500A) Processing helix chain 'A' and resid 2034 through 2048 removed outlier: 3.598A pdb=" N LEU A2038 " --> pdb=" O PRO A2034 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASN A2039 " --> pdb=" O MET A2035 " (cutoff:3.500A) Processing helix chain 'A' and resid 2049 through 2054 removed outlier: 3.634A pdb=" N ARG A2053 " --> pdb=" O GLY A2049 " (cutoff:3.500A) Processing helix chain 'A' and resid 2054 through 2069 removed outlier: 3.677A pdb=" N TYR A2058 " --> pdb=" O HIS A2054 " (cutoff:3.500A) Processing helix chain 'A' and resid 2098 through 2111 removed outlier: 3.626A pdb=" N GLN A2109 " --> pdb=" O LEU A2105 " (cutoff:3.500A) Processing helix chain 'A' and resid 2117 through 2126 Processing helix chain 'A' and resid 2129 through 2133 removed outlier: 3.659A pdb=" N MET A2133 " --> pdb=" O ALA A2130 " (cutoff:3.500A) Processing helix chain 'A' and resid 2143 through 2145 No H-bonds generated for 'chain 'A' and resid 2143 through 2145' Processing helix chain 'A' and resid 2146 through 2159 Processing helix chain 'A' and resid 2164 through 2184 removed outlier: 3.639A pdb=" N GLN A2184 " --> pdb=" O GLY A2180 " (cutoff:3.500A) Processing helix chain 'A' and resid 2202 through 2211 removed outlier: 3.961A pdb=" N PHE A2211 " --> pdb=" O LEU A2207 " (cutoff:3.500A) Processing helix chain 'A' and resid 2216 through 2218 No H-bonds generated for 'chain 'A' and resid 2216 through 2218' Processing helix chain 'A' and resid 2219 through 2232 removed outlier: 3.607A pdb=" N ALA A2226 " --> pdb=" O THR A2222 " (cutoff:3.500A) Processing helix chain 'A' and resid 2233 through 2237 removed outlier: 3.875A pdb=" N LEU A2237 " --> pdb=" O VAL A2234 " (cutoff:3.500A) Processing helix chain 'A' and resid 2238 through 2242 Processing helix chain 'A' and resid 2246 through 2269 removed outlier: 4.620A pdb=" N ASP A2250 " --> pdb=" O GLU A2246 " (cutoff:3.500A) Processing helix chain 'A' and resid 2273 through 2288 Processing helix chain 'A' and resid 2290 through 2298 removed outlier: 3.599A pdb=" N VAL A2296 " --> pdb=" O GLY A2292 " (cutoff:3.500A) Processing helix chain 'A' and resid 2302 through 2322 Processing helix chain 'A' and resid 2355 through 2371 removed outlier: 3.709A pdb=" N THR A2359 " --> pdb=" O PRO A2355 " (cutoff:3.500A) Processing helix chain 'A' and resid 2380 through 2384 removed outlier: 4.222A pdb=" N SER A2384 " --> pdb=" O LYS A2381 " (cutoff:3.500A) Processing helix chain 'A' and resid 2390 through 2403 Processing helix chain 'A' and resid 2404 through 2412 removed outlier: 4.626A pdb=" N SER A2409 " --> pdb=" O PRO A2405 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N TYR A2410 " --> pdb=" O LEU A2406 " (cutoff:3.500A) Processing helix chain 'A' and resid 2414 through 2420 removed outlier: 3.616A pdb=" N TRP A2418 " --> pdb=" O PRO A2414 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU A2420 " --> pdb=" O LEU A2416 " (cutoff:3.500A) Processing helix chain 'A' and resid 2438 through 2442 Processing helix chain 'A' and resid 2444 through 2459 Processing helix chain 'A' and resid 2462 through 2478 Processing helix chain 'A' and resid 2499 through 2515 removed outlier: 3.798A pdb=" N ALA A2515 " --> pdb=" O LEU A2511 " (cutoff:3.500A) Processing helix chain 'A' and resid 2544 through 2565 removed outlier: 3.632A pdb=" N LYS A2548 " --> pdb=" O ARG A2544 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE A2551 " --> pdb=" O ARG A2547 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL A2556 " --> pdb=" O ILE A2552 " (cutoff:3.500A) Processing helix chain 'A' and resid 2595 through 2599 Processing helix chain 'A' and resid 2620 through 2628 removed outlier: 3.554A pdb=" N ASN A2628 " --> pdb=" O VAL A2624 " (cutoff:3.500A) Processing helix chain 'A' and resid 2669 through 2683 removed outlier: 3.759A pdb=" N CYS A2673 " --> pdb=" O ASP A2669 " (cutoff:3.500A) Processing helix chain 'A' and resid 2695 through 2710 removed outlier: 3.799A pdb=" N GLU A2701 " --> pdb=" O ILE A2697 " (cutoff:3.500A) Processing helix chain 'A' and resid 2715 through 2733 removed outlier: 3.708A pdb=" N PHE A2719 " --> pdb=" O GLU A2715 " (cutoff:3.500A) Processing helix chain 'A' and resid 2740 through 2755 Proline residue: A2746 - end of helix Processing helix chain 'A' and resid 2764 through 2774 removed outlier: 4.405A pdb=" N LEU A2768 " --> pdb=" O PRO A2764 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG A2774 " --> pdb=" O GLU A2770 " (cutoff:3.500A) Processing helix chain 'A' and resid 2777 through 2793 removed outlier: 4.176A pdb=" N ARG A2781 " --> pdb=" O HIS A2777 " (cutoff:3.500A) Processing helix chain 'A' and resid 2803 through 2819 removed outlier: 3.702A pdb=" N TYR A2811 " --> pdb=" O VAL A2807 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS A2817 " --> pdb=" O LEU A2813 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLY A2818 " --> pdb=" O SER A2814 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ILE A2819 " --> pdb=" O ASN A2815 " (cutoff:3.500A) Processing helix chain 'A' and resid 2827 through 2845 Processing helix chain 'A' and resid 2855 through 2866 removed outlier: 3.574A pdb=" N GLN A2859 " --> pdb=" O ALA A2855 " (cutoff:3.500A) Processing helix chain 'A' and resid 2873 through 2890 Processing helix chain 'A' and resid 2898 through 2903 Processing helix chain 'A' and resid 2913 through 2931 Processing helix chain 'A' and resid 2954 through 2970 Processing helix chain 'A' and resid 2971 through 2990 Proline residue: A2983 - end of helix removed outlier: 3.501A pdb=" N PHE A2990 " --> pdb=" O LEU A2986 " (cutoff:3.500A) Processing helix chain 'A' and resid 2991 through 2994 Processing helix chain 'A' and resid 2995 through 3004 removed outlier: 3.618A pdb=" N ILE A3000 " --> pdb=" O MET A2996 " (cutoff:3.500A) Processing helix chain 'A' and resid 3010 through 3026 removed outlier: 3.547A pdb=" N MET A3014 " --> pdb=" O TYR A3010 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N THR A3016 " --> pdb=" O GLN A3012 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N HIS A3026 " --> pdb=" O PHE A3022 " (cutoff:3.500A) Processing helix chain 'A' and resid 3032 through 3040 Processing helix chain 'A' and resid 3050 through 3065 Processing helix chain 'A' and resid 3071 through 3073 No H-bonds generated for 'chain 'A' and resid 3071 through 3073' Processing helix chain 'A' and resid 3074 through 3080 Processing helix chain 'A' and resid 3086 through 3103 removed outlier: 3.613A pdb=" N HIS A3103 " --> pdb=" O ASP A3099 " (cutoff:3.500A) Processing helix chain 'A' and resid 3107 through 3119 removed outlier: 4.044A pdb=" N VAL A3117 " --> pdb=" O ALA A3113 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU A3118 " --> pdb=" O PHE A3114 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU A3119 " --> pdb=" O GLN A3115 " (cutoff:3.500A) Processing helix chain 'A' and resid 3120 through 3122 No H-bonds generated for 'chain 'A' and resid 3120 through 3122' Processing helix chain 'A' and resid 3128 through 3138 Processing helix chain 'B' and resid 84 through 106 removed outlier: 3.559A pdb=" N LEU B 96 " --> pdb=" O GLU B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 136 Processing helix chain 'B' and resid 137 through 155 Processing helix chain 'B' and resid 157 through 173 Processing helix chain 'B' and resid 176 through 194 Processing helix chain 'B' and resid 196 through 215 Processing helix chain 'B' and resid 260 through 281 removed outlier: 3.565A pdb=" N ASP B 264 " --> pdb=" O GLY B 260 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL B 265 " --> pdb=" O ALA B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 298 removed outlier: 3.728A pdb=" N LYS B 297 " --> pdb=" O GLN B 293 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TYR B 298 " --> pdb=" O THR B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 331 Processing helix chain 'B' and resid 333 through 345 Processing helix chain 'B' and resid 349 through 365 1322 hydrogen bonds defined for protein. 3846 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: 8.62 Time building geometry restraints manager: 9.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3867 1.33 - 1.45: 4919 1.45 - 1.57: 12328 1.57 - 1.69: 0 1.69 - 1.82: 190 Bond restraints: 21304 Sorted by residual: bond pdb=" C LEU A2982 " pdb=" N PRO A2983 " ideal model delta sigma weight residual 1.335 1.389 -0.054 1.38e-02 5.25e+03 1.56e+01 bond pdb=" C GLN A1447 " pdb=" N LYS A1448 " ideal model delta sigma weight residual 1.335 1.383 -0.049 1.31e-02 5.83e+03 1.38e+01 bond pdb=" N GLN A2270 " pdb=" CA GLN A2270 " ideal model delta sigma weight residual 1.457 1.503 -0.045 1.29e-02 6.01e+03 1.23e+01 bond pdb=" N CYS A1049 " pdb=" CA CYS A1049 " ideal model delta sigma weight residual 1.458 1.524 -0.066 1.90e-02 2.77e+03 1.21e+01 bond pdb=" N ILE A2995 " pdb=" CA ILE A2995 " ideal model delta sigma weight residual 1.460 1.490 -0.030 8.60e-03 1.35e+04 1.21e+01 ... (remaining 21299 not shown) Histogram of bond angle deviations from ideal: 98.68 - 105.81: 477 105.81 - 112.95: 11955 112.95 - 120.09: 7892 120.09 - 127.23: 8356 127.23 - 134.37: 254 Bond angle restraints: 28934 Sorted by residual: angle pdb=" N THR A 310 " pdb=" CA THR A 310 " pdb=" C THR A 310 " ideal model delta sigma weight residual 113.88 103.10 10.78 1.23e+00 6.61e-01 7.68e+01 angle pdb=" CA PRO A1936 " pdb=" C PRO A1936 " pdb=" N PRO A1937 " ideal model delta sigma weight residual 117.93 125.23 -7.30 1.20e+00 6.94e-01 3.70e+01 angle pdb=" N VAL A1066 " pdb=" CA VAL A1066 " pdb=" C VAL A1066 " ideal model delta sigma weight residual 111.58 105.65 5.93 1.06e+00 8.90e-01 3.13e+01 angle pdb=" N LEU A 106 " pdb=" CA LEU A 106 " pdb=" C LEU A 106 " ideal model delta sigma weight residual 113.43 106.80 6.63 1.26e+00 6.30e-01 2.77e+01 angle pdb=" N LEU A 153 " pdb=" CA LEU A 153 " pdb=" C LEU A 153 " ideal model delta sigma weight residual 111.07 105.51 5.56 1.07e+00 8.73e-01 2.70e+01 ... (remaining 28929 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 11571 17.92 - 35.84: 1053 35.84 - 53.75: 250 53.75 - 71.67: 52 71.67 - 89.59: 33 Dihedral angle restraints: 12959 sinusoidal: 5141 harmonic: 7818 Sorted by residual: dihedral pdb=" CB CYS A 109 " pdb=" SG CYS A 109 " pdb=" SG CYS A 152 " pdb=" CB CYS A 152 " ideal model delta sinusoidal sigma weight residual -86.00 -28.45 -57.55 1 1.00e+01 1.00e-02 4.45e+01 dihedral pdb=" C ASP A1468 " pdb=" N ASP A1468 " pdb=" CA ASP A1468 " pdb=" CB ASP A1468 " ideal model delta harmonic sigma weight residual -122.60 -135.04 12.44 0 2.50e+00 1.60e-01 2.48e+01 dihedral pdb=" CA GLN A1761 " pdb=" C GLN A1761 " pdb=" N LEU A1762 " pdb=" CA LEU A1762 " ideal model delta harmonic sigma weight residual -180.00 -156.38 -23.62 0 5.00e+00 4.00e-02 2.23e+01 ... (remaining 12956 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 3067 0.073 - 0.147: 297 0.147 - 0.220: 71 0.220 - 0.293: 11 0.293 - 0.366: 4 Chirality restraints: 3450 Sorted by residual: chirality pdb=" CA LEU A 940 " pdb=" N LEU A 940 " pdb=" C LEU A 940 " pdb=" CB LEU A 940 " both_signs ideal model delta sigma weight residual False 2.51 2.88 -0.37 2.00e-01 2.50e+01 3.36e+00 chirality pdb=" CA ASP A1468 " pdb=" N ASP A1468 " pdb=" C ASP A1468 " pdb=" CB ASP A1468 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.35e+00 chirality pdb=" CB VAL A3121 " pdb=" CA VAL A3121 " pdb=" CG1 VAL A3121 " pdb=" CG2 VAL A3121 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.29e+00 ... (remaining 3447 not shown) Planarity restraints: 3650 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A2267 " 0.017 2.00e-02 2.50e+03 3.48e-02 1.21e+01 pdb=" C ILE A2267 " -0.060 2.00e-02 2.50e+03 pdb=" O ILE A2267 " 0.022 2.00e-02 2.50e+03 pdb=" N HIS A2268 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A1064 " -0.014 2.00e-02 2.50e+03 2.95e-02 8.69e+00 pdb=" C CYS A1064 " 0.051 2.00e-02 2.50e+03 pdb=" O CYS A1064 " -0.019 2.00e-02 2.50e+03 pdb=" N THR A1065 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A2521 " -0.012 2.00e-02 2.50e+03 2.48e-02 6.14e+00 pdb=" C ALA A2521 " 0.043 2.00e-02 2.50e+03 pdb=" O ALA A2521 " -0.016 2.00e-02 2.50e+03 pdb=" N GLY A2522 " -0.015 2.00e-02 2.50e+03 ... (remaining 3647 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 115 2.54 - 3.13: 16700 3.13 - 3.72: 34129 3.72 - 4.31: 48871 4.31 - 4.90: 78552 Nonbonded interactions: 178367 Sorted by model distance: nonbonded pdb=" O ASN A2628 " pdb=" OD1 ASN A2628 " model vdw 1.953 3.040 nonbonded pdb=" OH TYR A2614 " pdb=" OD2 ASP A2711 " model vdw 2.202 2.440 nonbonded pdb=" O LEU A1617 " pdb=" OG SER A1657 " model vdw 2.212 2.440 nonbonded pdb=" OG1 THR A2300 " pdb=" OD2 ASP A2429 " model vdw 2.226 2.440 nonbonded pdb=" O ASP A1628 " pdb=" OD1 ASP A1628 " model vdw 2.231 3.040 ... (remaining 178362 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 130 5.16 5 C 13379 2.51 5 N 3603 2.21 5 O 3787 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 4.000 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: 20.210 Check model and map are aligned: 0.370 Convert atoms to be neutral: 0.160 Process input model: 56.540 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 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 : 0.006 0.066 21304 Z= 0.384 Angle : 0.808 10.776 28934 Z= 0.521 Chirality : 0.053 0.366 3450 Planarity : 0.005 0.051 3650 Dihedral : 15.456 89.588 7839 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.29 % Favored : 93.41 % Rotamer Outliers : 0.56 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.15), residues: 2625 helix: -0.90 (0.11), residues: 1854 sheet: None (None), residues: 0 loop : -2.35 (0.21), residues: 771 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2329 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 424 time to evaluate : 2.439 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 4 residues processed: 433 average time/residue: 1.4002 time to fit residues: 686.5702 Evaluate side-chains 239 residues out of total 2329 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 235 time to evaluate : 2.462 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 3.3664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 224 optimal weight: 0.9980 chunk 201 optimal weight: 2.9990 chunk 111 optimal weight: 0.2980 chunk 68 optimal weight: 0.9990 chunk 135 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 208 optimal weight: 0.8980 chunk 80 optimal weight: 0.4980 chunk 126 optimal weight: 2.9990 chunk 155 optimal weight: 0.8980 chunk 241 optimal weight: 7.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 169 GLN A 366 HIS A 898 HIS A 906 GLN A1539 HIS A1596 GLN A1630 HIS A1637 ASN A1847 HIS A1892 ASN A2054 HIS A2134 ASN A2139 ASN A2189 HIS A2305 HIS A2383 ASN A2628 ASN A2671 HIS B 106 GLN B 164 HIS B 291 HIS B 323 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 21304 Z= 0.244 Angle : 0.624 9.772 28934 Z= 0.315 Chirality : 0.040 0.168 3450 Planarity : 0.005 0.081 3650 Dihedral : 4.734 23.351 2853 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.07 % Favored : 94.78 % Rotamer Outliers : 3.13 % 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: -0.02 (0.16), residues: 2625 helix: 0.69 (0.12), residues: 1861 sheet: None (None), residues: 0 loop : -1.66 (0.23), residues: 764 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2329 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 263 time to evaluate : 2.730 Fit side-chains outliers start: 73 outliers final: 16 residues processed: 312 average time/residue: 1.2847 time to fit residues: 462.6007 Evaluate side-chains 248 residues out of total 2329 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 232 time to evaluate : 2.581 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 10 residues processed: 6 average time/residue: 0.4512 time to fit residues: 7.3472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 134 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 chunk 201 optimal weight: 7.9990 chunk 164 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 241 optimal weight: 5.9990 chunk 261 optimal weight: 0.5980 chunk 215 optimal weight: 3.9990 chunk 239 optimal weight: 5.9990 chunk 82 optimal weight: 0.9980 chunk 194 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 GLN A1278 GLN A2139 ASN A2218 GLN A2443 GLN A2499 GLN A2671 HIS ** A2733 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2993 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.052 21304 Z= 0.300 Angle : 0.615 10.257 28934 Z= 0.309 Chirality : 0.041 0.149 3450 Planarity : 0.005 0.092 3650 Dihedral : 4.626 21.628 2853 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.91 % Favored : 94.93 % Rotamer Outliers : 3.13 % 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: 0.59 (0.17), residues: 2625 helix: 1.11 (0.12), residues: 1877 sheet: None (None), residues: 0 loop : -1.41 (0.23), residues: 748 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2329 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 256 time to evaluate : 2.570 Fit side-chains outliers start: 73 outliers final: 26 residues processed: 303 average time/residue: 1.2806 time to fit residues: 449.5734 Evaluate side-chains 253 residues out of total 2329 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 227 time to evaluate : 2.518 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 16 residues processed: 11 average time/residue: 0.6011 time to fit residues: 11.8951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 239 optimal weight: 9.9990 chunk 181 optimal weight: 2.9990 chunk 125 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 chunk 115 optimal weight: 3.9990 chunk 162 optimal weight: 0.7980 chunk 242 optimal weight: 2.9990 chunk 257 optimal weight: 0.8980 chunk 126 optimal weight: 0.5980 chunk 230 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 GLN A2218 GLN A2499 GLN ** A2618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2671 HIS ** A2733 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 21304 Z= 0.229 Angle : 0.581 8.523 28934 Z= 0.291 Chirality : 0.039 0.160 3450 Planarity : 0.005 0.103 3650 Dihedral : 4.453 22.136 2853 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.57 % Favored : 95.28 % Rotamer Outliers : 2.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.17), residues: 2625 helix: 1.44 (0.12), residues: 1873 sheet: None (None), residues: 0 loop : -1.34 (0.23), residues: 752 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2329 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 242 time to evaluate : 2.301 Fit side-chains outliers start: 65 outliers final: 20 residues processed: 282 average time/residue: 1.2379 time to fit residues: 405.2102 Evaluate side-chains 245 residues out of total 2329 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 225 time to evaluate : 2.509 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 15 residues processed: 5 average time/residue: 0.7819 time to fit residues: 8.2409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 214 optimal weight: 1.9990 chunk 145 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 chunk 191 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 219 optimal weight: 0.8980 chunk 177 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 131 optimal weight: 0.7980 chunk 230 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1637 ASN A2218 GLN A2499 GLN ** A2618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2671 HIS ** A2733 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 21304 Z= 0.256 Angle : 0.594 7.886 28934 Z= 0.296 Chirality : 0.040 0.162 3450 Planarity : 0.005 0.105 3650 Dihedral : 4.408 21.467 2853 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.91 % Favored : 94.93 % Rotamer Outliers : 2.62 % 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: 1.15 (0.17), residues: 2625 helix: 1.54 (0.12), residues: 1878 sheet: None (None), residues: 0 loop : -1.26 (0.23), residues: 747 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2329 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 237 time to evaluate : 2.561 Fit side-chains revert: symmetry clash outliers start: 61 outliers final: 29 residues processed: 280 average time/residue: 1.3178 time to fit residues: 426.4633 Evaluate side-chains 249 residues out of total 2329 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 220 time to evaluate : 2.562 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 22 residues processed: 8 average time/residue: 0.4126 time to fit residues: 8.3271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 86 optimal weight: 0.9990 chunk 231 optimal weight: 0.2980 chunk 50 optimal weight: 0.9990 chunk 150 optimal weight: 0.5980 chunk 63 optimal weight: 0.5980 chunk 257 optimal weight: 0.9980 chunk 213 optimal weight: 2.9990 chunk 119 optimal weight: 0.7980 chunk 21 optimal weight: 4.9990 chunk 85 optimal weight: 0.5980 chunk 135 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 GLN A2055 GLN A2218 GLN A2499 GLN ** A2618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2671 HIS ** A2733 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 21304 Z= 0.196 Angle : 0.567 9.652 28934 Z= 0.281 Chirality : 0.038 0.152 3450 Planarity : 0.004 0.110 3650 Dihedral : 4.269 22.038 2853 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.42 % Favored : 95.43 % Rotamer Outliers : 3.05 % 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: 1.41 (0.17), residues: 2625 helix: 1.72 (0.12), residues: 1878 sheet: None (None), residues: 0 loop : -1.12 (0.24), residues: 747 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2329 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 241 time to evaluate : 2.662 Fit side-chains outliers start: 71 outliers final: 31 residues processed: 290 average time/residue: 1.3288 time to fit residues: 448.1388 Evaluate side-chains 250 residues out of total 2329 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 219 time to evaluate : 2.574 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 24 residues processed: 9 average time/residue: 0.8985 time to fit residues: 13.4660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 248 optimal weight: 0.7980 chunk 29 optimal weight: 0.0050 chunk 146 optimal weight: 3.9990 chunk 187 optimal weight: 0.0770 chunk 145 optimal weight: 0.9990 chunk 216 optimal weight: 0.6980 chunk 143 optimal weight: 4.9990 chunk 256 optimal weight: 2.9990 chunk 160 optimal weight: 0.6980 chunk 156 optimal weight: 0.0980 chunk 118 optimal weight: 0.8980 overall best weight: 0.3152 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 GLN A2218 GLN ** A2618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2892 GLN A2993 GLN ** A3047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 21304 Z= 0.170 Angle : 0.573 11.536 28934 Z= 0.281 Chirality : 0.037 0.152 3450 Planarity : 0.004 0.091 3650 Dihedral : 4.152 20.852 2853 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.15 % Favored : 95.73 % Rotamer Outliers : 2.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.17), residues: 2625 helix: 1.90 (0.12), residues: 1875 sheet: None (None), residues: 0 loop : -1.06 (0.24), residues: 750 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2329 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 246 time to evaluate : 2.535 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 24 residues processed: 281 average time/residue: 1.2169 time to fit residues: 397.1964 Evaluate side-chains 240 residues out of total 2329 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 216 time to evaluate : 2.715 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 22 residues processed: 4 average time/residue: 0.3172 time to fit residues: 5.7420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 158 optimal weight: 2.9990 chunk 102 optimal weight: 0.7980 chunk 153 optimal weight: 1.9990 chunk 77 optimal weight: 0.3980 chunk 50 optimal weight: 0.6980 chunk 49 optimal weight: 0.7980 chunk 162 optimal weight: 0.6980 chunk 174 optimal weight: 0.8980 chunk 126 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 201 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 GLN A1459 GLN A1637 ASN A2218 GLN ** A2618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2671 HIS A2892 GLN A2993 GLN ** A3047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 21304 Z= 0.225 Angle : 0.592 10.581 28934 Z= 0.292 Chirality : 0.038 0.161 3450 Planarity : 0.005 0.121 3650 Dihedral : 4.171 20.223 2853 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.46 % Favored : 95.39 % Rotamer Outliers : 2.15 % 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: 1.61 (0.17), residues: 2625 helix: 1.88 (0.12), residues: 1873 sheet: None (None), residues: 0 loop : -1.02 (0.24), residues: 752 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2329 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 227 time to evaluate : 2.479 Fit side-chains revert: symmetry clash outliers start: 50 outliers final: 27 residues processed: 263 average time/residue: 1.2782 time to fit residues: 392.1874 Evaluate side-chains 244 residues out of total 2329 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 217 time to evaluate : 2.721 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 25 residues processed: 5 average time/residue: 0.6342 time to fit residues: 7.8364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 233 optimal weight: 9.9990 chunk 245 optimal weight: 0.7980 chunk 224 optimal weight: 4.9990 chunk 238 optimal weight: 0.5980 chunk 143 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 187 optimal weight: 0.9980 chunk 73 optimal weight: 0.6980 chunk 215 optimal weight: 1.9990 chunk 225 optimal weight: 0.8980 chunk 156 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 GLN A1637 ASN A2218 GLN ** A2618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2892 GLN ** A3047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 21304 Z= 0.242 Angle : 0.611 11.521 28934 Z= 0.302 Chirality : 0.039 0.200 3450 Planarity : 0.005 0.120 3650 Dihedral : 4.221 24.703 2853 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.34 % Favored : 95.50 % Rotamer Outliers : 1.93 % 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: 1.60 (0.17), residues: 2625 helix: 1.85 (0.12), residues: 1872 sheet: None (None), residues: 0 loop : -0.99 (0.24), residues: 753 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2329 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 222 time to evaluate : 2.546 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 26 residues processed: 256 average time/residue: 1.2657 time to fit residues: 377.3078 Evaluate side-chains 244 residues out of total 2329 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 218 time to evaluate : 2.760 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 26 residues processed: 2 average time/residue: 0.4100 time to fit residues: 4.9796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 252 optimal weight: 0.8980 chunk 154 optimal weight: 0.9980 chunk 119 optimal weight: 0.6980 chunk 175 optimal weight: 0.5980 chunk 265 optimal weight: 0.5980 chunk 243 optimal weight: 0.9990 chunk 211 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 163 optimal weight: 0.9980 chunk 129 optimal weight: 2.9990 chunk 167 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 GLN A2218 GLN ** A2618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2892 GLN ** A3047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 21304 Z= 0.229 Angle : 0.602 12.211 28934 Z= 0.297 Chirality : 0.039 0.183 3450 Planarity : 0.005 0.124 3650 Dihedral : 4.210 24.577 2853 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.30 % Favored : 95.54 % Rotamer Outliers : 1.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.17), residues: 2625 helix: 1.88 (0.12), residues: 1871 sheet: None (None), residues: 0 loop : -0.94 (0.24), residues: 754 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2329 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 219 time to evaluate : 2.600 Fit side-chains revert: symmetry clash outliers start: 36 outliers final: 27 residues processed: 252 average time/residue: 1.2965 time to fit residues: 380.3519 Evaluate side-chains 246 residues out of total 2329 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 219 time to evaluate : 2.427 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 26 residues processed: 3 average time/residue: 0.7093 time to fit residues: 6.0935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 224 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 194 optimal weight: 0.2980 chunk 31 optimal weight: 0.9990 chunk 58 optimal weight: 0.6980 chunk 211 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 217 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 185 optimal weight: 1.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 GLN A2218 GLN ** A2618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2892 GLN ** A3047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.138345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.100798 restraints weight = 26925.075| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 1.94 r_work: 0.3177 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 1.71 restraints_weight: 0.2500 r_work: 0.3141 rms_B_bonded: 1.78 restraints_weight: 0.1250 r_work: 0.3122 rms_B_bonded: 1.90 restraints_weight: 0.0625 r_work: 0.3101 rms_B_bonded: 2.07 restraints_weight: 0.0312 r_work: 0.3079 rms_B_bonded: 2.29 restraints_weight: 0.0156 r_work: 0.3054 rms_B_bonded: 2.57 restraints_weight: 0.0078 r_work: 0.3027 rms_B_bonded: 2.92 restraints_weight: 0.0039 r_work: 0.2997 rms_B_bonded: 3.33 restraints_weight: 0.0020 r_work: 0.2964 rms_B_bonded: 3.83 restraints_weight: 0.0010 r_work: 0.2927 rms_B_bonded: 4.42 restraints_weight: 0.0005 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.061 21304 Z= 0.243 Angle : 0.618 12.232 28934 Z= 0.304 Chirality : 0.039 0.181 3450 Planarity : 0.005 0.128 3650 Dihedral : 4.216 24.619 2853 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.42 % Favored : 95.43 % Rotamer Outliers : 1.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.17), residues: 2625 helix: 1.88 (0.12), residues: 1871 sheet: None (None), residues: 0 loop : -0.94 (0.24), residues: 754 =============================================================================== Job complete usr+sys time: 6982.01 seconds wall clock time: 125 minutes 20.39 seconds (7520.39 seconds total)