Starting phenix.real_space_refine on Wed Apr 10 08:37:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jb5_36141/04_2024/8jb5_36141.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jb5_36141/04_2024/8jb5_36141.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jb5_36141/04_2024/8jb5_36141.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jb5_36141/04_2024/8jb5_36141.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jb5_36141/04_2024/8jb5_36141.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jb5_36141/04_2024/8jb5_36141.pdb" } resolution = 2.9 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= 0.005 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 47 5.16 5 C 12183 2.51 5 N 3022 2.21 5 O 3774 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 21": "OE1" <-> "OE2" Residue "A ASP 22": "OD1" <-> "OD2" Residue "A GLU 23": "OE1" <-> "OE2" Residue "A TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 32": "OE1" <-> "OE2" Residue "A GLU 33": "OE1" <-> "OE2" Residue "A TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 44": "OE1" <-> "OE2" Residue "A TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 77": "OE1" <-> "OE2" Residue "A GLU 82": "OE1" <-> "OE2" Residue "A GLU 85": "OE1" <-> "OE2" Residue "A GLU 95": "OE1" <-> "OE2" Residue "A PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 147": "OE1" <-> "OE2" Residue "A GLU 155": "OE1" <-> "OE2" Residue "A GLU 159": "OE1" <-> "OE2" Residue "A GLU 165": "OE1" <-> "OE2" Residue "A PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 177": "OE1" <-> "OE2" Residue "A TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 195": "OE1" <-> "OE2" Residue "A GLU 196": "OE1" <-> "OE2" Residue "A TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 213": "OE1" <-> "OE2" Residue "A TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 226": "OE1" <-> "OE2" Residue "A GLU 227": "OE1" <-> "OE2" Residue "A GLU 244": "OE1" <-> "OE2" Residue "A PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 258": "OE1" <-> "OE2" Residue "A GLU 261": "OE1" <-> "OE2" Residue "A ASP 270": "OD1" <-> "OD2" Residue "A GLU 279": "OE1" <-> "OE2" Residue "A TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 305": "OD1" <-> "OD2" Residue "A GLU 313": "OE1" <-> "OE2" Residue "A GLU 318": "OE1" <-> "OE2" Residue "A TYR 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 339": "OD1" <-> "OD2" Residue "A GLU 340": "OE1" <-> "OE2" Residue "A GLU 347": "OE1" <-> "OE2" Residue "A GLU 358": "OE1" <-> "OE2" Residue "A ASP 364": "OD1" <-> "OD2" Residue "A GLU 372": "OE1" <-> "OE2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 420": "OE1" <-> "OE2" Residue "A ASP 423": "OD1" <-> "OD2" Residue "A PHE 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 486": "OD1" <-> "OD2" Residue "A GLU 495": "OE1" <-> "OE2" Residue "A PHE 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 502": "OE1" <-> "OE2" Residue "A GLU 513": "OE1" <-> "OE2" Residue "A GLU 515": "OE1" <-> "OE2" Residue "A PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 532": "OE1" <-> "OE2" Residue "A TYR 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 540": "OE1" <-> "OE2" Residue "A TYR 561": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 573": "NH1" <-> "NH2" Residue "A GLU 576": "OE1" <-> "OE2" Residue "A TYR 577": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 587": "OD1" <-> "OD2" Residue "A TYR 591": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 592": "OE1" <-> "OE2" Residue "A PHE 598": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 608": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 616": "OE1" <-> "OE2" Residue "A TYR 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 621": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 630": "OE1" <-> "OE2" Residue "A ASP 632": "OD1" <-> "OD2" Residue "A TYR 634": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 657": "OE1" <-> "OE2" Residue "A PHE 658": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 663": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 674": "OE1" <-> "OE2" Residue "A GLU 676": "OE1" <-> "OE2" Residue "A ASP 685": "OD1" <-> "OD2" Residue "A GLU 692": "OE1" <-> "OE2" Residue "A TYR 703": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 708": "OE1" <-> "OE2" Residue "A GLU 743": "OE1" <-> "OE2" Residue "A GLU 753": "OE1" <-> "OE2" Residue "A GLU 765": "OE1" <-> "OE2" Residue "A GLU 766": "OE1" <-> "OE2" Residue "A GLU 776": "OE1" <-> "OE2" Residue "A TYR 777": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 780": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 793": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 796": "OE1" <-> "OE2" Residue "A ARG 805": "NH1" <-> "NH2" Residue "A ASP 812": "OD1" <-> "OD2" Residue "A ASP 814": "OD1" <-> "OD2" Residue "A GLU 816": "OE1" <-> "OE2" Residue "A GLU 823": "OE1" <-> "OE2" Residue "A ASP 833": "OD1" <-> "OD2" Residue "A GLU 838": "OE1" <-> "OE2" Residue "A TYR 854": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 858": "OE1" <-> "OE2" Residue "A GLU 863": "OE1" <-> "OE2" Residue "A TYR 870": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 883": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 893": "OE1" <-> "OE2" Residue "A PHE 896": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 900": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 910": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 914": "OE1" <-> "OE2" Residue "A GLU 916": "OE1" <-> "OE2" Residue "A PHE 918": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 921": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 928": "OE1" <-> "OE2" Residue "A ASP 938": "OD1" <-> "OD2" Residue "A PHE 963": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 964": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 970": "OE1" <-> "OE2" Residue "A GLU 976": "OE1" <-> "OE2" Residue "A ASP 1037": "OD1" <-> "OD2" Residue "A GLU 1047": "OE1" <-> "OE2" Residue "A GLU 1050": "OE1" <-> "OE2" Residue "A GLU 1061": "OE1" <-> "OE2" Residue "A GLU 1110": "OE1" <-> "OE2" Residue "A ASP 1122": "OD1" <-> "OD2" Residue "A TYR 1123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1140": "OD1" <-> "OD2" Residue "A ASP 1141": "OD1" <-> "OD2" Residue "A ASP 1149": "OD1" <-> "OD2" Residue "A GLU 1154": "OE1" <-> "OE2" Residue "A ASP 1156": "OD1" <-> "OD2" Residue "A PHE 1157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1182": "OD1" <-> "OD2" Residue "A PHE 1188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1204": "OD1" <-> "OD2" Residue "A GLU 1211": "OE1" <-> "OE2" Residue "A PHE 1230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1283": "OE1" <-> "OE2" Residue "A ASP 1284": "OD1" <-> "OD2" Residue "A PHE 1298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1306": "OE1" <-> "OE2" Residue "A PHE 1316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1335": "OD1" <-> "OD2" Residue "A GLU 1358": "OE1" <-> "OE2" Residue "A GLU 1366": "OE1" <-> "OE2" Residue "A TYR 1392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1417": "OE1" <-> "OE2" Residue "A ASP 1442": "OD1" <-> "OD2" Residue "A PHE 1452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1466": "OD1" <-> "OD2" Residue "A PHE 1474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1476": "OD1" <-> "OD2" Residue "A TYR 1477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1487": "OE1" <-> "OE2" Residue "A PHE 1488": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1491": "OE1" <-> "OE2" Residue "A TYR 1531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1532": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1542": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1545": "OE1" <-> "OE2" Residue "A TYR 1556": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1559": "OE1" <-> "OE2" Residue "A PHE 1568": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1585": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1587": "OE1" <-> "OE2" Residue "A TYR 1596": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1611": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1622": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1623": "OE1" <-> "OE2" Residue "A TYR 1635": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1643": "OE1" <-> "OE2" Residue "A TYR 1646": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1659": "OE1" <-> "OE2" Residue "A TYR 1662": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1677": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1683": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1702": "OE1" <-> "OE2" Residue "A TYR 1709": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1713": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1717": "OE1" <-> "OE2" Residue "A TYR 1741": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1757": "OE1" <-> "OE2" Residue "A GLU 1758": "OE1" <-> "OE2" Residue "A PHE 1768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1779": "OD1" <-> "OD2" Residue "A PHE 1800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1810": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1812": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1813": "OE1" <-> "OE2" Residue "A PHE 1814": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1820": "OD1" <-> "OD2" Residue "A PHE 1824": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1825": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1845": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1846": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1861": "OD1" <-> "OD2" Residue "A TYR 1865": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1866": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1879": "OE1" <-> "OE2" Residue "A TYR 1887": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1908": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1917": "OE1" <-> "OE2" Residue "A GLU 1920": "OE1" <-> "OE2" Residue "A GLU 1922": "OE1" <-> "OE2" Residue "A PHE 1926": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1937": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1938": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1940": "OE1" <-> "OE2" Residue "A GLU 1948": "OE1" <-> "OE2" Residue "A TYR 1958": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1965": "OE1" <-> "OE2" Residue "A ASP 1975": "OD1" <-> "OD2" Residue "A TYR 1978": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1980": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1990": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1998": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1999": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2000": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2003": "OD1" <-> "OD2" Residue "A TYR 2010": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2012": "OE1" <-> "OE2" Residue "A PHE 2018": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2019": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2020": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2025": "OE1" <-> "OE2" Residue "A ASP 2035": "OD1" <-> "OD2" Residue "A PHE 2037": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2039": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2044": "OD1" <-> "OD2" Residue "A ASP 2045": "OD1" <-> "OD2" Residue "A GLU 2053": "OE1" <-> "OE2" Residue "A PHE 2063": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2068": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2069": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2070": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2084": "OD1" <-> "OD2" Residue "A TYR 2089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2090": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2091": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2093": "OD1" <-> "OD2" Residue "A ASP 2107": "OD1" <-> "OD2" Residue "A TYR 2110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2114": "OD1" <-> "OD2" Residue "A PHE 2130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2134": "OE1" <-> "OE2" Residue "A GLU 2139": "OE1" <-> "OE2" Residue "A TYR 2149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2154": "OE1" <-> "OE2" Residue "A PHE 2163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2197": "OE1" <-> "OE2" Residue "A GLU 2204": "OE1" <-> "OE2" Residue "A TYR 2220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2223": "OD1" <-> "OD2" Residue "A TYR 2230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2237": "OD1" <-> "OD2" Residue "A ASP 2238": "OD1" <-> "OD2" Residue "A TYR 2242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2244": "OD1" <-> "OD2" Residue "A PHE 2256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2257": "OE1" <-> "OE2" Residue "A TYR 2261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2265": "OE1" <-> "OE2" Residue "A ASP 2266": "OD1" <-> "OD2" Residue "A PHE 2271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2298": "OD1" <-> "OD2" Residue "A TYR 2302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2311": "OE1" <-> "OE2" Residue "A PHE 2313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2314": "OE1" <-> "OE2" Residue "A GLU 2316": "OE1" <-> "OE2" Residue "A TYR 2320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2325": "OD1" <-> "OD2" Residue "A ASP 2327": "OD1" <-> "OD2" Residue "A TYR 2331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2336": "OE1" <-> "OE2" Residue "A TYR 2351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2356": "OD1" <-> "OD2" Residue "A GLU 2359": "OE1" <-> "OE2" Residue "A GLU 2364": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 19027 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 19026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2355, 19026 Classifications: {'peptide': 2355} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 2298} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5704 SG CYS A 698 81.942 22.758 87.073 1.00 23.67 S Time building chain proxies: 10.10, per 1000 atoms: 0.53 Number of scatterers: 19027 At special positions: 0 Unit cell: (180.442, 161.963, 208.704, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 47 16.00 O 3774 8.00 N 3022 7.00 C 12183 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.17 Conformation dependent library (CDL) restraints added in 4.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A3000 " pdb="ZN ZN A3000 " - pdb=" SG CYS A 698 " pdb="ZN ZN A3000 " - pdb=" NE2 HIS A 757 " pdb="ZN ZN A3000 " - pdb=" ND1 HIS A 653 " 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4446 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 44 sheets defined 31.8% alpha, 22.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.65 Creating SS restraints... Processing helix chain 'A' and resid 5 through 13 Processing helix chain 'A' and resid 21 through 36 Processing helix chain 'A' and resid 41 through 63 Processing helix chain 'A' and resid 68 through 87 Processing helix chain 'A' and resid 108 through 122 removed outlier: 3.902A pdb=" N GLN A 117 " --> pdb=" O ASN A 113 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N TRP A 118 " --> pdb=" O TYR A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 156 removed outlier: 3.553A pdb=" N LEU A 141 " --> pdb=" O LEU A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 197 Processing helix chain 'A' and resid 201 through 214 removed outlier: 3.521A pdb=" N ILE A 205 " --> pdb=" O ILE A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 234 Processing helix chain 'A' and resid 248 through 261 Processing helix chain 'A' and resid 264 through 280 removed outlier: 3.976A pdb=" N ILE A 274 " --> pdb=" O ASP A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 324 Processing helix chain 'A' and resid 339 through 353 removed outlier: 3.967A pdb=" N SER A 352 " --> pdb=" O SER A 348 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N LYS A 353 " --> pdb=" O ALA A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 358 Processing helix chain 'A' and resid 393 through 420 removed outlier: 3.533A pdb=" N ASP A 397 " --> pdb=" O SER A 393 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE A 409 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Proline residue: A 416 - end of helix Processing helix chain 'A' and resid 423 through 438 Processing helix chain 'A' and resid 443 through 450 Processing helix chain 'A' and resid 452 through 456 Processing helix chain 'A' and resid 464 through 469 Processing helix chain 'A' and resid 470 through 484 removed outlier: 3.955A pdb=" N TYR A 474 " --> pdb=" O GLY A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 499 Processing helix chain 'A' and resid 500 through 502 No H-bonds generated for 'chain 'A' and resid 500 through 502' Processing helix chain 'A' and resid 504 through 506 No H-bonds generated for 'chain 'A' and resid 504 through 506' Processing helix chain 'A' and resid 512 through 519 Processing helix chain 'A' and resid 523 through 539 Processing helix chain 'A' and resid 558 through 568 Processing helix chain 'A' and resid 587 through 601 removed outlier: 3.833A pdb=" N ASP A 601 " --> pdb=" O LEU A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 642 removed outlier: 4.531A pdb=" N ASN A 642 " --> pdb=" O TYR A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 683 Processing helix chain 'A' and resid 706 through 709 Processing helix chain 'A' and resid 710 through 727 removed outlier: 4.662A pdb=" N ASP A 721 " --> pdb=" O LEU A 717 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N ARG A 722 " --> pdb=" O LYS A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 733 No H-bonds generated for 'chain 'A' and resid 731 through 733' Processing helix chain 'A' and resid 764 through 775 removed outlier: 3.778A pdb=" N LYS A 775 " --> pdb=" O ASP A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 809 removed outlier: 3.511A pdb=" N LEU A 797 " --> pdb=" O TYR A 793 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR A 799 " --> pdb=" O HIS A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 839 Processing helix chain 'A' and resid 850 through 876 removed outlier: 3.704A pdb=" N ASN A 876 " --> pdb=" O LEU A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 936 removed outlier: 3.542A pdb=" N ALA A 922 " --> pdb=" O PHE A 918 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER A 926 " --> pdb=" O ALA A 922 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N THR A 935 " --> pdb=" O ASN A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 971 removed outlier: 4.418A pdb=" N THR A 958 " --> pdb=" O HIS A 954 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N PHE A 964 " --> pdb=" O ASN A 960 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE A 965 " --> pdb=" O SER A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 995 Processing helix chain 'A' and resid 997 through 1001 Processing helix chain 'A' and resid 1003 through 1017 Processing helix chain 'A' and resid 1042 through 1051 removed outlier: 3.513A pdb=" N GLU A1050 " --> pdb=" O LYS A1046 " (cutoff:3.500A) Processing helix chain 'A' and resid 1053 through 1065 Processing helix chain 'A' and resid 1072 through 1087 Processing helix chain 'A' and resid 1116 through 1133 removed outlier: 4.213A pdb=" N ALA A1130 " --> pdb=" O HIS A1126 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N GLU A1131 " --> pdb=" O ILE A1127 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N THR A1132 " --> pdb=" O SER A1128 " (cutoff:3.500A) Processing helix chain 'A' and resid 1203 through 1206 Processing helix chain 'A' and resid 1245 through 1258 Processing helix chain 'A' and resid 1305 through 1310 Processing helix chain 'A' and resid 1348 through 1352 Processing helix chain 'A' and resid 1370 through 1373 Processing helix chain 'A' and resid 1432 through 1439 Processing helix chain 'A' and resid 1439 through 1450 removed outlier: 3.748A pdb=" N ILE A1450 " --> pdb=" O LYS A1446 " (cutoff:3.500A) Processing helix chain 'A' and resid 1558 through 1572 Processing helix chain 'A' and resid 1580 through 1589 Processing helix chain 'A' and resid 1651 through 1653 No H-bonds generated for 'chain 'A' and resid 1651 through 1653' Processing helix chain 'A' and resid 1680 through 1683 Processing helix chain 'A' and resid 1685 through 1689 removed outlier: 3.758A pdb=" N VAL A1689 " --> pdb=" O ASP A1686 " (cutoff:3.500A) Processing helix chain 'A' and resid 1774 through 1779 removed outlier: 3.871A pdb=" N ALA A1778 " --> pdb=" O SER A1774 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASP A1779 " --> pdb=" O ASP A1775 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1774 through 1779' Processing helix chain 'A' and resid 1792 through 1800 Processing helix chain 'A' and resid 1868 through 1872 removed outlier: 3.588A pdb=" N SER A1872 " --> pdb=" O PRO A1869 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 92 through 93 Processing sheet with id=AA2, first strand: chain 'A' and resid 237 through 239 removed outlier: 6.170A pdb=" N LEU A 98 " --> pdb=" O LYS A 128 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N PHE A 130 " --> pdb=" O LEU A 98 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N PHE A 100 " --> pdb=" O PHE A 130 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N ILE A 101 " --> pdb=" O LEU A 285 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N GLN A 385 " --> pdb=" O LYS A 374 " (cutoff:3.500A) removed outlier: 11.302A pdb=" N LYS A 374 " --> pdb=" O GLN A 385 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 360 through 361 removed outlier: 4.520A pdb=" N GLY A 292 " --> pdb=" O LEU A 361 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A 290 " --> pdb=" O SER A 509 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 605 through 609 removed outlier: 6.746A pdb=" N ILE A 646 " --> pdb=" O GLU A 692 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N ASN A 694 " --> pdb=" O ILE A 646 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LEU A 648 " --> pdb=" O ASN A 694 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N LEU A 696 " --> pdb=" O LEU A 648 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N PHE A 650 " --> pdb=" O LEU A 696 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 617 through 622 Processing sheet with id=AA6, first strand: chain 'A' and resid 744 through 746 Processing sheet with id=AA7, first strand: chain 'A' and resid 777 through 781 removed outlier: 4.610A pdb=" N TYR A 777 " --> pdb=" O LYS A 790 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 882 through 884 Processing sheet with id=AA9, first strand: chain 'A' and resid 882 through 884 Processing sheet with id=AB1, first strand: chain 'A' and resid 938 through 940 removed outlier: 3.810A pdb=" N ASP A 938 " --> pdb=" O VAL A 945 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1035 through 1036 Processing sheet with id=AB3, first strand: chain 'A' and resid 1067 through 1068 removed outlier: 5.485A pdb=" N ASP A1515 " --> pdb=" O ASN A1530 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ASN A1530 " --> pdb=" O ASP A1515 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N LYS A1525 " --> pdb=" O ILE A1544 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ILE A1544 " --> pdb=" O LYS A1525 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N LYS A1537 " --> pdb=" O LEU A1557 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N LEU A1557 " --> pdb=" O LYS A1537 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N SER A1539 " --> pdb=" O VAL A1555 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N VAL A1555 " --> pdb=" O SER A1539 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N SER A1541 " --> pdb=" O ASN A1553 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N GLY A1554 " --> pdb=" O ASP A1608 " (cutoff:3.500A) removed outlier: 11.142A pdb=" N ASN A1610 " --> pdb=" O GLY A1554 " (cutoff:3.500A) removed outlier: 11.055A pdb=" N TYR A1556 " --> pdb=" O ASN A1610 " (cutoff:3.500A) removed outlier: 11.380A pdb=" N ILE A1612 " --> pdb=" O TYR A1556 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N PHE A1611 " --> pdb=" O CYS A1626 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N CYS A1626 " --> pdb=" O PHE A1611 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N GLN A1621 " --> pdb=" O ILE A1637 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ILE A1637 " --> pdb=" O GLN A1621 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N GLU A1623 " --> pdb=" O TYR A1635 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU A1656 " --> pdb=" O ILE A1693 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL A1718 " --> pdb=" O ARG A1767 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N SER A1801 " --> pdb=" O TYR A1741 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1105 through 1107 Processing sheet with id=AB5, first strand: chain 'A' and resid 1136 through 1139 removed outlier: 6.963A pdb=" N ILE A1144 " --> pdb=" O VAL A1221 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL A1345 " --> pdb=" O TYR A1323 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU A1325 " --> pdb=" O VAL A1345 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ASP A1347 " --> pdb=" O LEU A1325 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N TRP A1344 " --> pdb=" O SER A1403 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N THR A1405 " --> pdb=" O TRP A1344 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ILE A1346 " --> pdb=" O THR A1405 " (cutoff:3.500A) removed outlier: 8.551A pdb=" N SER A1407 " --> pdb=" O ILE A1346 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1161 through 1164 removed outlier: 6.950A pdb=" N SER A1161 " --> pdb=" O ILE A1155 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ILE A1155 " --> pdb=" O SER A1161 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N THR A1163 " --> pdb=" O SER A1153 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N SER A1153 " --> pdb=" O ARG A1288 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N ASN A1290 " --> pdb=" O SER A1153 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ILE A1155 " --> pdb=" O ASN A1290 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N TYR A1314 " --> pdb=" O ASP A1335 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N ASN A1337 " --> pdb=" O TYR A1314 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N PHE A1316 " --> pdb=" O ASN A1337 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N THR A1388 " --> pdb=" O ILE A1334 " (cutoff:3.500A) removed outlier: 9.004A pdb=" N LEU A1336 " --> pdb=" O THR A1388 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N ASN A1390 " --> pdb=" O LEU A1336 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N LEU A1338 " --> pdb=" O ASN A1390 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N TYR A1392 " --> pdb=" O LEU A1338 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1168 through 1169 Processing sheet with id=AB8, first strand: chain 'A' and resid 1171 through 1173 Processing sheet with id=AB9, first strand: chain 'A' and resid 1179 through 1181 removed outlier: 6.650A pdb=" N ASP A1185 " --> pdb=" O PHE A1267 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N ILE A1275 " --> pdb=" O GLY A1235 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N GLY A1235 " --> pdb=" O ILE A1275 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1353 through 1358 removed outlier: 4.242A pdb=" N ASN A1354 " --> pdb=" O GLY A1365 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1459 through 1466 Processing sheet with id=AC3, first strand: chain 'A' and resid 1674 through 1678 removed outlier: 6.400A pdb=" N ILE A1675 " --> pdb=" O ASN A1704 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N THR A1706 " --> pdb=" O ILE A1675 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N PHE A1677 " --> pdb=" O THR A1706 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ILE A1703 " --> pdb=" O ASN A1733 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ILE A1730 " --> pdb=" O SER A1782 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N ASN A1784 " --> pdb=" O ILE A1730 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N VAL A1732 " --> pdb=" O ASN A1784 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'A' and resid 1815 through 1819 Processing sheet with id=AC5, first strand: chain 'A' and resid 1835 through 1839 removed outlier: 3.722A pdb=" N ASN A1852 " --> pdb=" O LYS A1847 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 1856 through 1860 Processing sheet with id=AC7, first strand: chain 'A' and resid 1878 through 1882 Processing sheet with id=AC8, first strand: chain 'A' and resid 1898 through 1902 removed outlier: 3.765A pdb=" N GLU A1922 " --> pdb=" O ALA A1910 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 1928 through 1932 Processing sheet with id=AD1, first strand: chain 'A' and resid 1969 through 1973 removed outlier: 4.567A pdb=" N TYR A1979 " --> pdb=" O GLN A1987 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 1991 through 1992 Processing sheet with id=AD3, first strand: chain 'A' and resid 2009 through 2013 Processing sheet with id=AD4, first strand: chain 'A' and resid 2029 through 2033 Processing sheet with id=AD5, first strand: chain 'A' and resid 2059 through 2063 Processing sheet with id=AD6, first strand: chain 'A' and resid 2079 through 2082 Processing sheet with id=AD7, first strand: chain 'A' and resid 2101 through 2105 Processing sheet with id=AD8, first strand: chain 'A' and resid 2143 through 2145 Processing sheet with id=AD9, first strand: chain 'A' and resid 2161 through 2165 removed outlier: 4.695A pdb=" N TYR A2171 " --> pdb=" O VAL A2187 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN A2185 " --> pdb=" O ALA A2173 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 2191 through 2194 Processing sheet with id=AE2, first strand: chain 'A' and resid 2211 through 2215 Processing sheet with id=AE3, first strand: chain 'A' and resid 2232 through 2236 Processing sheet with id=AE4, first strand: chain 'A' and resid 2252 through 2256 Processing sheet with id=AE5, first strand: chain 'A' and resid 2272 through 2276 Processing sheet with id=AE6, first strand: chain 'A' and resid 2292 through 2296 removed outlier: 4.544A pdb=" N TYR A2302 " --> pdb=" O ILE A2318 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'A' and resid 2322 through 2326 Processing sheet with id=AE8, first strand: chain 'A' and resid 2343 through 2346 832 hydrogen bonds defined for protein. 2232 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: 13.58 Time building geometry restraints manager: 6.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4718 1.33 - 1.45: 3944 1.45 - 1.57: 10663 1.57 - 1.69: 0 1.69 - 1.82: 84 Bond restraints: 19409 Sorted by residual: bond pdb=" C ILE A 409 " pdb=" O ILE A 409 " ideal model delta sigma weight residual 1.237 1.307 -0.070 1.13e-02 7.83e+03 3.85e+01 bond pdb=" C ASN A 413 " pdb=" O ASN A 413 " ideal model delta sigma weight residual 1.237 1.293 -0.056 1.19e-02 7.06e+03 2.23e+01 bond pdb=" C ASP A 412 " pdb=" O ASP A 412 " ideal model delta sigma weight residual 1.236 1.285 -0.049 1.15e-02 7.56e+03 1.78e+01 bond pdb=" C ARG A 406 " pdb=" O ARG A 406 " ideal model delta sigma weight residual 1.237 1.280 -0.043 1.19e-02 7.06e+03 1.32e+01 bond pdb=" N ILE A1019 " pdb=" CA ILE A1019 " ideal model delta sigma weight residual 1.456 1.496 -0.039 1.14e-02 7.69e+03 1.19e+01 ... (remaining 19404 not shown) Histogram of bond angle deviations from ideal: 93.65 - 101.77: 34 101.77 - 109.88: 2548 109.88 - 118.00: 11791 118.00 - 126.11: 11732 126.11 - 134.23: 156 Bond angle restraints: 26261 Sorted by residual: angle pdb=" CA PRO A 416 " pdb=" N PRO A 416 " pdb=" CD PRO A 416 " ideal model delta sigma weight residual 112.00 93.65 18.35 1.40e+00 5.10e-01 1.72e+02 angle pdb=" C VAL A1947 " pdb=" N GLU A1948 " pdb=" CA GLU A1948 " ideal model delta sigma weight residual 121.54 132.77 -11.23 1.91e+00 2.74e-01 3.46e+01 angle pdb=" N VAL A1069 " pdb=" CA VAL A1069 " pdb=" C VAL A1069 " ideal model delta sigma weight residual 111.91 107.22 4.69 8.90e-01 1.26e+00 2.78e+01 angle pdb=" O LEU A1021 " pdb=" C LEU A1021 " pdb=" N LEU A1022 " ideal model delta sigma weight residual 122.09 127.29 -5.20 1.08e+00 8.57e-01 2.32e+01 angle pdb=" CA ASN A 415 " pdb=" C ASN A 415 " pdb=" N PRO A 416 " ideal model delta sigma weight residual 120.52 124.43 -3.91 8.30e-01 1.45e+00 2.21e+01 ... (remaining 26256 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 9886 17.95 - 35.90: 1332 35.90 - 53.85: 301 53.85 - 71.81: 68 71.81 - 89.76: 26 Dihedral angle restraints: 11613 sinusoidal: 4669 harmonic: 6944 Sorted by residual: dihedral pdb=" CA GLY A1028 " pdb=" C GLY A1028 " pdb=" N LEU A1029 " pdb=" CA LEU A1029 " ideal model delta harmonic sigma weight residual 180.00 92.75 87.25 0 5.00e+00 4.00e-02 3.04e+02 dihedral pdb=" CA PHE A1452 " pdb=" C PHE A1452 " pdb=" N ASN A1453 " pdb=" CA ASN A1453 " ideal model delta harmonic sigma weight residual 180.00 148.03 31.97 0 5.00e+00 4.00e-02 4.09e+01 dihedral pdb=" C ASN A1602 " pdb=" N ASN A1602 " pdb=" CA ASN A1602 " pdb=" CB ASN A1602 " ideal model delta harmonic sigma weight residual -122.60 -137.36 14.76 0 2.50e+00 1.60e-01 3.48e+01 ... (remaining 11610 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 2550 0.097 - 0.193: 326 0.193 - 0.290: 18 0.290 - 0.387: 2 0.387 - 0.484: 2 Chirality restraints: 2898 Sorted by residual: chirality pdb=" CA ASN A1602 " pdb=" N ASN A1602 " pdb=" C ASN A1602 " pdb=" CB ASN A1602 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.85e+00 chirality pdb=" CA ASN A 419 " pdb=" N ASN A 419 " pdb=" C ASN A 419 " pdb=" CB ASN A 419 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.99e+00 chirality pdb=" CA SER A 706 " pdb=" N SER A 706 " pdb=" C SER A 706 " pdb=" CB SER A 706 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.44e+00 ... (remaining 2895 not shown) Planarity restraints: 3394 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 415 " 0.120 5.00e-02 4.00e+02 1.65e-01 4.37e+01 pdb=" N PRO A 416 " -0.285 5.00e-02 4.00e+02 pdb=" CA PRO A 416 " 0.075 5.00e-02 4.00e+02 pdb=" CD PRO A 416 " 0.090 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY A2342 " 0.022 2.00e-02 2.50e+03 4.46e-02 1.99e+01 pdb=" C GLY A2342 " -0.077 2.00e-02 2.50e+03 pdb=" O GLY A2342 " 0.029 2.00e-02 2.50e+03 pdb=" N SER A2343 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 413 " 0.020 2.00e-02 2.50e+03 4.03e-02 1.62e+01 pdb=" C ASN A 413 " -0.070 2.00e-02 2.50e+03 pdb=" O ASN A 413 " 0.026 2.00e-02 2.50e+03 pdb=" N LEU A 414 " 0.024 2.00e-02 2.50e+03 ... (remaining 3391 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 96 2.47 - 3.08: 12846 3.08 - 3.68: 27753 3.68 - 4.29: 42859 4.29 - 4.90: 70372 Nonbonded interactions: 153926 Sorted by model distance: nonbonded pdb=" CG2 THR A1956 " pdb=" N MET A1986 " model vdw 1.861 3.540 nonbonded pdb=" CG PRO A1023 " pdb=" OH TYR A1649 " model vdw 1.925 3.440 nonbonded pdb=" O ASP A1534 " pdb=" OD1 ASP A1535 " model vdw 1.962 3.040 nonbonded pdb=" O LYS A1795 " pdb=" OG1 THR A1799 " model vdw 2.029 2.440 nonbonded pdb=" O ILE A1507 " pdb=" OD1 ASN A1598 " model vdw 2.031 3.040 ... (remaining 153921 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 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: 1.240 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: 6.610 Check model and map are aligned: 0.300 Set scattering table: 0.180 Process input model: 62.480 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.070 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:11.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 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 : 0.008 0.070 19409 Z= 0.477 Angle : 0.884 18.347 26261 Z= 0.585 Chirality : 0.062 0.484 2898 Planarity : 0.006 0.165 3394 Dihedral : 17.400 89.757 7167 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.74 % Favored : 94.00 % Rotamer: Outliers : 6.34 % Allowed : 17.18 % Favored : 76.48 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.73 (0.16), residues: 2351 helix: 0.08 (0.20), residues: 664 sheet: -1.13 (0.22), residues: 453 loop : -1.87 (0.15), residues: 1234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 102 HIS 0.005 0.001 HIS A 99 PHE 0.016 0.002 PHE A 503 TYR 0.019 0.002 TYR A1646 ARG 0.005 0.001 ARG A1241 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 200 time to evaluate : 2.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 GLU cc_start: 0.6787 (tt0) cc_final: 0.6519 (tt0) REVERT: A 197 ASN cc_start: 0.7715 (t0) cc_final: 0.7485 (t0) REVERT: A 333 LYS cc_start: 0.8463 (ttpt) cc_final: 0.8257 (ttpt) REVERT: A 428 MET cc_start: 0.8629 (tpt) cc_final: 0.8392 (mmm) REVERT: A 651 ILE cc_start: 0.9497 (OUTLIER) cc_final: 0.9246 (mm) REVERT: A 1327 LEU cc_start: 0.7239 (OUTLIER) cc_final: 0.6843 (OUTLIER) REVERT: A 1462 TYR cc_start: 0.7125 (OUTLIER) cc_final: 0.5038 (p90) REVERT: A 1490 ASN cc_start: 0.7438 (p0) cc_final: 0.7042 (p0) REVERT: A 1496 ASN cc_start: 0.7331 (t0) cc_final: 0.6567 (m-40) REVERT: A 1499 MET cc_start: 0.6669 (tpp) cc_final: 0.5515 (ttp) REVERT: A 1576 LEU cc_start: 0.2556 (OUTLIER) cc_final: 0.1786 (mp) REVERT: A 1819 LEU cc_start: 0.8442 (mt) cc_final: 0.8229 (mt) REVERT: A 1955 GLU cc_start: 0.5589 (OUTLIER) cc_final: 0.5352 (mp0) REVERT: A 2181 ASN cc_start: 0.1215 (OUTLIER) cc_final: -0.0697 (m-40) outliers start: 135 outliers final: 77 residues processed: 320 average time/residue: 1.0962 time to fit residues: 408.1166 Evaluate side-chains 211 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 129 time to evaluate : 2.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 464 SER Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 574 ASN Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 703 TYR Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain A residue 879 ASP Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 936 ILE Chi-restraints excluded: chain A residue 958 THR Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 1002 THR Chi-restraints excluded: chain A residue 1010 LEU Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1019 ILE Chi-restraints excluded: chain A residue 1055 LEU Chi-restraints excluded: chain A residue 1143 ILE Chi-restraints excluded: chain A residue 1144 ILE Chi-restraints excluded: chain A residue 1167 CYS Chi-restraints excluded: chain A residue 1205 VAL Chi-restraints excluded: chain A residue 1285 THR Chi-restraints excluded: chain A residue 1297 SER Chi-restraints excluded: chain A residue 1305 THR Chi-restraints excluded: chain A residue 1324 SER Chi-restraints excluded: chain A residue 1327 LEU Chi-restraints excluded: chain A residue 1368 ILE Chi-restraints excluded: chain A residue 1392 TYR Chi-restraints excluded: chain A residue 1433 CYS Chi-restraints excluded: chain A residue 1462 TYR Chi-restraints excluded: chain A residue 1515 ASP Chi-restraints excluded: chain A residue 1543 THR Chi-restraints excluded: chain A residue 1547 THR Chi-restraints excluded: chain A residue 1576 LEU Chi-restraints excluded: chain A residue 1591 ILE Chi-restraints excluded: chain A residue 1598 ASN Chi-restraints excluded: chain A residue 1602 ASN Chi-restraints excluded: chain A residue 1618 SER Chi-restraints excluded: chain A residue 1662 TYR Chi-restraints excluded: chain A residue 1671 SER Chi-restraints excluded: chain A residue 1726 ILE Chi-restraints excluded: chain A residue 1771 VAL Chi-restraints excluded: chain A residue 1776 THR Chi-restraints excluded: chain A residue 1801 SER Chi-restraints excluded: chain A residue 1814 PHE Chi-restraints excluded: chain A residue 1821 ASN Chi-restraints excluded: chain A residue 1870 THR Chi-restraints excluded: chain A residue 1902 THR Chi-restraints excluded: chain A residue 1914 THR Chi-restraints excluded: chain A residue 1927 ILE Chi-restraints excluded: chain A residue 1947 VAL Chi-restraints excluded: chain A residue 1955 GLU Chi-restraints excluded: chain A residue 1963 THR Chi-restraints excluded: chain A residue 1988 THR Chi-restraints excluded: chain A residue 1992 THR Chi-restraints excluded: chain A residue 1995 ASP Chi-restraints excluded: chain A residue 2005 VAL Chi-restraints excluded: chain A residue 2078 VAL Chi-restraints excluded: chain A residue 2181 ASN Chi-restraints excluded: chain A residue 2235 VAL Chi-restraints excluded: chain A residue 2259 ASN Chi-restraints excluded: chain A residue 2362 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 198 optimal weight: 0.1980 chunk 178 optimal weight: 0.6980 chunk 98 optimal weight: 0.2980 chunk 60 optimal weight: 0.7980 chunk 120 optimal weight: 7.9990 chunk 95 optimal weight: 0.9980 chunk 184 optimal weight: 0.9980 chunk 71 optimal weight: 0.6980 chunk 112 optimal weight: 10.0000 chunk 137 optimal weight: 20.0000 chunk 213 optimal weight: 6.9990 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 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 106 GLN ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 574 ASN A 639 GLN A 732 GLN A 741 GLN ** A 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 876 ASN A 941 ASN A 949 ASN A 988 GLN A1109 ASN A1453 ASN A1584 ASN A1590 ASN A1593 ASN A1621 GLN A1631 ASN A1724 ASN A1761 GLN A1763 GLN A2058 ASN A2143 GLN ** A2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2319 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 19409 Z= 0.145 Angle : 0.531 9.434 26261 Z= 0.289 Chirality : 0.045 0.167 2898 Planarity : 0.004 0.087 3394 Dihedral : 7.183 66.737 2670 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.30 % Favored : 95.62 % Rotamer: Outliers : 3.62 % Allowed : 21.69 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.40 (0.17), residues: 2351 helix: 1.63 (0.20), residues: 665 sheet: -0.57 (0.22), residues: 468 loop : -1.24 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1949 HIS 0.004 0.001 HIS A 924 PHE 0.018 0.001 PHE A 937 TYR 0.017 0.001 TYR A 990 ARG 0.003 0.000 ARG A 526 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 152 time to evaluate : 2.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 LYS cc_start: 0.8437 (ttpt) cc_final: 0.8197 (ttpt) REVERT: A 1230 PHE cc_start: 0.1051 (OUTLIER) cc_final: 0.0056 (m-80) REVERT: A 1332 MET cc_start: 0.3261 (pmm) cc_final: 0.0485 (ttp) REVERT: A 1462 TYR cc_start: 0.7051 (OUTLIER) cc_final: 0.4648 (p90) REVERT: A 1490 ASN cc_start: 0.7411 (p0) cc_final: 0.7040 (p0) REVERT: A 1499 MET cc_start: 0.6479 (tpp) cc_final: 0.5416 (ttp) REVERT: A 1775 ASP cc_start: 0.5235 (OUTLIER) cc_final: 0.3991 (m-30) REVERT: A 2006 MET cc_start: 0.4228 (tpt) cc_final: 0.2414 (ttt) outliers start: 77 outliers final: 34 residues processed: 221 average time/residue: 1.1238 time to fit residues: 288.6757 Evaluate side-chains 168 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 131 time to evaluate : 2.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 574 ASN Chi-restraints excluded: chain A residue 576 GLU Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain A residue 874 HIS Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1018 THR Chi-restraints excluded: chain A residue 1019 ILE Chi-restraints excluded: chain A residue 1034 THR Chi-restraints excluded: chain A residue 1080 THR Chi-restraints excluded: chain A residue 1150 LEU Chi-restraints excluded: chain A residue 1167 CYS Chi-restraints excluded: chain A residue 1213 ILE Chi-restraints excluded: chain A residue 1230 PHE Chi-restraints excluded: chain A residue 1234 MET Chi-restraints excluded: chain A residue 1305 THR Chi-restraints excluded: chain A residue 1368 ILE Chi-restraints excluded: chain A residue 1418 ILE Chi-restraints excluded: chain A residue 1462 TYR Chi-restraints excluded: chain A residue 1547 THR Chi-restraints excluded: chain A residue 1598 ASN Chi-restraints excluded: chain A residue 1662 TYR Chi-restraints excluded: chain A residue 1726 ILE Chi-restraints excluded: chain A residue 1775 ASP Chi-restraints excluded: chain A residue 1776 THR Chi-restraints excluded: chain A residue 1814 PHE Chi-restraints excluded: chain A residue 1988 THR Chi-restraints excluded: chain A residue 2092 ASP Chi-restraints excluded: chain A residue 2143 GLN Chi-restraints excluded: chain A residue 2235 VAL Chi-restraints excluded: chain A residue 2253 LEU Chi-restraints excluded: chain A residue 2362 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 118 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 chunk 177 optimal weight: 5.9990 chunk 145 optimal weight: 6.9990 chunk 58 optimal weight: 0.1980 chunk 213 optimal weight: 30.0000 chunk 230 optimal weight: 2.9990 chunk 190 optimal weight: 8.9990 chunk 212 optimal weight: 9.9990 chunk 72 optimal weight: 2.9990 chunk 171 optimal weight: 2.9990 overall best weight: 2.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 413 ASN A 487 ASN A 795 HIS A1453 ASN A1580 ASN A1724 ASN A2058 ASN A2260 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 19409 Z= 0.311 Angle : 0.596 9.110 26261 Z= 0.321 Chirality : 0.048 0.175 2898 Planarity : 0.004 0.086 3394 Dihedral : 5.961 57.567 2576 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 4.74 % Allowed : 21.92 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.27 (0.17), residues: 2351 helix: 1.68 (0.20), residues: 664 sheet: -0.56 (0.23), residues: 472 loop : -1.08 (0.17), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 118 HIS 0.004 0.001 HIS A 99 PHE 0.027 0.002 PHE A 937 TYR 0.016 0.002 TYR A1646 ARG 0.005 0.001 ARG A1495 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 135 time to evaluate : 2.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 646 ILE cc_start: 0.9079 (OUTLIER) cc_final: 0.8580 (tp) REVERT: A 751 LYS cc_start: 0.8414 (OUTLIER) cc_final: 0.8163 (mttm) REVERT: A 1212 LYS cc_start: 0.2027 (OUTLIER) cc_final: 0.1392 (mmtm) REVERT: A 1230 PHE cc_start: 0.0977 (OUTLIER) cc_final: -0.0066 (m-80) REVERT: A 1302 VAL cc_start: 0.5491 (OUTLIER) cc_final: 0.4969 (p) REVERT: A 1327 LEU cc_start: 0.7616 (OUTLIER) cc_final: 0.7177 (tp) REVERT: A 1332 MET cc_start: 0.3574 (pmm) cc_final: 0.0478 (ttp) REVERT: A 1462 TYR cc_start: 0.7361 (OUTLIER) cc_final: 0.4357 (p90) REVERT: A 1490 ASN cc_start: 0.7395 (p0) cc_final: 0.7035 (p0) REVERT: A 1576 LEU cc_start: 0.2159 (OUTLIER) cc_final: 0.1535 (mp) REVERT: A 1795 LYS cc_start: 0.8648 (OUTLIER) cc_final: 0.8411 (tttt) REVERT: A 2006 MET cc_start: 0.4232 (tpt) cc_final: 0.2422 (ttt) REVERT: A 2198 ASP cc_start: 0.1759 (OUTLIER) cc_final: 0.0934 (t0) outliers start: 101 outliers final: 48 residues processed: 227 average time/residue: 0.9971 time to fit residues: 265.1896 Evaluate side-chains 176 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 118 time to evaluate : 1.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 223 LYS Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 574 ASN Chi-restraints excluded: chain A residue 576 GLU Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 751 LYS Chi-restraints excluded: chain A residue 830 SER Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 958 THR Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1018 THR Chi-restraints excluded: chain A residue 1019 ILE Chi-restraints excluded: chain A residue 1080 THR Chi-restraints excluded: chain A residue 1150 LEU Chi-restraints excluded: chain A residue 1167 CYS Chi-restraints excluded: chain A residue 1212 LYS Chi-restraints excluded: chain A residue 1213 ILE Chi-restraints excluded: chain A residue 1230 PHE Chi-restraints excluded: chain A residue 1234 MET Chi-restraints excluded: chain A residue 1302 VAL Chi-restraints excluded: chain A residue 1305 THR Chi-restraints excluded: chain A residue 1327 LEU Chi-restraints excluded: chain A residue 1368 ILE Chi-restraints excluded: chain A residue 1418 ILE Chi-restraints excluded: chain A residue 1462 TYR Chi-restraints excluded: chain A residue 1515 ASP Chi-restraints excluded: chain A residue 1547 THR Chi-restraints excluded: chain A residue 1576 LEU Chi-restraints excluded: chain A residue 1598 ASN Chi-restraints excluded: chain A residue 1626 CYS Chi-restraints excluded: chain A residue 1650 VAL Chi-restraints excluded: chain A residue 1662 TYR Chi-restraints excluded: chain A residue 1726 ILE Chi-restraints excluded: chain A residue 1775 ASP Chi-restraints excluded: chain A residue 1776 THR Chi-restraints excluded: chain A residue 1779 ASP Chi-restraints excluded: chain A residue 1795 LYS Chi-restraints excluded: chain A residue 1821 ASN Chi-restraints excluded: chain A residue 1927 ILE Chi-restraints excluded: chain A residue 1947 VAL Chi-restraints excluded: chain A residue 1988 THR Chi-restraints excluded: chain A residue 1995 ASP Chi-restraints excluded: chain A residue 2092 ASP Chi-restraints excluded: chain A residue 2176 ASN Chi-restraints excluded: chain A residue 2198 ASP Chi-restraints excluded: chain A residue 2235 VAL Chi-restraints excluded: chain A residue 2362 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 211 optimal weight: 0.0570 chunk 160 optimal weight: 4.9990 chunk 110 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 102 optimal weight: 10.0000 chunk 143 optimal weight: 6.9990 chunk 214 optimal weight: 1.9990 chunk 227 optimal weight: 0.8980 chunk 112 optimal weight: 0.5980 chunk 203 optimal weight: 20.0000 chunk 61 optimal weight: 3.9990 overall best weight: 1.5102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 ASN A1453 ASN A1530 ASN A1580 ASN A1724 ASN A2058 ASN A2143 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19409 Z= 0.210 Angle : 0.542 9.784 26261 Z= 0.291 Chirality : 0.046 0.180 2898 Planarity : 0.004 0.085 3394 Dihedral : 5.558 58.322 2573 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 4.79 % Allowed : 22.44 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: 0.03 (0.17), residues: 2351 helix: 1.98 (0.20), residues: 664 sheet: -0.43 (0.23), residues: 472 loop : -0.91 (0.17), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 118 HIS 0.003 0.001 HIS A 924 PHE 0.026 0.001 PHE A1474 TYR 0.017 0.001 TYR A 990 ARG 0.004 0.000 ARG A1495 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 130 time to evaluate : 2.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 646 ILE cc_start: 0.9026 (OUTLIER) cc_final: 0.8564 (tp) REVERT: A 814 ASP cc_start: 0.7688 (OUTLIER) cc_final: 0.7224 (p0) REVERT: A 897 ARG cc_start: 0.6552 (OUTLIER) cc_final: 0.6261 (ptm160) REVERT: A 1046 LYS cc_start: 0.7309 (tppt) cc_final: 0.7103 (tppt) REVERT: A 1230 PHE cc_start: 0.1062 (OUTLIER) cc_final: -0.0018 (m-80) REVERT: A 1302 VAL cc_start: 0.5702 (OUTLIER) cc_final: 0.5234 (p) REVERT: A 1332 MET cc_start: 0.3598 (pmm) cc_final: 0.0627 (ttp) REVERT: A 1462 TYR cc_start: 0.7210 (OUTLIER) cc_final: 0.4614 (p90) REVERT: A 1490 ASN cc_start: 0.7440 (p0) cc_final: 0.7088 (p0) REVERT: A 1499 MET cc_start: 0.6821 (tpp) cc_final: 0.5773 (ttp) REVERT: A 1576 LEU cc_start: 0.2067 (OUTLIER) cc_final: 0.1479 (mp) REVERT: A 2006 MET cc_start: 0.4053 (tpt) cc_final: 0.2283 (ttt) REVERT: A 2198 ASP cc_start: 0.1911 (OUTLIER) cc_final: 0.1040 (t0) outliers start: 102 outliers final: 56 residues processed: 218 average time/residue: 1.0956 time to fit residues: 280.6153 Evaluate side-chains 184 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 120 time to evaluate : 2.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 574 ASN Chi-restraints excluded: chain A residue 576 GLU Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 814 ASP Chi-restraints excluded: chain A residue 830 SER Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain A residue 874 HIS Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 890 SER Chi-restraints excluded: chain A residue 897 ARG Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1018 THR Chi-restraints excluded: chain A residue 1019 ILE Chi-restraints excluded: chain A residue 1055 LEU Chi-restraints excluded: chain A residue 1080 THR Chi-restraints excluded: chain A residue 1150 LEU Chi-restraints excluded: chain A residue 1167 CYS Chi-restraints excluded: chain A residue 1213 ILE Chi-restraints excluded: chain A residue 1230 PHE Chi-restraints excluded: chain A residue 1234 MET Chi-restraints excluded: chain A residue 1302 VAL Chi-restraints excluded: chain A residue 1305 THR Chi-restraints excluded: chain A residue 1368 ILE Chi-restraints excluded: chain A residue 1418 ILE Chi-restraints excluded: chain A residue 1462 TYR Chi-restraints excluded: chain A residue 1515 ASP Chi-restraints excluded: chain A residue 1547 THR Chi-restraints excluded: chain A residue 1576 LEU Chi-restraints excluded: chain A residue 1591 ILE Chi-restraints excluded: chain A residue 1626 CYS Chi-restraints excluded: chain A residue 1650 VAL Chi-restraints excluded: chain A residue 1662 TYR Chi-restraints excluded: chain A residue 1726 ILE Chi-restraints excluded: chain A residue 1748 SER Chi-restraints excluded: chain A residue 1775 ASP Chi-restraints excluded: chain A residue 1776 THR Chi-restraints excluded: chain A residue 1779 ASP Chi-restraints excluded: chain A residue 1821 ASN Chi-restraints excluded: chain A residue 1842 SER Chi-restraints excluded: chain A residue 1895 LEU Chi-restraints excluded: chain A residue 1927 ILE Chi-restraints excluded: chain A residue 1930 LEU Chi-restraints excluded: chain A residue 1947 VAL Chi-restraints excluded: chain A residue 1976 ASN Chi-restraints excluded: chain A residue 1988 THR Chi-restraints excluded: chain A residue 1995 ASP Chi-restraints excluded: chain A residue 2092 ASP Chi-restraints excluded: chain A residue 2143 GLN Chi-restraints excluded: chain A residue 2198 ASP Chi-restraints excluded: chain A residue 2235 VAL Chi-restraints excluded: chain A residue 2253 LEU Chi-restraints excluded: chain A residue 2361 VAL Chi-restraints excluded: chain A residue 2362 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 189 optimal weight: 6.9990 chunk 128 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 169 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 193 optimal weight: 0.8980 chunk 157 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 115 optimal weight: 0.9990 chunk 203 optimal weight: 20.0000 chunk 57 optimal weight: 0.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 ASN A1453 ASN A1580 ASN A1724 ASN A2058 ASN A2143 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19409 Z= 0.196 Angle : 0.529 10.492 26261 Z= 0.283 Chirality : 0.046 0.197 2898 Planarity : 0.004 0.082 3394 Dihedral : 5.379 55.289 2570 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 4.84 % Allowed : 22.49 % Favored : 72.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: 0.22 (0.17), residues: 2351 helix: 2.12 (0.20), residues: 665 sheet: -0.30 (0.23), residues: 484 loop : -0.80 (0.17), residues: 1202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 118 HIS 0.003 0.001 HIS A 924 PHE 0.030 0.001 PHE A1474 TYR 0.014 0.001 TYR A 793 ARG 0.002 0.000 ARG A1517 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 133 time to evaluate : 2.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8076 (tpt) cc_final: 0.7839 (tpt) REVERT: A 646 ILE cc_start: 0.9027 (OUTLIER) cc_final: 0.8564 (tp) REVERT: A 814 ASP cc_start: 0.7649 (OUTLIER) cc_final: 0.7197 (p0) REVERT: A 897 ARG cc_start: 0.6545 (OUTLIER) cc_final: 0.6188 (ptm160) REVERT: A 1230 PHE cc_start: 0.1093 (OUTLIER) cc_final: -0.0027 (m-80) REVERT: A 1302 VAL cc_start: 0.5637 (OUTLIER) cc_final: 0.5160 (p) REVERT: A 1327 LEU cc_start: 0.7624 (OUTLIER) cc_final: 0.7169 (tp) REVERT: A 1462 TYR cc_start: 0.7296 (OUTLIER) cc_final: 0.4544 (p90) REVERT: A 1490 ASN cc_start: 0.7375 (p0) cc_final: 0.7019 (p0) REVERT: A 1499 MET cc_start: 0.6729 (tpp) cc_final: 0.5644 (ttp) REVERT: A 1576 LEU cc_start: 0.2024 (OUTLIER) cc_final: 0.1391 (mp) REVERT: A 1598 ASN cc_start: 0.7157 (OUTLIER) cc_final: 0.6770 (p0) REVERT: A 1775 ASP cc_start: 0.5113 (OUTLIER) cc_final: 0.3938 (m-30) REVERT: A 2006 MET cc_start: 0.3976 (tpt) cc_final: 0.2138 (ttt) REVERT: A 2198 ASP cc_start: 0.2122 (OUTLIER) cc_final: 0.1167 (t0) outliers start: 103 outliers final: 62 residues processed: 224 average time/residue: 1.0438 time to fit residues: 276.7928 Evaluate side-chains 190 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 117 time to evaluate : 2.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 574 ASN Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain A residue 814 ASP Chi-restraints excluded: chain A residue 830 SER Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain A residue 874 HIS Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 890 SER Chi-restraints excluded: chain A residue 897 ARG Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 951 ASP Chi-restraints excluded: chain A residue 958 THR Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1018 THR Chi-restraints excluded: chain A residue 1019 ILE Chi-restraints excluded: chain A residue 1055 LEU Chi-restraints excluded: chain A residue 1080 THR Chi-restraints excluded: chain A residue 1150 LEU Chi-restraints excluded: chain A residue 1167 CYS Chi-restraints excluded: chain A residue 1205 VAL Chi-restraints excluded: chain A residue 1230 PHE Chi-restraints excluded: chain A residue 1234 MET Chi-restraints excluded: chain A residue 1302 VAL Chi-restraints excluded: chain A residue 1305 THR Chi-restraints excluded: chain A residue 1327 LEU Chi-restraints excluded: chain A residue 1328 SER Chi-restraints excluded: chain A residue 1368 ILE Chi-restraints excluded: chain A residue 1418 ILE Chi-restraints excluded: chain A residue 1462 TYR Chi-restraints excluded: chain A residue 1515 ASP Chi-restraints excluded: chain A residue 1543 THR Chi-restraints excluded: chain A residue 1547 THR Chi-restraints excluded: chain A residue 1576 LEU Chi-restraints excluded: chain A residue 1591 ILE Chi-restraints excluded: chain A residue 1598 ASN Chi-restraints excluded: chain A residue 1602 ASN Chi-restraints excluded: chain A residue 1626 CYS Chi-restraints excluded: chain A residue 1650 VAL Chi-restraints excluded: chain A residue 1662 TYR Chi-restraints excluded: chain A residue 1726 ILE Chi-restraints excluded: chain A residue 1775 ASP Chi-restraints excluded: chain A residue 1776 THR Chi-restraints excluded: chain A residue 1779 ASP Chi-restraints excluded: chain A residue 1821 ASN Chi-restraints excluded: chain A residue 1842 SER Chi-restraints excluded: chain A residue 1927 ILE Chi-restraints excluded: chain A residue 1930 LEU Chi-restraints excluded: chain A residue 1947 VAL Chi-restraints excluded: chain A residue 1976 ASN Chi-restraints excluded: chain A residue 1988 THR Chi-restraints excluded: chain A residue 1995 ASP Chi-restraints excluded: chain A residue 2092 ASP Chi-restraints excluded: chain A residue 2143 GLN Chi-restraints excluded: chain A residue 2176 ASN Chi-restraints excluded: chain A residue 2198 ASP Chi-restraints excluded: chain A residue 2235 VAL Chi-restraints excluded: chain A residue 2253 LEU Chi-restraints excluded: chain A residue 2361 VAL Chi-restraints excluded: chain A residue 2362 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 76 optimal weight: 2.9990 chunk 204 optimal weight: 3.9990 chunk 44 optimal weight: 0.3980 chunk 133 optimal weight: 9.9990 chunk 56 optimal weight: 1.9990 chunk 227 optimal weight: 20.0000 chunk 188 optimal weight: 3.9990 chunk 105 optimal weight: 10.0000 chunk 18 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 119 optimal weight: 0.9980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 ASN A 574 ASN A1453 ASN A1580 ASN A1724 ASN A2058 ASN A2143 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19409 Z= 0.186 Angle : 0.523 10.959 26261 Z= 0.280 Chirality : 0.045 0.202 2898 Planarity : 0.004 0.081 3394 Dihedral : 5.271 53.066 2570 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 4.51 % Allowed : 22.77 % Favored : 72.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: 0.33 (0.17), residues: 2351 helix: 2.17 (0.20), residues: 667 sheet: -0.22 (0.23), residues: 483 loop : -0.71 (0.18), residues: 1201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 118 HIS 0.003 0.001 HIS A 924 PHE 0.031 0.001 PHE A1474 TYR 0.019 0.001 TYR A 990 ARG 0.002 0.000 ARG A1495 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 132 time to evaluate : 2.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8080 (tpt) cc_final: 0.7834 (tpt) REVERT: A 197 ASN cc_start: 0.7008 (m-40) cc_final: 0.6787 (t0) REVERT: A 646 ILE cc_start: 0.9016 (OUTLIER) cc_final: 0.8552 (tp) REVERT: A 751 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.8073 (mttm) REVERT: A 814 ASP cc_start: 0.7595 (OUTLIER) cc_final: 0.7111 (p0) REVERT: A 1230 PHE cc_start: 0.1107 (OUTLIER) cc_final: -0.0031 (m-80) REVERT: A 1302 VAL cc_start: 0.5830 (OUTLIER) cc_final: 0.5399 (p) REVERT: A 1327 LEU cc_start: 0.7704 (OUTLIER) cc_final: 0.7234 (tp) REVERT: A 1332 MET cc_start: 0.3578 (pmm) cc_final: 0.0303 (ttp) REVERT: A 1462 TYR cc_start: 0.7359 (OUTLIER) cc_final: 0.4551 (p90) REVERT: A 1490 ASN cc_start: 0.7325 (p0) cc_final: 0.6967 (p0) REVERT: A 1499 MET cc_start: 0.6618 (tpp) cc_final: 0.5532 (ttp) REVERT: A 1576 LEU cc_start: 0.1948 (OUTLIER) cc_final: 0.1323 (mp) REVERT: A 1598 ASN cc_start: 0.7106 (OUTLIER) cc_final: 0.6777 (p0) REVERT: A 1641 ILE cc_start: 0.8066 (mt) cc_final: 0.7780 (mt) REVERT: A 1775 ASP cc_start: 0.5058 (OUTLIER) cc_final: 0.3813 (m-30) REVERT: A 2006 MET cc_start: 0.3863 (tpt) cc_final: 0.2023 (ttt) outliers start: 96 outliers final: 60 residues processed: 217 average time/residue: 1.0540 time to fit residues: 268.8240 Evaluate side-chains 193 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 123 time to evaluate : 2.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 574 ASN Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 751 LYS Chi-restraints excluded: chain A residue 814 ASP Chi-restraints excluded: chain A residue 830 SER Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain A residue 874 HIS Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 890 SER Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 958 THR Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1019 ILE Chi-restraints excluded: chain A residue 1055 LEU Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain A residue 1080 THR Chi-restraints excluded: chain A residue 1167 CYS Chi-restraints excluded: chain A residue 1205 VAL Chi-restraints excluded: chain A residue 1213 ILE Chi-restraints excluded: chain A residue 1230 PHE Chi-restraints excluded: chain A residue 1234 MET Chi-restraints excluded: chain A residue 1264 TRP Chi-restraints excluded: chain A residue 1302 VAL Chi-restraints excluded: chain A residue 1305 THR Chi-restraints excluded: chain A residue 1327 LEU Chi-restraints excluded: chain A residue 1328 SER Chi-restraints excluded: chain A residue 1368 ILE Chi-restraints excluded: chain A residue 1418 ILE Chi-restraints excluded: chain A residue 1443 ILE Chi-restraints excluded: chain A residue 1462 TYR Chi-restraints excluded: chain A residue 1515 ASP Chi-restraints excluded: chain A residue 1543 THR Chi-restraints excluded: chain A residue 1547 THR Chi-restraints excluded: chain A residue 1576 LEU Chi-restraints excluded: chain A residue 1591 ILE Chi-restraints excluded: chain A residue 1598 ASN Chi-restraints excluded: chain A residue 1626 CYS Chi-restraints excluded: chain A residue 1650 VAL Chi-restraints excluded: chain A residue 1662 TYR Chi-restraints excluded: chain A residue 1714 ILE Chi-restraints excluded: chain A residue 1726 ILE Chi-restraints excluded: chain A residue 1748 SER Chi-restraints excluded: chain A residue 1775 ASP Chi-restraints excluded: chain A residue 1776 THR Chi-restraints excluded: chain A residue 1821 ASN Chi-restraints excluded: chain A residue 1842 SER Chi-restraints excluded: chain A residue 1927 ILE Chi-restraints excluded: chain A residue 1947 VAL Chi-restraints excluded: chain A residue 1976 ASN Chi-restraints excluded: chain A residue 1988 THR Chi-restraints excluded: chain A residue 1995 ASP Chi-restraints excluded: chain A residue 2092 ASP Chi-restraints excluded: chain A residue 2125 ILE Chi-restraints excluded: chain A residue 2235 VAL Chi-restraints excluded: chain A residue 2253 LEU Chi-restraints excluded: chain A residue 2361 VAL Chi-restraints excluded: chain A residue 2362 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 219 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 129 optimal weight: 10.0000 chunk 166 optimal weight: 0.9990 chunk 128 optimal weight: 6.9990 chunk 191 optimal weight: 10.0000 chunk 126 optimal weight: 0.7980 chunk 226 optimal weight: 0.0170 chunk 141 optimal weight: 10.0000 chunk 138 optimal weight: 3.9990 chunk 104 optimal weight: 6.9990 overall best weight: 1.7624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 ASN A1445 GLN A1580 ASN ** A1652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1724 ASN A2058 ASN ** A2143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 19409 Z= 0.234 Angle : 0.548 11.825 26261 Z= 0.294 Chirality : 0.046 0.217 2898 Planarity : 0.004 0.080 3394 Dihedral : 5.310 50.145 2570 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 4.79 % Allowed : 23.15 % Favored : 72.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: 0.28 (0.17), residues: 2351 helix: 2.07 (0.20), residues: 666 sheet: -0.20 (0.23), residues: 481 loop : -0.73 (0.18), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 118 HIS 0.003 0.001 HIS A 99 PHE 0.031 0.001 PHE A1474 TYR 0.014 0.001 TYR A1646 ARG 0.005 0.000 ARG A1653 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 124 time to evaluate : 2.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8055 (tpt) cc_final: 0.7836 (tpt) REVERT: A 2 ASN cc_start: 0.8201 (OUTLIER) cc_final: 0.7842 (t0) REVERT: A 570 MET cc_start: 0.9014 (OUTLIER) cc_final: 0.7800 (mmt) REVERT: A 646 ILE cc_start: 0.9044 (OUTLIER) cc_final: 0.8540 (tp) REVERT: A 814 ASP cc_start: 0.7715 (OUTLIER) cc_final: 0.7240 (p0) REVERT: A 1212 LYS cc_start: 0.2301 (OUTLIER) cc_final: 0.1622 (mmtm) REVERT: A 1230 PHE cc_start: 0.1121 (OUTLIER) cc_final: -0.0036 (m-80) REVERT: A 1302 VAL cc_start: 0.5798 (OUTLIER) cc_final: 0.5367 (p) REVERT: A 1327 LEU cc_start: 0.7763 (OUTLIER) cc_final: 0.7266 (tp) REVERT: A 1332 MET cc_start: 0.3829 (pmm) cc_final: 0.0611 (tpp) REVERT: A 1470 LYS cc_start: 0.7716 (OUTLIER) cc_final: 0.7379 (mtmm) REVERT: A 1490 ASN cc_start: 0.7258 (p0) cc_final: 0.6935 (p0) REVERT: A 1495 ARG cc_start: 0.7144 (mtp-110) cc_final: 0.6927 (mmm-85) REVERT: A 1499 MET cc_start: 0.6541 (tpp) cc_final: 0.5462 (ttp) REVERT: A 1576 LEU cc_start: 0.2072 (OUTLIER) cc_final: 0.1366 (mp) REVERT: A 1598 ASN cc_start: 0.7114 (OUTLIER) cc_final: 0.6799 (p0) REVERT: A 1641 ILE cc_start: 0.8102 (mt) cc_final: 0.7816 (mt) REVERT: A 1775 ASP cc_start: 0.4964 (OUTLIER) cc_final: 0.3833 (m-30) REVERT: A 2006 MET cc_start: 0.3836 (tpt) cc_final: 0.2397 (ttt) REVERT: A 2198 ASP cc_start: 0.2700 (OUTLIER) cc_final: 0.1495 (t0) outliers start: 102 outliers final: 67 residues processed: 213 average time/residue: 1.0402 time to fit residues: 261.6762 Evaluate side-chains 203 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 123 time to evaluate : 2.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASN Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 444 MET Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 574 ASN Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain A residue 796 GLU Chi-restraints excluded: chain A residue 814 ASP Chi-restraints excluded: chain A residue 830 SER Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 890 SER Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 958 THR Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1055 LEU Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain A residue 1080 THR Chi-restraints excluded: chain A residue 1150 LEU Chi-restraints excluded: chain A residue 1167 CYS Chi-restraints excluded: chain A residue 1205 VAL Chi-restraints excluded: chain A residue 1212 LYS Chi-restraints excluded: chain A residue 1213 ILE Chi-restraints excluded: chain A residue 1230 PHE Chi-restraints excluded: chain A residue 1234 MET Chi-restraints excluded: chain A residue 1264 TRP Chi-restraints excluded: chain A residue 1302 VAL Chi-restraints excluded: chain A residue 1305 THR Chi-restraints excluded: chain A residue 1327 LEU Chi-restraints excluded: chain A residue 1328 SER Chi-restraints excluded: chain A residue 1368 ILE Chi-restraints excluded: chain A residue 1418 ILE Chi-restraints excluded: chain A residue 1443 ILE Chi-restraints excluded: chain A residue 1462 TYR Chi-restraints excluded: chain A residue 1470 LYS Chi-restraints excluded: chain A residue 1515 ASP Chi-restraints excluded: chain A residue 1543 THR Chi-restraints excluded: chain A residue 1547 THR Chi-restraints excluded: chain A residue 1576 LEU Chi-restraints excluded: chain A residue 1591 ILE Chi-restraints excluded: chain A residue 1598 ASN Chi-restraints excluded: chain A residue 1626 CYS Chi-restraints excluded: chain A residue 1650 VAL Chi-restraints excluded: chain A residue 1662 TYR Chi-restraints excluded: chain A residue 1714 ILE Chi-restraints excluded: chain A residue 1726 ILE Chi-restraints excluded: chain A residue 1748 SER Chi-restraints excluded: chain A residue 1775 ASP Chi-restraints excluded: chain A residue 1776 THR Chi-restraints excluded: chain A residue 1821 ASN Chi-restraints excluded: chain A residue 1842 SER Chi-restraints excluded: chain A residue 1927 ILE Chi-restraints excluded: chain A residue 1930 LEU Chi-restraints excluded: chain A residue 1947 VAL Chi-restraints excluded: chain A residue 1976 ASN Chi-restraints excluded: chain A residue 1988 THR Chi-restraints excluded: chain A residue 1995 ASP Chi-restraints excluded: chain A residue 2092 ASP Chi-restraints excluded: chain A residue 2176 ASN Chi-restraints excluded: chain A residue 2198 ASP Chi-restraints excluded: chain A residue 2235 VAL Chi-restraints excluded: chain A residue 2253 LEU Chi-restraints excluded: chain A residue 2320 TYR Chi-restraints excluded: chain A residue 2361 VAL Chi-restraints excluded: chain A residue 2362 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 63.5418 > 50: distance: 84 - 89: 4.047 distance: 89 - 90: 4.248 distance: 90 - 91: 6.923 distance: 90 - 93: 8.662 distance: 91 - 92: 8.494 distance: 91 - 98: 7.381 distance: 93 - 94: 10.875 distance: 94 - 95: 9.284 distance: 95 - 96: 8.204 distance: 95 - 97: 4.294 distance: 98 - 99: 11.011 distance: 99 - 100: 10.303 distance: 99 - 102: 9.305 distance: 100 - 101: 3.988 distance: 100 - 106: 8.580 distance: 103 - 104: 9.920 distance: 106 - 107: 4.258 distance: 107 - 108: 8.027 distance: 107 - 110: 4.988 distance: 108 - 109: 11.148 distance: 108 - 113: 9.114 distance: 110 - 111: 10.778 distance: 110 - 112: 17.408 distance: 113 - 114: 12.762 distance: 114 - 115: 4.368 distance: 114 - 117: 7.902 distance: 115 - 116: 6.892 distance: 115 - 119: 7.012 distance: 117 - 118: 16.635 distance: 119 - 120: 10.613 distance: 120 - 121: 13.839 distance: 120 - 123: 8.219 distance: 121 - 122: 10.614 distance: 121 - 126: 10.704 distance: 122 - 149: 11.061 distance: 123 - 124: 11.971 distance: 123 - 125: 15.334 distance: 126 - 127: 4.220 distance: 127 - 128: 7.002 distance: 127 - 130: 7.031 distance: 128 - 129: 7.095 distance: 128 - 132: 5.029 distance: 129 - 157: 39.082 distance: 130 - 131: 7.895 distance: 132 - 133: 4.164 distance: 133 - 134: 11.929 distance: 133 - 136: 5.650 distance: 134 - 135: 13.138 distance: 134 - 141: 11.516 distance: 135 - 163: 22.286 distance: 136 - 137: 26.147 distance: 138 - 139: 16.964 distance: 139 - 140: 10.893 distance: 141 - 142: 5.687 distance: 142 - 143: 12.166 distance: 142 - 145: 21.513 distance: 143 - 144: 25.244 distance: 143 - 149: 21.885 distance: 144 - 170: 28.411 distance: 145 - 146: 5.601 distance: 145 - 147: 17.850 distance: 146 - 148: 26.374 distance: 149 - 150: 53.363 distance: 150 - 151: 14.259 distance: 150 - 153: 17.533 distance: 151 - 157: 14.423 distance: 153 - 154: 46.587 distance: 153 - 155: 14.242 distance: 154 - 156: 36.708 distance: 157 - 158: 46.125 distance: 158 - 159: 11.989 distance: 159 - 160: 27.314 distance: 159 - 163: 26.981 distance: 161 - 162: 39.878