Starting phenix.real_space_refine on Sat Jun 29 15:36:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x2i_38011/06_2024/8x2i_38011.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x2i_38011/06_2024/8x2i_38011.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x2i_38011/06_2024/8x2i_38011.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x2i_38011/06_2024/8x2i_38011.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x2i_38011/06_2024/8x2i_38011.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x2i_38011/06_2024/8x2i_38011.pdb" } resolution = 2.5 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= 0.107 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 46 5.16 5 C 11942 2.51 5 N 2959 2.21 5 O 3697 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 GLU 23": "OE1" <-> "OE2" Residue "A TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 32": "OE1" <-> "OE2" Residue "A TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 39": "OE1" <-> "OE2" 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 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 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 GLU 199": "OE1" <-> "OE2" Residue "A TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 213": "OE1" <-> "OE2" Residue "A GLU 219": "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 GLU 313": "OE1" <-> "OE2" Residue "A GLU 318": "OE1" <-> "OE2" 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 ASP 355": "OD1" <-> "OD2" Residue "A GLU 358": "OE1" <-> "OE2" Residue "A ASP 364": "OD1" <-> "OD2" Residue "A ASP 365": "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 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 GLU 495": "OE1" <-> "OE2" Residue "A GLU 502": "OE1" <-> "OE2" Residue "A GLU 513": "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 ASP 560": "OD1" <-> "OD2" Residue "A TYR 561": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 573": "NH1" <-> "NH2" 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 ASP 601": "OD1" <-> "OD2" Residue "A TYR 608": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 613": "OE1" <-> "OE2" Residue "A TYR 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 621": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 625": "OD1" <-> "OD2" 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 PHE 658": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 663": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 667": "OD1" <-> "OD2" Residue "A GLU 674": "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 ASP 756": "OD1" <-> "OD2" 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 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 823": "OE1" <-> "OE2" Residue "A GLU 825": "OE1" <-> "OE2" Residue "A ASP 833": "OD1" <-> "OD2" Residue "A ASP 850": "OD1" <-> "OD2" Residue "A TYR 854": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 863": "OE1" <-> "OE2" Residue "A ASP 867": "OD1" <-> "OD2" Residue "A TYR 870": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 883": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 896": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 900": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 PHE 937": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 955": "OE1" <-> "OE2" Residue "A PHE 963": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 964": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 970": "OE1" <-> "OE2" Residue "A TYR 990": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 994": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1110": "OE1" <-> "OE2" Residue "A TYR 1123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1131": "OE1" <-> "OE2" Residue "A GLU 1133": "OE1" <-> "OE2" Residue "A ASP 1140": "OD1" <-> "OD2" Residue "A ASP 1141": "OD1" <-> "OD2" Residue "A GLU 1168": "OE1" <-> "OE2" Residue "A GLU 1173": "OE1" <-> "OE2" Residue "A ASP 1183": "OD1" <-> "OD2" Residue "A PHE 1188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1211": "OE1" <-> "OE2" Residue "A ASP 1214": "OD1" <-> "OD2" Residue "A PHE 1230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1233": "OE1" <-> "OE2" Residue "A ASP 1246": "OD1" <-> "OD2" Residue "A TYR 1258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1272": "OD1" <-> "OD2" Residue "A ASP 1284": "OD1" <-> "OD2" Residue "A PHE 1298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1306": "OE1" <-> "OE2" Residue "A ASP 1335": "OD1" <-> "OD2" Residue "A ASP 1342": "OD1" <-> "OD2" Residue "A ASP 1349": "OD1" <-> "OD2" Residue "A GLU 1358": "OE1" <-> "OE2" Residue "A GLU 1361": "OE1" <-> "OE2" Residue "A GLU 1366": "OE1" <-> "OE2" Residue "A GLU 1369": "OE1" <-> "OE2" Residue "A PHE 1391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1394": "OD1" <-> "OD2" Residue "A GLU 1397": "OE1" <-> "OE2" Residue "A PHE 1401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1410": "OE1" <-> "OE2" Residue "A ASP 1419": "OD1" <-> "OD2" Residue "A PHE 1452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1455": "OE1" <-> "OE2" Residue "A ASP 1466": "OD1" <-> "OD2" Residue "A TYR 1471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1487": "OE1" <-> "OE2" Residue "A PHE 1506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1523": "OD1" <-> "OD2" Residue "A TYR 1531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1532": "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 GLU 1587": "OE1" <-> "OE2" Residue "A PHE 1605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1608": "OD1" <-> "OD2" Residue "A PHE 1622": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1635": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1639": "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 1688": "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 ASP 1746": "OD1" <-> "OD2" 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 1783": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1785": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ASP 1820": "OD1" <-> "OD2" Residue "A PHE 1824": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1841": "OD1" <-> "OD2" 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 1866": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1879": "OE1" <-> "OE2" Residue "A ASP 1886": "OD1" <-> "OD2" Residue "A TYR 1887": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1908": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1916": "OD1" <-> "OD2" Residue "A GLU 1917": "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-5370/modules/chem_data/mon_lib" Total number of atoms: 18645 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 18644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2303, 18644 Classifications: {'peptide': 2303} Link IDs: {'PCIS': 1, 'PTRANS': 53, 'TRANS': 2248} Chain breaks: 3 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 63.049 86.639 163.551 1.00 8.69 S Time building chain proxies: 10.01, per 1000 atoms: 0.54 Number of scatterers: 18645 At special positions: 0 Unit cell: (144.571, 119.57, 247.836, 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 46 16.00 O 3697 8.00 N 2959 7.00 C 11942 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: 6.57 Conformation dependent library (CDL) restraints added in 3.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A3000 " pdb="ZN ZN A3000 " - pdb=" ND1 HIS A 653 " pdb="ZN ZN A3000 " - pdb=" SG CYS A 698 " pdb="ZN ZN A3000 " - pdb=" NE2 HIS A 757 " 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4352 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 40 sheets defined 31.4% alpha, 23.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.63 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 88 removed outlier: 3.502A pdb=" N ASN A 88 " --> pdb=" O LEU A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 122 removed outlier: 3.572A pdb=" N ILE A 112 " --> pdb=" O ASN A 108 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN A 117 " --> pdb=" O ASN A 113 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N TRP A 118 " --> pdb=" O TYR A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 156 Processing helix chain 'A' and resid 167 through 197 Processing helix chain 'A' and resid 201 through 214 removed outlier: 3.577A 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 281 removed outlier: 3.958A 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: 3.972A pdb=" N SER A 352 " --> pdb=" O SER A 348 " (cutoff:3.500A) removed outlier: 4.434A 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 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 451 through 456 removed outlier: 4.682A pdb=" N LEU A 454 " --> pdb=" O THR A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 468 Processing helix chain 'A' and resid 470 through 484 removed outlier: 3.826A 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: 3.750A pdb=" N ASP A 601 " --> pdb=" O LEU A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 643 removed outlier: 4.265A pdb=" N ASN A 642 " --> pdb=" O GLN A 639 " (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: 4.891A pdb=" N ASP A 721 " --> pdb=" O LEU A 717 " (cutoff:3.500A) removed outlier: 5.246A 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 774 Processing helix chain 'A' and resid 793 through 809 removed outlier: 3.821A pdb=" N LEU A 797 " --> pdb=" O TYR A 793 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 839 Processing helix chain 'A' and resid 850 through 876 removed outlier: 3.527A pdb=" N ASN A 876 " --> pdb=" O LEU A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 934 Processing helix chain 'A' and resid 954 through 971 removed outlier: 3.992A pdb=" N THR A 958 " --> pdb=" O HIS A 954 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N PHE A 964 " --> pdb=" O ASN A 960 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR A 971 " --> pdb=" O SER A 967 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 995 removed outlier: 3.592A pdb=" N SER A 995 " --> pdb=" O ALA A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1001 Processing helix chain 'A' and resid 1003 through 1017 Processing helix chain 'A' and resid 1073 through 1090 Processing helix chain 'A' and resid 1116 through 1129 Processing helix chain 'A' and resid 1129 through 1134 Processing helix chain 'A' and resid 1245 through 1258 removed outlier: 3.594A pdb=" N TYR A1258 " --> pdb=" O ILE A1254 " (cutoff:3.500A) Processing helix chain 'A' and resid 1305 through 1311 Processing helix chain 'A' and resid 1348 through 1352 Processing helix chain 'A' and resid 1370 through 1374 removed outlier: 3.721A pdb=" N SER A1373 " --> pdb=" O ASN A1370 " (cutoff:3.500A) Processing helix chain 'A' and resid 1432 through 1448 removed outlier: 5.639A pdb=" N SER A1441 " --> pdb=" O ILE A1437 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N ASP A1442 " --> pdb=" O GLU A1438 " (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 Processing helix chain 'A' and resid 1737 through 1739 No H-bonds generated for 'chain 'A' and resid 1737 through 1739' Processing helix chain 'A' and resid 1776 through 1779 removed outlier: 3.532A pdb=" N ASP A1779 " --> pdb=" O THR A1776 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1776 through 1779' Processing helix chain 'A' and resid 1792 through 1800 removed outlier: 3.805A pdb=" N ILE A1797 " --> pdb=" O VAL A1793 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER A1798 " --> pdb=" O SER A1794 " (cutoff:3.500A) Processing helix chain 'A' and resid 1868 through 1872 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: 7.195A pdb=" N ASN A 238 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N VAL A 129 " --> pdb=" O ASN A 238 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N LEU A 98 " --> pdb=" O LYS A 128 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N PHE A 130 " --> pdb=" O LEU A 98 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N PHE A 100 " --> pdb=" O PHE A 130 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N ILE A 101 " --> pdb=" O LEU A 285 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N GLN A 385 " --> pdb=" O LYS A 374 " (cutoff:3.500A) removed outlier: 11.200A 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: 4.313A pdb=" N GLY A 292 " --> pdb=" O LEU A 361 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 627 through 632 removed outlier: 7.434A pdb=" N THR A 617 " --> pdb=" O GLN A 609 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N GLN A 609 " --> pdb=" O THR A 617 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N TYR A 621 " --> pdb=" O SER A 605 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N SER A 605 " --> pdb=" O TYR A 621 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ILE A 578 " --> pdb=" O LYS A 647 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N THR A 649 " --> pdb=" O ILE A 578 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N TYR A 580 " --> pdb=" O THR A 649 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N ILE A 651 " --> pdb=" O TYR A 580 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N VAL A 582 " --> pdb=" O ILE A 651 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 744 through 746 Processing sheet with id=AA6, first strand: chain 'A' and resid 777 through 781 removed outlier: 4.710A pdb=" N TYR A 777 " --> pdb=" O LYS A 790 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 882 through 884 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 1105 through 1107 Processing sheet with id=AB1, first strand: chain 'A' and resid 1136 through 1139 removed outlier: 6.644A pdb=" N ILE A1144 " --> pdb=" O VAL A1221 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N MET A1220 " --> pdb=" O SER A1297 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ILE A1299 " --> pdb=" O MET A1220 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ARG A1296 " --> pdb=" O SER A1324 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N SER A1326 " --> pdb=" O ARG A1296 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N PHE A1298 " --> pdb=" O SER A1326 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU A1325 " --> pdb=" O VAL A1345 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N TRP A1344 " --> pdb=" O SER A1403 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N THR A1405 " --> pdb=" O TRP A1344 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ILE A1346 " --> pdb=" O THR A1405 " (cutoff:3.500A) removed outlier: 8.742A pdb=" N SER A1407 " --> pdb=" O ILE A1346 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1161 through 1164 removed outlier: 6.834A pdb=" N SER A1161 " --> pdb=" O ILE A1155 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ILE A1155 " --> pdb=" O SER A1161 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N THR A1163 " --> pdb=" O SER A1153 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N SER A1153 " --> pdb=" O ARG A1288 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N ASN A1290 " --> pdb=" O SER A1153 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ILE A1155 " --> pdb=" O ASN A1290 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N THR A1285 " --> pdb=" O SER A1313 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N SER A1315 " --> pdb=" O THR A1285 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N VAL A1287 " --> pdb=" O SER A1315 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N TYR A1317 " --> pdb=" O VAL A1287 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ILE A1289 " --> pdb=" O TYR A1317 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ILE A1334 " --> pdb=" O THR A1388 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A1336 " --> pdb=" O ASN A1390 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1171 through 1173 Processing sheet with id=AB4, first strand: chain 'A' and resid 1179 through 1181 removed outlier: 6.737A pdb=" N ASP A1185 " --> pdb=" O PHE A1267 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N ILE A1275 " --> pdb=" O GLY A1235 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N GLY A1235 " --> pdb=" O ILE A1275 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASN A1227 " --> pdb=" O GLU A1283 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1353 through 1358 removed outlier: 4.354A pdb=" N GLU A1366 " --> pdb=" O ASN A1354 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N THR A1356 " --> pdb=" O LYS A1364 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N LYS A1364 " --> pdb=" O THR A1356 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N GLU A1358 " --> pdb=" O ILE A1362 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ILE A1362 " --> pdb=" O GLU A1358 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1460 through 1464 Processing sheet with id=AB7, first strand: chain 'A' and resid 1514 through 1521 removed outlier: 4.022A pdb=" N ILE A1516 " --> pdb=" O ILE A1528 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ILE A1528 " --> pdb=" O ILE A1516 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N ILE A1518 " --> pdb=" O LEU A1526 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LEU A1526 " --> pdb=" O ILE A1518 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N ASN A1520 " --> pdb=" O VAL A1524 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL A1524 " --> pdb=" O ASN A1520 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N LYS A1525 " --> pdb=" O ILE A1544 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N ILE A1544 " --> pdb=" O LYS A1525 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N LYS A1537 " --> pdb=" O LEU A1557 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N LEU A1557 " --> pdb=" O LYS A1537 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N SER A1539 " --> pdb=" O VAL A1555 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N VAL A1555 " --> pdb=" O SER A1539 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N SER A1541 " --> pdb=" O ASN A1553 " (cutoff:3.500A) removed outlier: 14.824A pdb=" N THR A1549 " --> pdb=" O ASP A1608 " (cutoff:3.500A) removed outlier: 15.698A pdb=" N ASN A1610 " --> pdb=" O THR A1549 " (cutoff:3.500A) removed outlier: 12.095A pdb=" N LYS A1551 " --> pdb=" O ASN A1610 " (cutoff:3.500A) removed outlier: 10.284A pdb=" N ILE A1612 " --> pdb=" O LYS A1551 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ASN A1553 " --> pdb=" O ILE A1612 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N SER A1614 " --> pdb=" O ASN A1553 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N VAL A1555 " --> pdb=" O SER A1614 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N SER A1616 " --> pdb=" O VAL A1555 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU A1557 " --> pdb=" O SER A1616 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N PHE A1611 " --> pdb=" O CYS A1626 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N CYS A1626 " --> pdb=" O PHE A1611 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N GLN A1621 " --> pdb=" O ILE A1637 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ILE A1637 " --> pdb=" O GLN A1621 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N GLU A1623 " --> pdb=" O TYR A1635 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N TYR A1649 " --> pdb=" O ASN A1655 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N ASN A1655 " --> pdb=" O TYR A1649 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N VAL A1692 " --> pdb=" O ILE A1719 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N VAL A1718 " --> pdb=" O ARG A1767 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1674 through 1678 removed outlier: 6.610A pdb=" N ILE A1675 " --> pdb=" O ASN A1704 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N THR A1706 " --> pdb=" O ILE A1675 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N PHE A1677 " --> pdb=" O THR A1706 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N PHE A1785 " --> pdb=" O GLN A1789 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N GLN A1789 " --> pdb=" O PHE A1785 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1815 through 1819 Processing sheet with id=AC1, first strand: chain 'A' and resid 1835 through 1839 removed outlier: 3.642A pdb=" N ASN A1852 " --> pdb=" O LYS A1847 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1856 through 1860 Processing sheet with id=AC3, first strand: chain 'A' and resid 1878 through 1882 Processing sheet with id=AC4, first strand: chain 'A' and resid 1898 through 1902 removed outlier: 3.766A pdb=" N GLU A1922 " --> pdb=" O ALA A1910 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 1928 through 1932 Processing sheet with id=AC6, 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=AC7, first strand: chain 'A' and resid 1991 through 1992 Processing sheet with id=AC8, first strand: chain 'A' and resid 2009 through 2013 Processing sheet with id=AC9, first strand: chain 'A' and resid 2029 through 2033 Processing sheet with id=AD1, first strand: chain 'A' and resid 2059 through 2063 Processing sheet with id=AD2, first strand: chain 'A' and resid 2079 through 2082 Processing sheet with id=AD3, first strand: chain 'A' and resid 2101 through 2105 Processing sheet with id=AD4, first strand: chain 'A' and resid 2143 through 2145 Processing sheet with id=AD5, first strand: chain 'A' and resid 2161 through 2165 removed outlier: 4.696A 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=AD6, first strand: chain 'A' and resid 2191 through 2194 Processing sheet with id=AD7, first strand: chain 'A' and resid 2211 through 2215 Processing sheet with id=AD8, first strand: chain 'A' and resid 2232 through 2236 Processing sheet with id=AD9, first strand: chain 'A' and resid 2252 through 2256 Processing sheet with id=AE1, first strand: chain 'A' and resid 2272 through 2276 Processing sheet with id=AE2, 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=AE3, first strand: chain 'A' and resid 2322 through 2326 Processing sheet with id=AE4, first strand: chain 'A' and resid 2343 through 2346 803 hydrogen bonds defined for protein. 2154 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: 11.64 Time building geometry restraints manager: 7.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3588 1.32 - 1.44: 4798 1.44 - 1.57: 10554 1.57 - 1.69: 1 1.69 - 1.81: 82 Bond restraints: 19023 Sorted by residual: bond pdb=" N VAL A1924 " pdb=" CA VAL A1924 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.11e-02 8.12e+03 1.11e+01 bond pdb=" CA ARG A 499 " pdb=" C ARG A 499 " ideal model delta sigma weight residual 1.523 1.465 0.058 1.80e-02 3.09e+03 1.04e+01 bond pdb=" N GLN A1633 " pdb=" CA GLN A1633 " ideal model delta sigma weight residual 1.457 1.417 0.040 1.41e-02 5.03e+03 7.91e+00 bond pdb=" N TYR A1957 " pdb=" CA TYR A1957 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.18e-02 7.18e+03 7.67e+00 bond pdb=" N ASN A1925 " pdb=" CA ASN A1925 " ideal model delta sigma weight residual 1.458 1.491 -0.034 1.24e-02 6.50e+03 7.49e+00 ... (remaining 19018 not shown) Histogram of bond angle deviations from ideal: 96.57 - 104.12: 161 104.12 - 111.66: 7810 111.66 - 119.20: 7559 119.20 - 126.75: 10076 126.75 - 134.29: 128 Bond angle restraints: 25734 Sorted by residual: angle pdb=" C VAL A1947 " pdb=" N GLU A1948 " pdb=" CA GLU A1948 " ideal model delta sigma weight residual 121.54 132.75 -11.21 1.91e+00 2.74e-01 3.44e+01 angle pdb=" N GLN A1763 " pdb=" CA GLN A1763 " pdb=" C GLN A1763 " ideal model delta sigma weight residual 111.37 118.96 -7.59 1.64e+00 3.72e-01 2.14e+01 angle pdb=" C LEU A 91 " pdb=" N THR A 92 " pdb=" CA THR A 92 " ideal model delta sigma weight residual 122.36 133.55 -11.19 2.42e+00 1.71e-01 2.14e+01 angle pdb=" C PRO A1762 " pdb=" N GLN A1763 " pdb=" CA GLN A1763 " ideal model delta sigma weight residual 121.19 128.02 -6.83 1.59e+00 3.96e-01 1.85e+01 angle pdb=" C LEU A1015 " pdb=" N ASP A1016 " pdb=" CA ASP A1016 " ideal model delta sigma weight residual 121.92 114.64 7.28 1.73e+00 3.34e-01 1.77e+01 ... (remaining 25729 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.10: 9561 18.10 - 36.20: 1272 36.20 - 54.29: 410 54.29 - 72.39: 90 72.39 - 90.49: 37 Dihedral angle restraints: 11370 sinusoidal: 4574 harmonic: 6796 Sorted by residual: dihedral pdb=" CA LYS A1511 " pdb=" C LYS A1511 " pdb=" N ASP A1512 " pdb=" CA ASP A1512 " ideal model delta harmonic sigma weight residual 180.00 -128.34 -51.66 0 5.00e+00 4.00e-02 1.07e+02 dihedral pdb=" CA ASP A 364 " pdb=" C ASP A 364 " pdb=" N ASP A 365 " pdb=" CA ASP A 365 " ideal model delta harmonic sigma weight residual -180.00 -147.84 -32.16 0 5.00e+00 4.00e-02 4.14e+01 dihedral pdb=" CA LEU A 243 " pdb=" C LEU A 243 " pdb=" N GLU A 244 " pdb=" CA GLU A 244 " ideal model delta harmonic sigma weight residual 180.00 150.94 29.06 0 5.00e+00 4.00e-02 3.38e+01 ... (remaining 11367 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 2055 0.061 - 0.122: 655 0.122 - 0.184: 108 0.184 - 0.245: 9 0.245 - 0.306: 4 Chirality restraints: 2831 Sorted by residual: chirality pdb=" CB ILE A 508 " pdb=" CA ILE A 508 " pdb=" CG1 ILE A 508 " pdb=" CG2 ILE A 508 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" CB ILE A 969 " pdb=" CA ILE A 969 " pdb=" CG1 ILE A 969 " pdb=" CG2 ILE A 969 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CA ASN A1925 " pdb=" N ASN A1925 " pdb=" C ASN A1925 " pdb=" CB ASN A1925 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.56e+00 ... (remaining 2828 not shown) Planarity restraints: 3324 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A2342 " -0.022 2.00e-02 2.50e+03 4.41e-02 1.95e+01 pdb=" C GLY A2342 " 0.076 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=" CB PHE A 186 " 0.043 2.00e-02 2.50e+03 2.77e-02 1.35e+01 pdb=" CG PHE A 186 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 PHE A 186 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE A 186 " -0.029 2.00e-02 2.50e+03 pdb=" CE1 PHE A 186 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE A 186 " 0.021 2.00e-02 2.50e+03 pdb=" CZ PHE A 186 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A1761 " 0.055 5.00e-02 4.00e+02 8.32e-02 1.11e+01 pdb=" N PRO A1762 " -0.144 5.00e-02 4.00e+02 pdb=" CA PRO A1762 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO A1762 " 0.045 5.00e-02 4.00e+02 ... (remaining 3321 not shown) Histogram of nonbonded interaction distances: 1.06 - 1.83: 6 1.83 - 2.59: 178 2.59 - 3.36: 23221 3.36 - 4.13: 46762 4.13 - 4.90: 83046 Nonbonded interactions: 153213 Sorted by model distance: nonbonded pdb=" OD1 ASN A1925 " pdb=" CD1 TYR A1943 " model vdw 1.057 3.340 nonbonded pdb=" ND2 ASN A1925 " pdb=" CE1 TYR A1943 " model vdw 1.091 3.420 nonbonded pdb=" ND2 ASN A1925 " pdb=" CZ TYR A1943 " model vdw 1.196 3.340 nonbonded pdb=" OD1 ASN A1925 " pdb=" CG TYR A1943 " model vdw 1.353 3.260 nonbonded pdb=" CG ASN A1925 " pdb=" CD1 TYR A1943 " model vdw 1.499 3.570 ... (remaining 153208 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: 3.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 14.120 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 56.220 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6539 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.086 19023 Z= 0.554 Angle : 0.931 13.219 25734 Z= 0.532 Chirality : 0.060 0.306 2831 Planarity : 0.006 0.083 3324 Dihedral : 19.082 90.491 7018 Min Nonbonded Distance : 1.057 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.58 % Favored : 94.25 % Rotamer: Outliers : 8.96 % Allowed : 21.41 % Favored : 69.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: -2.37 (0.15), residues: 2295 helix: -1.04 (0.18), residues: 625 sheet: -1.56 (0.22), residues: 457 loop : -1.84 (0.15), residues: 1213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP A 102 HIS 0.010 0.002 HIS A 35 PHE 0.043 0.003 PHE A 186 TYR 0.047 0.003 TYR A 46 ARG 0.010 0.001 ARG A1296 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 145 time to evaluate : 1.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 PHE cc_start: 0.6756 (m-10) cc_final: 0.6343 (m-10) REVERT: A 166 PHE cc_start: 0.5349 (t80) cc_final: 0.4689 (t80) REVERT: A 195 GLU cc_start: 0.6054 (OUTLIER) cc_final: 0.5765 (mp0) REVERT: A 314 MET cc_start: 0.7776 (mtp) cc_final: 0.7529 (mtp) REVERT: A 439 SER cc_start: 0.8697 (OUTLIER) cc_final: 0.8346 (t) REVERT: A 450 ILE cc_start: 0.9077 (OUTLIER) cc_final: 0.8771 (pp) REVERT: A 526 ARG cc_start: 0.7692 (ttm-80) cc_final: 0.7391 (tpm170) REVERT: A 800 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7931 (mt) REVERT: A 980 ASN cc_start: 0.4512 (OUTLIER) cc_final: 0.4019 (p0) REVERT: A 1116 LYS cc_start: 0.2422 (OUTLIER) cc_final: 0.1080 (ttmt) REVERT: A 1129 LEU cc_start: 0.3554 (OUTLIER) cc_final: 0.3283 (tt) REVERT: A 1270 ILE cc_start: 0.0581 (OUTLIER) cc_final: 0.0139 (pp) REVERT: A 1310 LYS cc_start: 0.3785 (OUTLIER) cc_final: 0.3541 (tppt) REVERT: A 1409 LEU cc_start: 0.2026 (OUTLIER) cc_final: 0.1682 (mp) REVERT: A 1434 MET cc_start: 0.1535 (OUTLIER) cc_final: 0.1204 (mtp) REVERT: A 1465 ILE cc_start: 0.4517 (OUTLIER) cc_final: 0.4273 (tt) REVERT: A 1512 ASP cc_start: 0.5732 (OUTLIER) cc_final: 0.5502 (m-30) REVERT: A 1647 THR cc_start: 0.8172 (OUTLIER) cc_final: 0.7849 (m) REVERT: A 1779 ASP cc_start: 0.6717 (OUTLIER) cc_final: 0.6455 (m-30) REVERT: A 1857 PHE cc_start: 0.5182 (OUTLIER) cc_final: 0.3996 (m-80) REVERT: A 1952 LEU cc_start: 0.0542 (OUTLIER) cc_final: 0.0239 (mm) outliers start: 187 outliers final: 90 residues processed: 313 average time/residue: 0.9394 time to fit residues: 344.8631 Evaluate side-chains 229 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 122 time to evaluate : 1.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 74 LYS Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 223 LYS Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 444 MET Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 518 SER Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 532 GLU Chi-restraints excluded: chain A residue 576 GLU Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 622 SER Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 667 ASP Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 774 SER Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 825 GLU Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 830 SER Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 849 SER Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain A residue 890 SER Chi-restraints excluded: chain A residue 920 GLU Chi-restraints excluded: chain A residue 937 PHE Chi-restraints excluded: chain A residue 945 VAL Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 979 SER Chi-restraints excluded: chain A residue 980 ASN Chi-restraints excluded: chain A residue 1002 THR Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain A residue 1072 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1116 LYS Chi-restraints excluded: chain A residue 1129 LEU Chi-restraints excluded: chain A residue 1161 SER Chi-restraints excluded: chain A residue 1169 ILE Chi-restraints excluded: chain A residue 1181 THR Chi-restraints excluded: chain A residue 1197 LYS Chi-restraints excluded: chain A residue 1214 ASP Chi-restraints excluded: chain A residue 1228 ARG Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain A residue 1310 LYS Chi-restraints excluded: chain A residue 1345 VAL Chi-restraints excluded: chain A residue 1409 LEU Chi-restraints excluded: chain A residue 1434 MET Chi-restraints excluded: chain A residue 1435 LYS Chi-restraints excluded: chain A residue 1465 ILE Chi-restraints excluded: chain A residue 1478 SER Chi-restraints excluded: chain A residue 1512 ASP Chi-restraints excluded: chain A residue 1516 ILE Chi-restraints excluded: chain A residue 1524 VAL Chi-restraints excluded: chain A residue 1539 SER Chi-restraints excluded: chain A residue 1541 SER Chi-restraints excluded: chain A residue 1547 THR Chi-restraints excluded: chain A residue 1588 SER Chi-restraints excluded: chain A residue 1591 ILE Chi-restraints excluded: chain A residue 1610 ASN Chi-restraints excluded: chain A residue 1614 SER Chi-restraints excluded: chain A residue 1616 SER Chi-restraints excluded: chain A residue 1618 SER Chi-restraints excluded: chain A residue 1641 ILE Chi-restraints excluded: chain A residue 1645 SER Chi-restraints excluded: chain A residue 1647 THR Chi-restraints excluded: chain A residue 1662 TYR Chi-restraints excluded: chain A residue 1682 LEU Chi-restraints excluded: chain A residue 1698 LEU Chi-restraints excluded: chain A residue 1714 ILE Chi-restraints excluded: chain A residue 1722 ASP Chi-restraints excluded: chain A residue 1748 SER Chi-restraints excluded: chain A residue 1779 ASP Chi-restraints excluded: chain A residue 1782 SER Chi-restraints excluded: chain A residue 1801 SER Chi-restraints excluded: chain A residue 1841 ASP Chi-restraints excluded: chain A residue 1842 SER Chi-restraints excluded: chain A residue 1857 PHE Chi-restraints excluded: chain A residue 1914 THR Chi-restraints excluded: chain A residue 1952 LEU Chi-restraints excluded: chain A residue 1955 GLU Chi-restraints excluded: chain A residue 2235 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 194 optimal weight: 3.9990 chunk 174 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 117 optimal weight: 9.9990 chunk 93 optimal weight: 1.9990 chunk 180 optimal weight: 0.7980 chunk 69 optimal weight: 0.7980 chunk 109 optimal weight: 6.9990 chunk 134 optimal weight: 0.9990 chunk 208 optimal weight: 5.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 2 ASN A 106 GLN A 379 ASN A 405 ASN A 419 ASN A 579 HIS A 694 ASN A 741 GLN ** A 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 827 ASN A 876 ASN A 924 HIS A 988 GLN ** A1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1178 HIS A1207 ASN A1257 HIS A1333 ASN A1350 ASN A1385 ASN A1444 GLN A1449 HIS A1530 ASN A1548 ASN A1580 ASN A1598 ASN A1663 HIS A1690 ASN A1727 ASN A1763 GLN A1976 ASN A2058 ASN A2143 GLN ** A2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2319 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6470 moved from start: 0.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 19023 Z= 0.234 Angle : 0.645 10.256 25734 Z= 0.347 Chirality : 0.048 0.210 2831 Planarity : 0.004 0.051 3324 Dihedral : 10.094 84.679 2681 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.49 % Favored : 95.47 % Rotamer: Outliers : 5.84 % Allowed : 24.81 % Favored : 69.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.11 (0.16), residues: 2295 helix: 0.66 (0.20), residues: 636 sheet: -1.12 (0.22), residues: 447 loop : -1.35 (0.16), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 102 HIS 0.005 0.001 HIS A 653 PHE 0.024 0.002 PHE A 186 TYR 0.027 0.002 TYR A 46 ARG 0.004 0.001 ARG A 262 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 132 time to evaluate : 1.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 PHE cc_start: 0.6490 (m-80) cc_final: 0.6193 (m-10) REVERT: A 166 PHE cc_start: 0.5223 (t80) cc_final: 0.4754 (t80) REVERT: A 276 MET cc_start: 0.8348 (mmt) cc_final: 0.8023 (mmm) REVERT: A 314 MET cc_start: 0.7639 (mtp) cc_final: 0.7358 (mtp) REVERT: A 526 ARG cc_start: 0.7603 (ttm-80) cc_final: 0.7348 (tpm170) REVERT: A 800 LEU cc_start: 0.7850 (OUTLIER) cc_final: 0.7647 (mt) REVERT: A 1116 LYS cc_start: 0.1603 (OUTLIER) cc_final: 0.0300 (ttmt) REVERT: A 1145 MET cc_start: 0.3270 (mmp) cc_final: 0.2964 (mmt) REVERT: A 1409 LEU cc_start: 0.1920 (OUTLIER) cc_final: 0.1578 (mp) REVERT: A 1465 ILE cc_start: 0.4363 (OUTLIER) cc_final: 0.4069 (tt) REVERT: A 1512 ASP cc_start: 0.5100 (OUTLIER) cc_final: 0.4870 (m-30) REVERT: A 1647 THR cc_start: 0.8071 (OUTLIER) cc_final: 0.7720 (m) REVERT: A 1857 PHE cc_start: 0.5016 (OUTLIER) cc_final: 0.4708 (m-80) REVERT: A 1986 MET cc_start: 0.0861 (mmt) cc_final: -0.0348 (tpp) REVERT: A 2143 GLN cc_start: -0.0012 (OUTLIER) cc_final: -0.0281 (mp-120) outliers start: 122 outliers final: 59 residues processed: 238 average time/residue: 0.9400 time to fit residues: 262.2853 Evaluate side-chains 189 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 122 time to evaluate : 2.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 74 LYS Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 518 SER Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 532 GLU Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 667 ASP Chi-restraints excluded: chain A residue 756 ASP Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain A residue 937 PHE Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 1072 THR Chi-restraints excluded: chain A residue 1116 LYS Chi-restraints excluded: chain A residue 1143 ILE Chi-restraints excluded: chain A residue 1169 ILE Chi-restraints excluded: chain A residue 1178 HIS Chi-restraints excluded: chain A residue 1181 THR Chi-restraints excluded: chain A residue 1228 ARG Chi-restraints excluded: chain A residue 1304 THR Chi-restraints excluded: chain A residue 1343 THR Chi-restraints excluded: chain A residue 1345 VAL Chi-restraints excluded: chain A residue 1385 ASN Chi-restraints excluded: chain A residue 1403 SER Chi-restraints excluded: chain A residue 1409 LEU Chi-restraints excluded: chain A residue 1465 ILE Chi-restraints excluded: chain A residue 1512 ASP Chi-restraints excluded: chain A residue 1516 ILE Chi-restraints excluded: chain A residue 1539 SER Chi-restraints excluded: chain A residue 1547 THR Chi-restraints excluded: chain A residue 1582 LEU Chi-restraints excluded: chain A residue 1591 ILE Chi-restraints excluded: chain A residue 1609 THR Chi-restraints excluded: chain A residue 1610 ASN Chi-restraints excluded: chain A residue 1614 SER Chi-restraints excluded: chain A residue 1641 ILE Chi-restraints excluded: chain A residue 1647 THR Chi-restraints excluded: chain A residue 1662 TYR Chi-restraints excluded: chain A residue 1682 LEU Chi-restraints excluded: chain A residue 1714 ILE Chi-restraints excluded: chain A residue 1722 ASP Chi-restraints excluded: chain A residue 1724 ASN Chi-restraints excluded: chain A residue 1837 ILE Chi-restraints excluded: chain A residue 1842 SER Chi-restraints excluded: chain A residue 1857 PHE Chi-restraints excluded: chain A residue 1978 TYR Chi-restraints excluded: chain A residue 2088 THR Chi-restraints excluded: chain A residue 2125 ILE Chi-restraints excluded: chain A residue 2143 GLN Chi-restraints excluded: chain A residue 2235 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 116 optimal weight: 0.7980 chunk 64 optimal weight: 6.9990 chunk 173 optimal weight: 0.6980 chunk 142 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 209 optimal weight: 0.9980 chunk 226 optimal weight: 7.9990 chunk 186 optimal weight: 10.0000 chunk 207 optimal weight: 0.2980 chunk 71 optimal weight: 0.0870 chunk 167 optimal weight: 3.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 379 ASN A 763 ASN ** A 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 931 ASN ** A1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1178 HIS A2058 ASN ** A2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6430 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19023 Z= 0.161 Angle : 0.562 8.992 25734 Z= 0.302 Chirality : 0.045 0.157 2831 Planarity : 0.004 0.051 3324 Dihedral : 7.988 82.995 2584 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 4.79 % Allowed : 25.53 % Favored : 69.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: -0.45 (0.17), residues: 2295 helix: 1.48 (0.21), residues: 639 sheet: -0.85 (0.23), residues: 443 loop : -1.05 (0.17), residues: 1213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 102 HIS 0.008 0.001 HIS A1178 PHE 0.017 0.001 PHE A 186 TYR 0.019 0.001 TYR A 46 ARG 0.004 0.000 ARG A1265 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 135 time to evaluate : 2.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 GLN cc_start: 0.8591 (OUTLIER) cc_final: 0.7183 (tp-100) REVERT: A 157 PHE cc_start: 0.6381 (m-80) cc_final: 0.6172 (m-80) REVERT: A 166 PHE cc_start: 0.5244 (t80) cc_final: 0.4779 (t80) REVERT: A 276 MET cc_start: 0.8370 (mmt) cc_final: 0.8077 (mmm) REVERT: A 314 MET cc_start: 0.7586 (mtp) cc_final: 0.7306 (mtp) REVERT: A 337 MET cc_start: 0.6918 (OUTLIER) cc_final: 0.6431 (mtp) REVERT: A 419 ASN cc_start: 0.7455 (m-40) cc_final: 0.7123 (t0) REVERT: A 423 ASP cc_start: 0.6664 (OUTLIER) cc_final: 0.6258 (p0) REVERT: A 1116 LYS cc_start: 0.1268 (OUTLIER) cc_final: -0.0103 (ttmt) REVERT: A 1145 MET cc_start: 0.2759 (mmp) cc_final: 0.1562 (mtm) REVERT: A 1228 ARG cc_start: 0.2235 (OUTLIER) cc_final: 0.1496 (ptm160) REVERT: A 1327 LEU cc_start: 0.2220 (OUTLIER) cc_final: 0.1949 (pt) REVERT: A 1332 MET cc_start: 0.0762 (ppp) cc_final: 0.0374 (mmm) REVERT: A 1409 LEU cc_start: 0.1953 (OUTLIER) cc_final: 0.1681 (mp) REVERT: A 1434 MET cc_start: 0.1459 (OUTLIER) cc_final: 0.1055 (mtm) REVERT: A 1499 MET cc_start: 0.3506 (mpt) cc_final: 0.2920 (mmm) REVERT: A 1533 LYS cc_start: 0.5496 (OUTLIER) cc_final: 0.5044 (tmtt) REVERT: A 1647 THR cc_start: 0.8052 (OUTLIER) cc_final: 0.7740 (m) REVERT: A 1857 PHE cc_start: 0.5136 (OUTLIER) cc_final: 0.4767 (m-80) REVERT: A 1986 MET cc_start: 0.1131 (mmt) cc_final: 0.0032 (tpp) REVERT: A 2212 TRP cc_start: 0.0406 (OUTLIER) cc_final: -0.0226 (t60) outliers start: 100 outliers final: 49 residues processed: 219 average time/residue: 1.0111 time to fit residues: 258.9473 Evaluate side-chains 179 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 118 time to evaluate : 1.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 532 GLU Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 667 ASP Chi-restraints excluded: chain A residue 721 ASP Chi-restraints excluded: chain A residue 756 ASP Chi-restraints excluded: chain A residue 757 HIS Chi-restraints excluded: chain A residue 774 SER Chi-restraints excluded: chain A residue 812 ASP Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 866 SER Chi-restraints excluded: chain A residue 937 PHE Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 956 VAL Chi-restraints excluded: chain A residue 1005 SER Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain A residue 1072 THR Chi-restraints excluded: chain A residue 1116 LYS Chi-restraints excluded: chain A residue 1143 ILE Chi-restraints excluded: chain A residue 1169 ILE Chi-restraints excluded: chain A residue 1176 SER Chi-restraints excluded: chain A residue 1178 HIS Chi-restraints excluded: chain A residue 1181 THR Chi-restraints excluded: chain A residue 1194 THR Chi-restraints excluded: chain A residue 1228 ARG Chi-restraints excluded: chain A residue 1251 LEU Chi-restraints excluded: chain A residue 1327 LEU Chi-restraints excluded: chain A residue 1343 THR Chi-restraints excluded: chain A residue 1345 VAL Chi-restraints excluded: chain A residue 1380 ASN Chi-restraints excluded: chain A residue 1409 LEU Chi-restraints excluded: chain A residue 1434 MET Chi-restraints excluded: chain A residue 1512 ASP Chi-restraints excluded: chain A residue 1533 LYS Chi-restraints excluded: chain A residue 1547 THR Chi-restraints excluded: chain A residue 1582 LEU Chi-restraints excluded: chain A residue 1591 ILE Chi-restraints excluded: chain A residue 1609 THR Chi-restraints excluded: chain A residue 1610 ASN Chi-restraints excluded: chain A residue 1614 SER Chi-restraints excluded: chain A residue 1647 THR Chi-restraints excluded: chain A residue 1662 TYR Chi-restraints excluded: chain A residue 1724 ASN Chi-restraints excluded: chain A residue 1837 ILE Chi-restraints excluded: chain A residue 1841 ASP Chi-restraints excluded: chain A residue 1857 PHE Chi-restraints excluded: chain A residue 1956 THR Chi-restraints excluded: chain A residue 2212 TRP Chi-restraints excluded: chain A residue 2235 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 206 optimal weight: 0.7980 chunk 157 optimal weight: 1.9990 chunk 108 optimal weight: 8.9990 chunk 23 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 chunk 140 optimal weight: 5.9990 chunk 209 optimal weight: 10.0000 chunk 222 optimal weight: 10.0000 chunk 109 optimal weight: 5.9990 chunk 199 optimal weight: 20.0000 chunk 59 optimal weight: 5.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 379 ASN A 385 GLN ** A 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 639 GLN A 785 ASN ** A 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1114 GLN A1178 HIS A1633 GLN A1654 GLN ** A2058 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2143 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6544 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 19023 Z= 0.476 Angle : 0.771 10.600 25734 Z= 0.420 Chirality : 0.055 0.320 2831 Planarity : 0.005 0.058 3324 Dihedral : 8.212 94.581 2551 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 6.23 % Allowed : 25.67 % Favored : 68.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.85 (0.17), residues: 2295 helix: 0.69 (0.20), residues: 637 sheet: -0.92 (0.23), residues: 453 loop : -1.07 (0.17), residues: 1205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP A 102 HIS 0.014 0.002 HIS A1178 PHE 0.041 0.003 PHE A 186 TYR 0.038 0.003 TYR A 46 ARG 0.006 0.001 ARG A 406 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 116 time to evaluate : 1.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 PHE cc_start: 0.5597 (t80) cc_final: 0.4978 (t80) REVERT: A 253 ARG cc_start: 0.8325 (OUTLIER) cc_final: 0.7924 (ttp-110) REVERT: A 314 MET cc_start: 0.7733 (mtp) cc_final: 0.7515 (mtp) REVERT: A 337 MET cc_start: 0.6982 (OUTLIER) cc_final: 0.6413 (mtp) REVERT: A 560 ASP cc_start: 0.5036 (OUTLIER) cc_final: 0.4598 (t0) REVERT: A 597 LEU cc_start: 0.7871 (OUTLIER) cc_final: 0.7640 (tp) REVERT: A 800 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7966 (mt) REVERT: A 927 LYS cc_start: 0.7268 (OUTLIER) cc_final: 0.6985 (ttpp) REVERT: A 980 ASN cc_start: 0.4386 (OUTLIER) cc_final: 0.3827 (p0) REVERT: A 1145 MET cc_start: 0.2602 (mmp) cc_final: 0.1278 (mtm) REVERT: A 1327 LEU cc_start: 0.2502 (OUTLIER) cc_final: 0.2185 (pt) REVERT: A 1409 LEU cc_start: 0.2233 (OUTLIER) cc_final: 0.1912 (mp) REVERT: A 1499 MET cc_start: 0.3243 (mpt) cc_final: 0.2790 (mmm) REVERT: A 1647 THR cc_start: 0.8103 (OUTLIER) cc_final: 0.7866 (m) REVERT: A 1986 MET cc_start: 0.1271 (mmt) cc_final: 0.0172 (tpp) REVERT: A 2143 GLN cc_start: 0.0313 (OUTLIER) cc_final: 0.0061 (mp-120) REVERT: A 2212 TRP cc_start: 0.0316 (OUTLIER) cc_final: -0.0599 (t60) outliers start: 130 outliers final: 82 residues processed: 233 average time/residue: 0.9843 time to fit residues: 271.3840 Evaluate side-chains 208 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 114 time to evaluate : 2.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 143 LYS Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 253 ARG Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 444 MET Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 532 GLU Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 560 ASP Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 667 ASP Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 721 ASP Chi-restraints excluded: chain A residue 756 ASP Chi-restraints excluded: chain A residue 774 SER Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 812 ASP Chi-restraints excluded: chain A residue 825 GLU Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 881 SER Chi-restraints excluded: chain A residue 903 LYS Chi-restraints excluded: chain A residue 926 SER Chi-restraints excluded: chain A residue 927 LYS Chi-restraints excluded: chain A residue 937 PHE Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 969 ILE Chi-restraints excluded: chain A residue 978 LEU Chi-restraints excluded: chain A residue 980 ASN Chi-restraints excluded: chain A residue 1005 SER Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain A residue 1072 THR Chi-restraints excluded: chain A residue 1116 LYS Chi-restraints excluded: chain A residue 1143 ILE Chi-restraints excluded: chain A residue 1169 ILE Chi-restraints excluded: chain A residue 1176 SER Chi-restraints excluded: chain A residue 1181 THR Chi-restraints excluded: chain A residue 1194 THR Chi-restraints excluded: chain A residue 1228 ARG Chi-restraints excluded: chain A residue 1251 LEU Chi-restraints excluded: chain A residue 1304 THR Chi-restraints excluded: chain A residue 1327 LEU Chi-restraints excluded: chain A residue 1343 THR Chi-restraints excluded: chain A residue 1345 VAL Chi-restraints excluded: chain A residue 1390 ASN Chi-restraints excluded: chain A residue 1402 ILE Chi-restraints excluded: chain A residue 1403 SER Chi-restraints excluded: chain A residue 1409 LEU Chi-restraints excluded: chain A residue 1434 MET Chi-restraints excluded: chain A residue 1436 LEU Chi-restraints excluded: chain A residue 1512 ASP Chi-restraints excluded: chain A residue 1541 SER Chi-restraints excluded: chain A residue 1547 THR Chi-restraints excluded: chain A residue 1582 LEU Chi-restraints excluded: chain A residue 1588 SER Chi-restraints excluded: chain A residue 1591 ILE Chi-restraints excluded: chain A residue 1609 THR Chi-restraints excluded: chain A residue 1610 ASN Chi-restraints excluded: chain A residue 1614 SER Chi-restraints excluded: chain A residue 1616 SER Chi-restraints excluded: chain A residue 1647 THR Chi-restraints excluded: chain A residue 1662 TYR Chi-restraints excluded: chain A residue 1667 SER Chi-restraints excluded: chain A residue 1698 LEU Chi-restraints excluded: chain A residue 1714 ILE Chi-restraints excluded: chain A residue 1722 ASP Chi-restraints excluded: chain A residue 1724 ASN Chi-restraints excluded: chain A residue 1822 ASP Chi-restraints excluded: chain A residue 1837 ILE Chi-restraints excluded: chain A residue 1841 ASP Chi-restraints excluded: chain A residue 1857 PHE Chi-restraints excluded: chain A residue 1894 ILE Chi-restraints excluded: chain A residue 1956 THR Chi-restraints excluded: chain A residue 1978 TYR Chi-restraints excluded: chain A residue 2125 ILE Chi-restraints excluded: chain A residue 2143 GLN Chi-restraints excluded: chain A residue 2212 TRP Chi-restraints excluded: chain A residue 2235 VAL Chi-restraints excluded: chain A residue 2253 LEU Chi-restraints excluded: chain A residue 2323 TRP Chi-restraints excluded: chain A residue 2361 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 185 optimal weight: 0.0050 chunk 126 optimal weight: 8.9990 chunk 3 optimal weight: 0.5980 chunk 165 optimal weight: 0.5980 chunk 91 optimal weight: 0.8980 chunk 189 optimal weight: 9.9990 chunk 153 optimal weight: 9.9990 chunk 0 optimal weight: 0.9990 chunk 113 optimal weight: 0.6980 chunk 199 optimal weight: 6.9990 chunk 56 optimal weight: 0.2980 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 781 ASN A 795 HIS ** A1530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2058 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2143 GLN ** A2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6424 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 19023 Z= 0.142 Angle : 0.529 8.595 25734 Z= 0.285 Chirality : 0.045 0.159 2831 Planarity : 0.004 0.053 3324 Dihedral : 7.361 83.168 2551 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 4.84 % Allowed : 27.49 % Favored : 67.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.13 (0.17), residues: 2295 helix: 1.71 (0.21), residues: 635 sheet: -0.54 (0.25), residues: 428 loop : -0.87 (0.17), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 102 HIS 0.005 0.001 HIS A 757 PHE 0.014 0.001 PHE A1677 TYR 0.017 0.001 TYR A 46 ARG 0.002 0.000 ARG A1253 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 128 time to evaluate : 2.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 GLN cc_start: 0.8601 (OUTLIER) cc_final: 0.7025 (tp-100) REVERT: A 166 PHE cc_start: 0.5249 (t80) cc_final: 0.4787 (t80) REVERT: A 314 MET cc_start: 0.7559 (mtp) cc_final: 0.7275 (mtp) REVERT: A 419 ASN cc_start: 0.7497 (m-40) cc_final: 0.7149 (t0) REVERT: A 423 ASP cc_start: 0.6408 (OUTLIER) cc_final: 0.5970 (p0) REVERT: A 754 ILE cc_start: 0.7398 (OUTLIER) cc_final: 0.6998 (pp) REVERT: A 1114 GLN cc_start: 0.3275 (OUTLIER) cc_final: 0.2836 (mp-120) REVERT: A 1145 MET cc_start: 0.1625 (mmp) cc_final: 0.1186 (mtm) REVERT: A 1164 LEU cc_start: 0.3136 (OUTLIER) cc_final: 0.2807 (tm) REVERT: A 1228 ARG cc_start: 0.2645 (OUTLIER) cc_final: 0.2016 (ptm160) REVERT: A 1249 LYS cc_start: 0.3245 (OUTLIER) cc_final: 0.2993 (mmtt) REVERT: A 1327 LEU cc_start: 0.1682 (OUTLIER) cc_final: 0.1451 (pt) REVERT: A 1332 MET cc_start: 0.0793 (ppp) cc_final: 0.0249 (mmm) REVERT: A 1409 LEU cc_start: 0.1969 (OUTLIER) cc_final: 0.1713 (mp) REVERT: A 1533 LYS cc_start: 0.5531 (OUTLIER) cc_final: 0.5034 (tmtt) REVERT: A 1647 THR cc_start: 0.8063 (OUTLIER) cc_final: 0.7772 (m) REVERT: A 1857 PHE cc_start: 0.5431 (OUTLIER) cc_final: 0.4972 (m-80) REVERT: A 1956 THR cc_start: 0.3212 (OUTLIER) cc_final: 0.2985 (p) REVERT: A 1986 MET cc_start: 0.1610 (mmt) cc_final: 0.0520 (tpp) REVERT: A 2212 TRP cc_start: 0.0318 (OUTLIER) cc_final: -0.0483 (t60) outliers start: 101 outliers final: 51 residues processed: 219 average time/residue: 1.0026 time to fit residues: 256.3676 Evaluate side-chains 181 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 116 time to evaluate : 1.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 532 GLU Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 667 ASP Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 756 ASP Chi-restraints excluded: chain A residue 774 SER Chi-restraints excluded: chain A residue 812 ASP Chi-restraints excluded: chain A residue 881 SER Chi-restraints excluded: chain A residue 903 LYS Chi-restraints excluded: chain A residue 937 PHE Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 956 VAL Chi-restraints excluded: chain A residue 1005 SER Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain A residue 1072 THR Chi-restraints excluded: chain A residue 1114 GLN Chi-restraints excluded: chain A residue 1116 LYS Chi-restraints excluded: chain A residue 1143 ILE Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain A residue 1169 ILE Chi-restraints excluded: chain A residue 1176 SER Chi-restraints excluded: chain A residue 1181 THR Chi-restraints excluded: chain A residue 1194 THR Chi-restraints excluded: chain A residue 1228 ARG Chi-restraints excluded: chain A residue 1249 LYS Chi-restraints excluded: chain A residue 1251 LEU Chi-restraints excluded: chain A residue 1279 LYS Chi-restraints excluded: chain A residue 1327 LEU Chi-restraints excluded: chain A residue 1343 THR Chi-restraints excluded: chain A residue 1390 ASN Chi-restraints excluded: chain A residue 1409 LEU Chi-restraints excluded: chain A residue 1436 LEU Chi-restraints excluded: chain A residue 1533 LYS Chi-restraints excluded: chain A residue 1547 THR Chi-restraints excluded: chain A residue 1582 LEU Chi-restraints excluded: chain A residue 1591 ILE Chi-restraints excluded: chain A residue 1610 ASN Chi-restraints excluded: chain A residue 1614 SER Chi-restraints excluded: chain A residue 1616 SER Chi-restraints excluded: chain A residue 1645 SER Chi-restraints excluded: chain A residue 1647 THR Chi-restraints excluded: chain A residue 1662 TYR Chi-restraints excluded: chain A residue 1724 ASN Chi-restraints excluded: chain A residue 1841 ASP Chi-restraints excluded: chain A residue 1857 PHE Chi-restraints excluded: chain A residue 1956 THR Chi-restraints excluded: chain A residue 1978 TYR Chi-restraints excluded: chain A residue 2088 THR Chi-restraints excluded: chain A residue 2125 ILE Chi-restraints excluded: chain A residue 2212 TRP Chi-restraints excluded: chain A residue 2235 VAL Chi-restraints excluded: chain A residue 2253 LEU Chi-restraints excluded: chain A residue 2289 MET Chi-restraints excluded: chain A residue 2323 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 74 optimal weight: 0.5980 chunk 200 optimal weight: 0.0470 chunk 43 optimal weight: 0.6980 chunk 130 optimal weight: 8.9990 chunk 54 optimal weight: 0.7980 chunk 222 optimal weight: 9.9990 chunk 184 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 116 optimal weight: 20.0000 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 574 ASN A 639 GLN ** A 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1896 GLN ** A2001 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2058 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6439 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19023 Z= 0.163 Angle : 0.538 8.526 25734 Z= 0.289 Chirality : 0.045 0.145 2831 Planarity : 0.004 0.049 3324 Dihedral : 7.002 82.702 2544 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.01 % Favored : 95.95 % Rotamer: Outliers : 4.45 % Allowed : 27.78 % Favored : 67.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.05 (0.17), residues: 2295 helix: 1.81 (0.21), residues: 636 sheet: -0.38 (0.25), residues: 435 loop : -0.75 (0.17), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 102 HIS 0.004 0.001 HIS A 757 PHE 0.018 0.001 PHE A 186 TYR 0.020 0.001 TYR A 46 ARG 0.006 0.000 ARG A 722 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 125 time to evaluate : 1.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 GLN cc_start: 0.8623 (OUTLIER) cc_final: 0.7132 (tp-100) REVERT: A 166 PHE cc_start: 0.5067 (t80) cc_final: 0.4677 (t80) REVERT: A 314 MET cc_start: 0.7566 (mtp) cc_final: 0.7303 (mtp) REVERT: A 337 MET cc_start: 0.6926 (OUTLIER) cc_final: 0.6418 (mtp) REVERT: A 423 ASP cc_start: 0.6469 (OUTLIER) cc_final: 0.6061 (p0) REVERT: A 705 ILE cc_start: 0.7436 (OUTLIER) cc_final: 0.6937 (pp) REVERT: A 792 LYS cc_start: 0.5777 (OUTLIER) cc_final: 0.5569 (mttt) REVERT: A 1145 MET cc_start: 0.1738 (mmp) cc_final: 0.1281 (mtm) REVERT: A 1164 LEU cc_start: 0.3101 (OUTLIER) cc_final: 0.2776 (tm) REVERT: A 1647 THR cc_start: 0.8092 (OUTLIER) cc_final: 0.7796 (m) REVERT: A 1857 PHE cc_start: 0.5243 (OUTLIER) cc_final: 0.4777 (m-80) REVERT: A 1986 MET cc_start: 0.1419 (mmt) cc_final: 0.0226 (tpp) REVERT: A 2212 TRP cc_start: 0.0326 (OUTLIER) cc_final: -0.0516 (t60) outliers start: 93 outliers final: 56 residues processed: 204 average time/residue: 0.9976 time to fit residues: 237.6591 Evaluate side-chains 187 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 122 time to evaluate : 2.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 379 ASN Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 532 GLU Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 667 ASP Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 721 ASP Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 757 HIS Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 774 SER Chi-restraints excluded: chain A residue 792 LYS Chi-restraints excluded: chain A residue 812 ASP Chi-restraints excluded: chain A residue 903 LYS Chi-restraints excluded: chain A residue 937 PHE Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 956 VAL Chi-restraints excluded: chain A residue 978 LEU Chi-restraints excluded: chain A residue 1005 SER Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain A residue 1116 LYS Chi-restraints excluded: chain A residue 1143 ILE Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain A residue 1169 ILE Chi-restraints excluded: chain A residue 1181 THR Chi-restraints excluded: chain A residue 1194 THR Chi-restraints excluded: chain A residue 1228 ARG Chi-restraints excluded: chain A residue 1251 LEU Chi-restraints excluded: chain A residue 1374 LYS Chi-restraints excluded: chain A residue 1539 SER Chi-restraints excluded: chain A residue 1547 THR Chi-restraints excluded: chain A residue 1582 LEU Chi-restraints excluded: chain A residue 1591 ILE Chi-restraints excluded: chain A residue 1609 THR Chi-restraints excluded: chain A residue 1610 ASN Chi-restraints excluded: chain A residue 1614 SER Chi-restraints excluded: chain A residue 1616 SER Chi-restraints excluded: chain A residue 1645 SER Chi-restraints excluded: chain A residue 1647 THR Chi-restraints excluded: chain A residue 1650 VAL Chi-restraints excluded: chain A residue 1662 TYR Chi-restraints excluded: chain A residue 1667 SER Chi-restraints excluded: chain A residue 1724 ASN Chi-restraints excluded: chain A residue 1837 ILE Chi-restraints excluded: chain A residue 1841 ASP Chi-restraints excluded: chain A residue 1857 PHE Chi-restraints excluded: chain A residue 1978 TYR Chi-restraints excluded: chain A residue 2033 THR Chi-restraints excluded: chain A residue 2088 THR Chi-restraints excluded: chain A residue 2125 ILE Chi-restraints excluded: chain A residue 2212 TRP Chi-restraints excluded: chain A residue 2235 VAL Chi-restraints excluded: chain A residue 2253 LEU Chi-restraints excluded: chain A residue 2289 MET Chi-restraints excluded: chain A residue 2323 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 214 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 126 optimal weight: 8.9990 chunk 162 optimal weight: 0.6980 chunk 125 optimal weight: 8.9990 chunk 187 optimal weight: 8.9990 chunk 124 optimal weight: 10.0000 chunk 221 optimal weight: 0.9990 chunk 138 optimal weight: 10.0000 chunk 135 optimal weight: 7.9990 chunk 102 optimal weight: 7.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 2 ASN ** A 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 732 GLN ** A 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1413 ASN ** A1896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2001 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2058 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6529 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 19023 Z= 0.405 Angle : 0.713 11.826 25734 Z= 0.386 Chirality : 0.053 0.381 2831 Planarity : 0.005 0.055 3324 Dihedral : 7.530 92.394 2539 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.62 % Favored : 95.34 % Rotamer: Outliers : 5.12 % Allowed : 27.20 % Favored : 67.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: -0.42 (0.17), residues: 2295 helix: 1.02 (0.20), residues: 637 sheet: -0.56 (0.24), residues: 444 loop : -0.85 (0.17), residues: 1214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 102 HIS 0.006 0.001 HIS A 35 PHE 0.038 0.003 PHE A 186 TYR 0.033 0.003 TYR A 46 ARG 0.008 0.001 ARG A 722 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 119 time to evaluate : 2.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 GLN cc_start: 0.8678 (OUTLIER) cc_final: 0.7092 (tp-100) REVERT: A 166 PHE cc_start: 0.5097 (t80) cc_final: 0.4696 (t80) REVERT: A 314 MET cc_start: 0.7734 (mtp) cc_final: 0.7529 (mtp) REVERT: A 337 MET cc_start: 0.7038 (OUTLIER) cc_final: 0.6444 (mtp) REVERT: A 705 ILE cc_start: 0.7494 (OUTLIER) cc_final: 0.7059 (pp) REVERT: A 708 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.6852 (mt-10) REVERT: A 1114 GLN cc_start: 0.3436 (OUTLIER) cc_final: 0.2982 (mp-120) REVERT: A 1164 LEU cc_start: 0.3173 (OUTLIER) cc_final: 0.2849 (tm) REVERT: A 1332 MET cc_start: 0.0819 (ppp) cc_final: 0.0349 (mmm) REVERT: A 1633 GLN cc_start: 0.7777 (OUTLIER) cc_final: 0.7494 (tt0) REVERT: A 1647 THR cc_start: 0.8119 (OUTLIER) cc_final: 0.7857 (m) REVERT: A 1986 MET cc_start: 0.1561 (mmt) cc_final: 0.0309 (tpp) REVERT: A 2212 TRP cc_start: 0.0469 (OUTLIER) cc_final: -0.0563 (t60) REVERT: A 2323 TRP cc_start: 0.0569 (OUTLIER) cc_final: 0.0332 (p90) outliers start: 107 outliers final: 72 residues processed: 208 average time/residue: 1.0107 time to fit residues: 246.8180 Evaluate side-chains 201 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 119 time to evaluate : 1.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 143 LYS Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 223 LYS Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 379 ASN Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 532 GLU Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 667 ASP Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 708 GLU Chi-restraints excluded: chain A residue 721 ASP Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 756 ASP Chi-restraints excluded: chain A residue 774 SER Chi-restraints excluded: chain A residue 812 ASP Chi-restraints excluded: chain A residue 881 SER Chi-restraints excluded: chain A residue 903 LYS Chi-restraints excluded: chain A residue 937 PHE Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 969 ILE Chi-restraints excluded: chain A residue 978 LEU Chi-restraints excluded: chain A residue 1005 SER Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1114 GLN Chi-restraints excluded: chain A residue 1116 LYS Chi-restraints excluded: chain A residue 1143 ILE Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain A residue 1169 ILE Chi-restraints excluded: chain A residue 1176 SER Chi-restraints excluded: chain A residue 1181 THR Chi-restraints excluded: chain A residue 1194 THR Chi-restraints excluded: chain A residue 1228 ARG Chi-restraints excluded: chain A residue 1249 LYS Chi-restraints excluded: chain A residue 1251 LEU Chi-restraints excluded: chain A residue 1279 LYS Chi-restraints excluded: chain A residue 1402 ILE Chi-restraints excluded: chain A residue 1403 SER Chi-restraints excluded: chain A residue 1436 LEU Chi-restraints excluded: chain A residue 1539 SER Chi-restraints excluded: chain A residue 1547 THR Chi-restraints excluded: chain A residue 1582 LEU Chi-restraints excluded: chain A residue 1591 ILE Chi-restraints excluded: chain A residue 1609 THR Chi-restraints excluded: chain A residue 1610 ASN Chi-restraints excluded: chain A residue 1614 SER Chi-restraints excluded: chain A residue 1616 SER Chi-restraints excluded: chain A residue 1633 GLN Chi-restraints excluded: chain A residue 1645 SER Chi-restraints excluded: chain A residue 1647 THR Chi-restraints excluded: chain A residue 1662 TYR Chi-restraints excluded: chain A residue 1667 SER Chi-restraints excluded: chain A residue 1722 ASP Chi-restraints excluded: chain A residue 1724 ASN Chi-restraints excluded: chain A residue 1782 SER Chi-restraints excluded: chain A residue 1837 ILE Chi-restraints excluded: chain A residue 1841 ASP Chi-restraints excluded: chain A residue 1857 PHE Chi-restraints excluded: chain A residue 1894 ILE Chi-restraints excluded: chain A residue 1978 TYR Chi-restraints excluded: chain A residue 2033 THR Chi-restraints excluded: chain A residue 2125 ILE Chi-restraints excluded: chain A residue 2212 TRP Chi-restraints excluded: chain A residue 2235 VAL Chi-restraints excluded: chain A residue 2253 LEU Chi-restraints excluded: chain A residue 2289 MET Chi-restraints excluded: chain A residue 2323 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 137 optimal weight: 6.9990 chunk 88 optimal weight: 0.7980 chunk 132 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 chunk 43 optimal weight: 0.6980 chunk 42 optimal weight: 0.5980 chunk 140 optimal weight: 6.9990 chunk 151 optimal weight: 0.0070 chunk 109 optimal weight: 6.9990 chunk 20 optimal weight: 0.5980 chunk 174 optimal weight: 5.9990 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN ** A 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 574 ASN A 795 HIS A1413 ASN A2001 ASN ** A2058 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6435 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 19023 Z= 0.153 Angle : 0.537 8.558 25734 Z= 0.287 Chirality : 0.045 0.179 2831 Planarity : 0.004 0.055 3324 Dihedral : 6.917 83.243 2539 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.14 % Favored : 95.82 % Rotamer: Outliers : 4.26 % Allowed : 28.21 % Favored : 67.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 0.04 (0.18), residues: 2295 helix: 1.75 (0.21), residues: 634 sheet: -0.35 (0.25), residues: 445 loop : -0.74 (0.17), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 102 HIS 0.005 0.001 HIS A 757 PHE 0.023 0.001 PHE A 157 TYR 0.018 0.001 TYR A 46 ARG 0.007 0.000 ARG A 722 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 125 time to evaluate : 1.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 PHE cc_start: 0.4689 (t80) cc_final: 0.4382 (t80) REVERT: A 314 MET cc_start: 0.7595 (mtp) cc_final: 0.7356 (mtp) REVERT: A 337 MET cc_start: 0.6914 (OUTLIER) cc_final: 0.6424 (mtp) REVERT: A 423 ASP cc_start: 0.6448 (OUTLIER) cc_final: 0.6008 (p0) REVERT: A 708 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.6901 (mt-10) REVERT: A 1114 GLN cc_start: 0.3243 (OUTLIER) cc_final: 0.2842 (mp-120) REVERT: A 1164 LEU cc_start: 0.3103 (OUTLIER) cc_final: 0.2785 (tm) REVERT: A 1234 MET cc_start: 0.2565 (OUTLIER) cc_final: -0.0471 (mmm) REVERT: A 1533 LYS cc_start: 0.5533 (OUTLIER) cc_final: 0.5139 (tttt) REVERT: A 1647 THR cc_start: 0.8047 (OUTLIER) cc_final: 0.7735 (m) REVERT: A 1857 PHE cc_start: 0.5261 (OUTLIER) cc_final: 0.4556 (m-80) REVERT: A 1986 MET cc_start: 0.1306 (mmt) cc_final: 0.0152 (tpp) REVERT: A 2212 TRP cc_start: 0.0440 (OUTLIER) cc_final: -0.0468 (t60) REVERT: A 2323 TRP cc_start: 0.0605 (OUTLIER) cc_final: 0.0403 (p90) outliers start: 89 outliers final: 58 residues processed: 200 average time/residue: 0.9563 time to fit residues: 225.8469 Evaluate side-chains 188 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 119 time to evaluate : 1.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 143 LYS Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 379 ASN Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 532 GLU Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 667 ASP Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 708 GLU Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 774 SER Chi-restraints excluded: chain A residue 812 ASP Chi-restraints excluded: chain A residue 903 LYS Chi-restraints excluded: chain A residue 926 SER Chi-restraints excluded: chain A residue 937 PHE Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 1005 SER Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain A residue 1114 GLN Chi-restraints excluded: chain A residue 1116 LYS Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain A residue 1169 ILE Chi-restraints excluded: chain A residue 1176 SER Chi-restraints excluded: chain A residue 1181 THR Chi-restraints excluded: chain A residue 1194 THR Chi-restraints excluded: chain A residue 1228 ARG Chi-restraints excluded: chain A residue 1234 MET Chi-restraints excluded: chain A residue 1249 LYS Chi-restraints excluded: chain A residue 1251 LEU Chi-restraints excluded: chain A residue 1279 LYS Chi-restraints excluded: chain A residue 1436 LEU Chi-restraints excluded: chain A residue 1533 LYS Chi-restraints excluded: chain A residue 1547 THR Chi-restraints excluded: chain A residue 1582 LEU Chi-restraints excluded: chain A residue 1588 SER Chi-restraints excluded: chain A residue 1591 ILE Chi-restraints excluded: chain A residue 1609 THR Chi-restraints excluded: chain A residue 1610 ASN Chi-restraints excluded: chain A residue 1614 SER Chi-restraints excluded: chain A residue 1616 SER Chi-restraints excluded: chain A residue 1645 SER Chi-restraints excluded: chain A residue 1647 THR Chi-restraints excluded: chain A residue 1662 TYR Chi-restraints excluded: chain A residue 1667 SER Chi-restraints excluded: chain A residue 1724 ASN Chi-restraints excluded: chain A residue 1837 ILE Chi-restraints excluded: chain A residue 1841 ASP Chi-restraints excluded: chain A residue 1857 PHE Chi-restraints excluded: chain A residue 1978 TYR Chi-restraints excluded: chain A residue 2032 ASN Chi-restraints excluded: chain A residue 2033 THR Chi-restraints excluded: chain A residue 2125 ILE Chi-restraints excluded: chain A residue 2212 TRP Chi-restraints excluded: chain A residue 2235 VAL Chi-restraints excluded: chain A residue 2253 LEU Chi-restraints excluded: chain A residue 2289 MET Chi-restraints excluded: chain A residue 2323 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 201 optimal weight: 8.9990 chunk 212 optimal weight: 8.9990 chunk 193 optimal weight: 0.0470 chunk 206 optimal weight: 9.9990 chunk 124 optimal weight: 10.0000 chunk 89 optimal weight: 0.9980 chunk 162 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 186 optimal weight: 3.9990 chunk 195 optimal weight: 10.0000 chunk 205 optimal weight: 9.9990 overall best weight: 1.6082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 2 ASN ** A 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1413 ASN A1633 GLN ** A1896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2058 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6503 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 19023 Z= 0.300 Angle : 0.640 9.946 25734 Z= 0.344 Chirality : 0.049 0.190 2831 Planarity : 0.004 0.054 3324 Dihedral : 7.035 85.375 2536 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.23 % Favored : 95.73 % Rotamer: Outliers : 4.17 % Allowed : 28.45 % Favored : 67.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: -0.18 (0.17), residues: 2295 helix: 1.33 (0.20), residues: 639 sheet: -0.39 (0.24), residues: 458 loop : -0.79 (0.18), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 102 HIS 0.005 0.001 HIS A 757 PHE 0.035 0.002 PHE A 157 TYR 0.028 0.002 TYR A 46 ARG 0.007 0.001 ARG A 722 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 118 time to evaluate : 2.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 PHE cc_start: 0.4770 (t80) cc_final: 0.4437 (t80) REVERT: A 314 MET cc_start: 0.7621 (mtp) cc_final: 0.7397 (mtp) REVERT: A 337 MET cc_start: 0.7041 (OUTLIER) cc_final: 0.6450 (mtp) REVERT: A 708 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.6892 (mt-10) REVERT: A 1114 GLN cc_start: 0.3030 (OUTLIER) cc_final: 0.2672 (mp-120) REVERT: A 1164 LEU cc_start: 0.3151 (OUTLIER) cc_final: 0.2821 (tm) REVERT: A 1234 MET cc_start: 0.2532 (tpp) cc_final: -0.0462 (mmm) REVERT: A 1499 MET cc_start: 0.3127 (mpt) cc_final: 0.2186 (ttp) REVERT: A 1647 THR cc_start: 0.8115 (OUTLIER) cc_final: 0.7839 (m) REVERT: A 1986 MET cc_start: 0.1412 (mmt) cc_final: 0.0224 (tpp) REVERT: A 2212 TRP cc_start: 0.0575 (OUTLIER) cc_final: -0.0433 (t60) REVERT: A 2323 TRP cc_start: 0.0687 (OUTLIER) cc_final: 0.0456 (p90) outliers start: 87 outliers final: 68 residues processed: 194 average time/residue: 0.8999 time to fit residues: 207.4453 Evaluate side-chains 191 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 116 time to evaluate : 1.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 143 LYS Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 379 ASN Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 532 GLU Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 667 ASP Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 708 GLU Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 756 ASP Chi-restraints excluded: chain A residue 774 SER Chi-restraints excluded: chain A residue 812 ASP Chi-restraints excluded: chain A residue 881 SER Chi-restraints excluded: chain A residue 903 LYS Chi-restraints excluded: chain A residue 926 SER Chi-restraints excluded: chain A residue 937 PHE Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 978 LEU Chi-restraints excluded: chain A residue 1005 SER Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain A residue 1114 GLN Chi-restraints excluded: chain A residue 1116 LYS Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain A residue 1169 ILE Chi-restraints excluded: chain A residue 1176 SER Chi-restraints excluded: chain A residue 1181 THR Chi-restraints excluded: chain A residue 1194 THR Chi-restraints excluded: chain A residue 1228 ARG Chi-restraints excluded: chain A residue 1249 LYS Chi-restraints excluded: chain A residue 1251 LEU Chi-restraints excluded: chain A residue 1299 ILE Chi-restraints excluded: chain A residue 1304 THR Chi-restraints excluded: chain A residue 1434 MET Chi-restraints excluded: chain A residue 1539 SER Chi-restraints excluded: chain A residue 1541 SER Chi-restraints excluded: chain A residue 1547 THR Chi-restraints excluded: chain A residue 1582 LEU Chi-restraints excluded: chain A residue 1588 SER Chi-restraints excluded: chain A residue 1591 ILE Chi-restraints excluded: chain A residue 1609 THR Chi-restraints excluded: chain A residue 1610 ASN Chi-restraints excluded: chain A residue 1614 SER Chi-restraints excluded: chain A residue 1616 SER Chi-restraints excluded: chain A residue 1645 SER Chi-restraints excluded: chain A residue 1647 THR Chi-restraints excluded: chain A residue 1662 TYR Chi-restraints excluded: chain A residue 1667 SER Chi-restraints excluded: chain A residue 1724 ASN Chi-restraints excluded: chain A residue 1782 SER Chi-restraints excluded: chain A residue 1837 ILE Chi-restraints excluded: chain A residue 1841 ASP Chi-restraints excluded: chain A residue 1857 PHE Chi-restraints excluded: chain A residue 1978 TYR Chi-restraints excluded: chain A residue 2032 ASN Chi-restraints excluded: chain A residue 2033 THR Chi-restraints excluded: chain A residue 2125 ILE Chi-restraints excluded: chain A residue 2212 TRP Chi-restraints excluded: chain A residue 2235 VAL Chi-restraints excluded: chain A residue 2253 LEU Chi-restraints excluded: chain A residue 2289 MET Chi-restraints excluded: chain A residue 2323 TRP Chi-restraints excluded: chain A residue 2361 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 135 optimal weight: 2.9990 chunk 218 optimal weight: 8.9990 chunk 133 optimal weight: 0.1980 chunk 103 optimal weight: 0.0050 chunk 151 optimal weight: 0.0270 chunk 229 optimal weight: 3.9990 chunk 210 optimal weight: 0.6980 chunk 182 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 140 optimal weight: 3.9990 chunk 111 optimal weight: 10.0000 overall best weight: 0.3854 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 795 HIS A1413 ASN ** A2058 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6410 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 19023 Z= 0.136 Angle : 0.522 8.664 25734 Z= 0.277 Chirality : 0.044 0.190 2831 Planarity : 0.004 0.055 3324 Dihedral : 6.435 82.997 2536 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.97 % Favored : 95.99 % Rotamer: Outliers : 3.54 % Allowed : 29.17 % Favored : 67.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 0.25 (0.18), residues: 2295 helix: 1.99 (0.21), residues: 635 sheet: -0.23 (0.25), residues: 443 loop : -0.66 (0.18), residues: 1217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 312 HIS 0.004 0.000 HIS A 757 PHE 0.034 0.001 PHE A 157 TYR 0.016 0.001 TYR A 46 ARG 0.006 0.000 ARG A 722 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 127 time to evaluate : 2.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 PHE cc_start: 0.4413 (t80) cc_final: 0.4197 (t80) REVERT: A 314 MET cc_start: 0.7552 (mtp) cc_final: 0.7293 (mtp) REVERT: A 667 ASP cc_start: 0.7481 (OUTLIER) cc_final: 0.7189 (m-30) REVERT: A 708 GLU cc_start: 0.7490 (OUTLIER) cc_final: 0.6925 (mt-10) REVERT: A 754 ILE cc_start: 0.7398 (OUTLIER) cc_final: 0.6958 (pp) REVERT: A 1114 GLN cc_start: 0.3068 (OUTLIER) cc_final: 0.2679 (mp-120) REVERT: A 1164 LEU cc_start: 0.3088 (OUTLIER) cc_final: 0.2784 (tm) REVERT: A 1234 MET cc_start: 0.2525 (OUTLIER) cc_final: -0.0412 (mmm) REVERT: A 1332 MET cc_start: 0.0867 (ppp) cc_final: 0.0060 (mmm) REVERT: A 1499 MET cc_start: 0.2701 (mpt) cc_final: 0.1745 (ttp) REVERT: A 1647 THR cc_start: 0.8073 (OUTLIER) cc_final: 0.7780 (m) REVERT: A 1857 PHE cc_start: 0.5036 (OUTLIER) cc_final: 0.4260 (m-80) REVERT: A 1986 MET cc_start: 0.1340 (mmt) cc_final: 0.0145 (tpp) REVERT: A 2212 TRP cc_start: 0.0537 (OUTLIER) cc_final: -0.0413 (t60) REVERT: A 2323 TRP cc_start: 0.0746 (OUTLIER) cc_final: 0.0502 (p90) outliers start: 74 outliers final: 49 residues processed: 192 average time/residue: 1.0209 time to fit residues: 229.8769 Evaluate side-chains 181 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 122 time to evaluate : 1.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 143 LYS Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 379 ASN Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 532 GLU Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 667 ASP Chi-restraints excluded: chain A residue 708 GLU Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 774 SER Chi-restraints excluded: chain A residue 903 LYS Chi-restraints excluded: chain A residue 926 SER Chi-restraints excluded: chain A residue 937 PHE Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 969 ILE Chi-restraints excluded: chain A residue 1005 SER Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain A residue 1114 GLN Chi-restraints excluded: chain A residue 1116 LYS Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain A residue 1169 ILE Chi-restraints excluded: chain A residue 1176 SER Chi-restraints excluded: chain A residue 1181 THR Chi-restraints excluded: chain A residue 1194 THR Chi-restraints excluded: chain A residue 1228 ARG Chi-restraints excluded: chain A residue 1234 MET Chi-restraints excluded: chain A residue 1251 LEU Chi-restraints excluded: chain A residue 1539 SER Chi-restraints excluded: chain A residue 1541 SER Chi-restraints excluded: chain A residue 1547 THR Chi-restraints excluded: chain A residue 1582 LEU Chi-restraints excluded: chain A residue 1591 ILE Chi-restraints excluded: chain A residue 1609 THR Chi-restraints excluded: chain A residue 1610 ASN Chi-restraints excluded: chain A residue 1614 SER Chi-restraints excluded: chain A residue 1616 SER Chi-restraints excluded: chain A residue 1645 SER Chi-restraints excluded: chain A residue 1647 THR Chi-restraints excluded: chain A residue 1662 TYR Chi-restraints excluded: chain A residue 1667 SER Chi-restraints excluded: chain A residue 1724 ASN Chi-restraints excluded: chain A residue 1837 ILE Chi-restraints excluded: chain A residue 1857 PHE Chi-restraints excluded: chain A residue 1978 TYR Chi-restraints excluded: chain A residue 2032 ASN Chi-restraints excluded: chain A residue 2033 THR Chi-restraints excluded: chain A residue 2212 TRP Chi-restraints excluded: chain A residue 2235 VAL Chi-restraints excluded: chain A residue 2253 LEU Chi-restraints excluded: chain A residue 2289 MET Chi-restraints excluded: chain A residue 2323 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 144 optimal weight: 6.9990 chunk 194 optimal weight: 1.9990 chunk 55 optimal weight: 0.0980 chunk 168 optimal weight: 0.0870 chunk 26 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 182 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 187 optimal weight: 9.9990 chunk 23 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 overall best weight: 0.5962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 795 HIS A1413 ASN A1633 GLN ** A2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4889 r_free = 0.4889 target = 0.277382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4758 r_free = 0.4758 target = 0.261806 restraints weight = 19982.673| |-----------------------------------------------------------------------------| r_work (start): 0.4764 rms_B_bonded: 0.73 r_work: 0.4639 rms_B_bonded: 1.06 restraints_weight: 0.5000 r_work: 0.4612 rms_B_bonded: 1.37 restraints_weight: 0.2500 r_work: 0.4487 rms_B_bonded: 3.70 restraints_weight: 0.1250 r_work (final): 0.4487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6248 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19023 Z= 0.164 Angle : 0.545 8.505 25734 Z= 0.290 Chirality : 0.045 0.201 2831 Planarity : 0.004 0.052 3324 Dihedral : 6.330 82.472 2536 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.01 % Favored : 95.95 % Rotamer: Outliers : 3.21 % Allowed : 29.65 % Favored : 67.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 0.30 (0.18), residues: 2295 helix: 2.00 (0.21), residues: 638 sheet: -0.18 (0.25), residues: 443 loop : -0.62 (0.18), residues: 1214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 102 HIS 0.005 0.001 HIS A 757 PHE 0.049 0.001 PHE A 157 TYR 0.020 0.001 TYR A 46 ARG 0.006 0.000 ARG A 722 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6065.59 seconds wall clock time: 107 minutes 20.46 seconds (6440.46 seconds total)