Starting phenix.real_space_refine on Wed Aug 7 09:27:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x2h_38010/08_2024/8x2h_38010.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x2h_38010/08_2024/8x2h_38010.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x2h_38010/08_2024/8x2h_38010.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x2h_38010/08_2024/8x2h_38010.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x2h_38010/08_2024/8x2h_38010.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x2h_38010/08_2024/8x2h_38010.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.052 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 47 5.16 5 C 12219 2.51 5 N 3035 2.21 5 O 3786 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 39": "OE1" <-> "OE2" Residue "A TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 51": "OD1" <-> "OD2" Residue "A PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 85": "OE1" <-> "OE2" Residue "A PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 147": "OE1" <-> "OE2" Residue "A GLU 177": "OE1" <-> "OE2" Residue "A PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 195": "OE1" <-> "OE2" Residue "A GLU 196": "OE1" <-> "OE2" Residue "A TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 217": "OD1" <-> "OD2" Residue "A GLU 226": "OE1" <-> "OE2" Residue "A GLU 244": "OE1" <-> "OE2" Residue "A GLU 249": "OE1" <-> "OE2" Residue "A ASP 288": "OD1" <-> "OD2" Residue "A ASP 296": "OD1" <-> "OD2" Residue "A ASP 305": "OD1" <-> "OD2" Residue "A PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 355": "OD1" <-> "OD2" Residue "A GLU 358": "OE1" <-> "OE2" Residue "A PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 420": "OE1" <-> "OE2" Residue "A ASP 461": "OD1" <-> "OD2" Residue "A TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 486": "OD1" <-> "OD2" Residue "A GLU 495": "OE1" <-> "OE2" Residue "A GLU 497": "OE1" <-> "OE2" Residue "A PHE 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 547": "OD1" <-> "OD2" Residue "A TYR 577": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 580": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 613": "OE1" <-> "OE2" Residue "A GLU 616": "OE1" <-> "OE2" Residue "A ASP 625": "OD1" <-> "OD2" Residue "A ASP 632": "OD1" <-> "OD2" Residue "A TYR 634": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 650": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 661": "OD1" <-> "OD2" Residue "A ASP 667": "OD1" <-> "OD2" Residue "A GLU 676": "OE1" <-> "OE2" Residue "A PHE 701": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 709": "OE1" <-> "OE2" Residue "A TYR 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 722": "NH1" <-> "NH2" Residue "A GLU 776": "OE1" <-> "OE2" Residue "A TYR 777": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 784": "OE1" <-> "OE2" Residue "A GLU 803": "OE1" <-> "OE2" Residue "A ARG 805": "NH1" <-> "NH2" Residue "A GLU 816": "OE1" <-> "OE2" Residue "A GLU 825": "OE1" <-> "OE2" Residue "A ASP 833": "OD1" <-> "OD2" Residue "A ARG 834": "NH1" <-> "NH2" Residue "A GLU 838": "OE1" <-> "OE2" Residue "A ASP 850": "OD1" <-> "OD2" Residue "A TYR 854": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 859": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 870": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 880": "OD1" <-> "OD2" Residue "A PHE 883": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 887": "OE1" <-> "OE2" Residue "A ASP 888": "OD1" <-> "OD2" Residue "A PHE 900": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 904": "OE1" <-> "OE2" Residue "A PHE 910": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 912": "OE1" <-> "OE2" Residue "A GLU 914": "OE1" <-> "OE2" Residue "A GLU 916": "OE1" <-> "OE2" Residue "A GLU 920": "OE1" <-> "OE2" Residue "A TYR 921": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 963": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 964": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 970": "OE1" <-> "OE2" Residue "A GLU 976": "OE1" <-> "OE2" Residue "A PHE 994": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1009": "OE1" <-> "OE2" Residue "A GLU 1017": "OE1" <-> "OE2" Residue "A ASP 1037": "OD1" <-> "OD2" Residue "A GLU 1050": "OE1" <-> "OE2" Residue "A ARG 1057": "NH1" <-> "NH2" Residue "A GLU 1059": "OE1" <-> "OE2" Residue "A PHE 1089": "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 1133": "OE1" <-> "OE2" Residue "A ASP 1141": "OD1" <-> "OD2" Residue "A PHE 1157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1168": "OE1" <-> "OE2" Residue "A ASP 1183": "OD1" <-> "OD2" Residue "A ASP 1185": "OD1" <-> "OD2" Residue "A PHE 1188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1244": "OD1" <-> "OD2" Residue "A ASP 1252": "OD1" <-> "OD2" Residue "A GLU 1259": "OE1" <-> "OE2" Residue "A PHE 1262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1272": "OD1" <-> "OD2" Residue "A TYR 1282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1306": "OE1" <-> "OE2" Residue "A TYR 1314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1347": "OD1" <-> "OD2" Residue "A ASP 1349": "OD1" <-> "OD2" Residue "A ASP 1360": "OD1" <-> "OD2" Residue "A GLU 1366": "OE1" <-> "OE2" Residue "A PHE 1391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1394": "OD1" <-> "OD2" Residue "A GLU 1397": "OE1" <-> "OE2" Residue "A GLU 1410": "OE1" <-> "OE2" Residue "A PHE 1452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1455": "OE1" <-> "OE2" Residue "A TYR 1459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1488": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1498": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1501": "OD1" <-> "OD2" Residue "A PHE 1506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1532": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1534": "OD1" <-> "OD2" Residue "A PHE 1542": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1545": "OE1" <-> "OE2" Residue "A PHE 1585": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1587": "OE1" <-> "OE2" Residue "A TYR 1596": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1600": "OD1" <-> "OD2" Residue "A GLU 1604": "OE1" <-> "OE2" Residue "A PHE 1611": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1623": "OE1" <-> "OE2" Residue "A TYR 1635": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1646": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1659": "OE1" <-> "OE2" Residue "A TYR 1662": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1677": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1683": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1699": "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 1758": "OE1" <-> "OE2" Residue "A ASP 1759": "OD1" <-> "OD2" Residue "A PHE 1768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1783": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1790": "OD1" <-> "OD2" Residue "A PHE 1800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1807": "OD1" <-> "OD2" Residue "A PHE 1809": "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 TYR 1823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1824": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1825": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1838": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1844": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1845": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1846": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1865": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1866": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1879": "OE1" <-> "OE2" Residue "A ASP 1883": "OD1" <-> "OD2" Residue "A TYR 1887": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1904": "OD1" <-> "OD2" Residue "A TYR 1908": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1909": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1916": "OD1" <-> "OD2" Residue "A GLU 1917": "OE1" <-> "OE2" Residue "A GLU 1920": "OE1" <-> "OE2" Residue "A PHE 1926": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1933": "OD1" <-> "OD2" Residue "A TYR 1937": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1938": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1939": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1940": "OE1" <-> "OE2" Residue "A ASP 1941": "OD1" <-> "OD2" Residue "A ASP 1953": "OD1" <-> "OD2" Residue "A ASP 1954": "OD1" <-> "OD2" Residue "A GLU 1955": "OE1" <-> "OE2" Residue "A GLU 1965": "OE1" <-> "OE2" Residue "A TYR 1978": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1979": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1980": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1982": "OD1" <-> "OD2" 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 TYR 2010": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2012": "OE1" <-> "OE2" Residue "A PHE 2018": "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 2045": "OD1" <-> "OD2" Residue "A ASP 2046": "OD1" <-> "OD2" Residue "A GLU 2053": "OE1" <-> "OE2" 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 TYR 2089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2090": "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 2122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2127": "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 PHE 2150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2197": "OE1" <-> "OE2" Residue "A ASP 2198": "OD1" <-> "OD2" Residue "A TYR 2200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2209": "OE1" <-> "OE2" Residue "A GLU 2216": "OE1" <-> "OE2" Residue "A ASP 2218": "OD1" <-> "OD2" Residue "A PHE 2222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2223": "OD1" <-> "OD2" Residue "A TYR 2241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2250": "NH1" <-> "NH2" 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 ASP 2266": "OD1" <-> "OD2" Residue "A PHE 2271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2278": "OD1" <-> "OD2" Residue "A PHE 2283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2286": "OD1" <-> "OD2" Residue "A PHE 2300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2310": "OD1" <-> "OD2" Residue "A PHE 2313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2354": "OD1" <-> "OD2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 19088 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 19087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2363, 19087 Classifications: {'peptide': 2363} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 2306} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 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 5700 SG CYS A 698 46.893 50.407 184.224 1.00 66.12 S Time building chain proxies: 11.00, per 1000 atoms: 0.58 Number of scatterers: 19088 At special positions: 0 Unit cell: (97.83, 140.223, 223.922, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 47 16.00 O 3786 8.00 N 3035 7.00 C 12219 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: 7.40 Conformation dependent library (CDL) restraints added in 3.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A3000 " pdb="ZN ZN A3000 " - pdb=" SG CYS A 698 " pdb="ZN ZN A3000 " - pdb=" ND1 HIS A 653 " 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4462 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 43 sheets defined 27.9% alpha, 22.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.64 Creating SS restraints... Processing helix chain 'A' and resid 5 through 13 Processing helix chain 'A' and resid 21 through 34 Processing helix chain 'A' and resid 41 through 61 Processing helix chain 'A' and resid 68 through 90 removed outlier: 3.983A pdb=" N LYS A 74 " --> pdb=" O LYS A 70 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLU A 77 " --> pdb=" O LYS A 73 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N THR A 80 " --> pdb=" O LYS A 76 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU A 84 " --> pdb=" O THR A 80 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU A 85 " --> pdb=" O MET A 81 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER A 90 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 119 removed outlier: 3.623A pdb=" N ILE A 112 " --> pdb=" O ASN A 108 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N TYR A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N GLN A 117 " --> pdb=" O ASN A 113 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TRP A 118 " --> pdb=" O TYR A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 148 removed outlier: 3.501A pdb=" N LEU A 141 " --> pdb=" O LEU A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 156 removed outlier: 3.907A pdb=" N SER A 156 " --> pdb=" O ASN A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 194 removed outlier: 4.252A pdb=" N GLU A 177 " --> pdb=" O ARG A 173 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 215 removed outlier: 3.500A pdb=" N ILE A 205 " --> pdb=" O ILE A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 233 Processing helix chain 'A' and resid 251 through 261 removed outlier: 3.544A pdb=" N GLU A 261 " --> pdb=" O GLN A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 324 removed outlier: 3.619A pdb=" N TYR A 323 " --> pdb=" O ALA A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 337 removed outlier: 4.028A pdb=" N ASP A 336 " --> pdb=" O SER A 332 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N MET A 337 " --> pdb=" O LYS A 333 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 332 through 337' Processing helix chain 'A' and resid 339 through 349 Processing helix chain 'A' and resid 355 through 360 Processing helix chain 'A' and resid 394 through 421 removed outlier: 3.826A pdb=" N LEU A 398 " --> pdb=" O TYR A 394 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ILE A 400 " --> pdb=" O SER A 396 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASN A 413 " --> pdb=" O ILE A 409 " (cutoff:3.500A) Proline residue: A 416 - end of helix Processing helix chain 'A' and resid 423 through 436 Processing helix chain 'A' and resid 437 through 439 No H-bonds generated for 'chain 'A' and resid 437 through 439' Processing helix chain 'A' and resid 451 through 456 removed outlier: 4.638A pdb=" N LEU A 454 " --> pdb=" O THR A 451 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL A 456 " --> pdb=" O TYR A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 483 removed outlier: 3.783A pdb=" N TYR A 474 " --> pdb=" O GLY A 470 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR A 475 " --> pdb=" O PRO A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 502 removed outlier: 3.631A pdb=" N PHE A 501 " --> pdb=" O LEU A 498 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU A 502 " --> pdb=" O ARG A 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 498 through 502' Processing helix chain 'A' and resid 504 through 508 removed outlier: 4.039A pdb=" N ILE A 508 " --> pdb=" O LYS A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 519 Processing helix chain 'A' and resid 526 through 537 Processing helix chain 'A' and resid 558 through 568 Processing helix chain 'A' and resid 587 through 601 removed outlier: 3.764A pdb=" N TYR A 591 " --> pdb=" O ASP A 587 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP A 601 " --> pdb=" O LEU A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 641 removed outlier: 3.546A pdb=" N ILE A 640 " --> pdb=" O PRO A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 683 Processing helix chain 'A' and resid 710 through 715 Processing helix chain 'A' and resid 715 through 720 Processing helix chain 'A' and resid 764 through 773 Processing helix chain 'A' and resid 793 through 808 removed outlier: 4.233A pdb=" N LEU A 797 " --> pdb=" O TYR A 793 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 838 removed outlier: 3.639A pdb=" N LYS A 818 " --> pdb=" O ASP A 814 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N CYS A 824 " --> pdb=" O MET A 820 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE A 826 " --> pdb=" O THR A 822 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASN A 827 " --> pdb=" O GLU A 823 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU A 838 " --> pdb=" O ARG A 834 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 857 removed outlier: 3.764A pdb=" N SER A 851 " --> pdb=" O LEU A 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 860 through 876 removed outlier: 3.999A pdb=" N LEU A 872 " --> pdb=" O SER A 868 " (cutoff:3.500A) removed outlier: 3.544A 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 951 through 971 Processing helix chain 'A' and resid 975 through 980 Processing helix chain 'A' and resid 980 through 995 removed outlier: 3.768A pdb=" N ALA A 984 " --> pdb=" O ASN A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 1003 through 1017 removed outlier: 4.060A pdb=" N VAL A1008 " --> pdb=" O ALA A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1044 through 1049 removed outlier: 3.659A pdb=" N SER A1049 " --> pdb=" O ILE A1045 " (cutoff:3.500A) Processing helix chain 'A' and resid 1055 through 1058 removed outlier: 3.619A pdb=" N GLN A1058 " --> pdb=" O LEU A1055 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1055 through 1058' Processing helix chain 'A' and resid 1059 through 1064 removed outlier: 3.517A pdb=" N ILE A1064 " --> pdb=" O ILE A1060 " (cutoff:3.500A) Processing helix chain 'A' and resid 1072 through 1081 removed outlier: 4.299A pdb=" N ILE A1078 " --> pdb=" O ALA A1074 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1133 removed outlier: 4.160A pdb=" N ALA A1130 " --> pdb=" O HIS A1126 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N GLU A1131 " --> pdb=" O ILE A1127 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR A1132 " --> pdb=" O SER A1128 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU A1133 " --> pdb=" O LEU A1129 " (cutoff:3.500A) Processing helix chain 'A' and resid 1202 through 1206 removed outlier: 3.936A pdb=" N LEU A1206 " --> pdb=" O ILE A1202 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1202 through 1206' Processing helix chain 'A' and resid 1245 through 1258 removed outlier: 3.601A pdb=" N TYR A1258 " --> pdb=" O ILE A1254 " (cutoff:3.500A) Processing helix chain 'A' and resid 1305 through 1311 removed outlier: 4.030A pdb=" N ARG A1309 " --> pdb=" O THR A1305 " (cutoff:3.500A) Processing helix chain 'A' and resid 1348 through 1352 removed outlier: 3.808A pdb=" N VAL A1352 " --> pdb=" O VAL A1348 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1348 through 1352' Processing helix chain 'A' and resid 1396 through 1399 Processing helix chain 'A' and resid 1432 through 1439 Processing helix chain 'A' and resid 1439 through 1450 Processing helix chain 'A' and resid 1558 through 1572 Processing helix chain 'A' and resid 1582 through 1587 Processing helix chain 'A' and resid 1588 through 1590 No H-bonds generated for 'chain 'A' and resid 1588 through 1590' Processing helix chain 'A' and resid 1680 through 1683 Processing helix chain 'A' and resid 1792 through 1800 Processing helix chain 'A' and resid 1868 through 1872 removed outlier: 3.584A pdb=" N LYS A1871 " --> pdb=" O ASP A1868 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER A1872 " --> pdb=" O PRO A1869 " (cutoff:3.500A) No H-bonds generated for '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 126 through 130 removed outlier: 6.152A pdb=" N LEU A 98 " --> pdb=" O LYS A 128 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N PHE A 130 " --> pdb=" O LEU A 98 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N PHE A 100 " --> pdb=" O PHE A 130 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ASN A 97 " --> pdb=" O VAL A 283 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N LEU A 285 " --> pdb=" O ASN A 97 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N HIS A 99 " --> pdb=" O LEU A 285 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER A 381 " --> pdb=" O ALA A 378 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA A 376 " --> pdb=" O ILE A 383 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N GLN A 385 " --> pdb=" O LYS A 374 " (cutoff:3.500A) removed outlier: 11.806A pdb=" N LYS A 374 " --> pdb=" O GLN A 385 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 578 through 583 removed outlier: 6.796A pdb=" N ILE A 646 " --> pdb=" O GLU A 692 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N ASN A 694 " --> pdb=" O ILE A 646 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N LEU A 648 " --> pdb=" O ASN A 694 " (cutoff:3.500A) removed outlier: 8.347A pdb=" N LEU A 696 " --> pdb=" O LEU A 648 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N PHE A 650 " --> pdb=" O LEU A 696 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ILE A 691 " --> pdb=" O THR A 736 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 606 through 607 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 778 through 781 removed outlier: 3.742A pdb=" N LYS A 786 " --> pdb=" O ASN A 781 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 882 through 891 removed outlier: 9.901A pdb=" N PHE A 886 " --> pdb=" O ILE A 901 " (cutoff:3.500A) removed outlier: 11.628A pdb=" N ILE A 901 " --> pdb=" O PHE A 886 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N ASP A 888 " --> pdb=" O ARG A 899 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG A 899 " --> pdb=" O ASP A 888 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 936 through 939 removed outlier: 3.745A pdb=" N ASP A 938 " --> pdb=" O VAL A 945 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1066 through 1067 removed outlier: 4.165A pdb=" N ILE A1516 " --> pdb=" O ILE A1528 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ILE A1528 " --> pdb=" O ILE A1516 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ILE A1518 " --> pdb=" O LEU A1526 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LEU A1526 " --> pdb=" O ILE A1518 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ASN A1520 " --> pdb=" O VAL A1524 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N VAL A1524 " --> pdb=" O ASN A1520 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ILE A1550 " --> pdb=" O ILE A1606 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ASP A1608 " --> pdb=" O ILE A1550 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N LEU A1552 " --> pdb=" O ASP A1608 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ASN A1610 " --> pdb=" O LEU A1552 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N GLY A1554 " --> pdb=" O ASN A1610 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ILE A1612 " --> pdb=" O GLY A1554 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N TYR A1556 " --> pdb=" O ILE A1612 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N SER A1614 " --> pdb=" O TYR A1556 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ILE A1625 " --> pdb=" O PRO A1634 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1105 through 1107 Processing sheet with id=AB2, first strand: chain 'A' and resid 1136 through 1139 Processing sheet with id=AB3, first strand: chain 'A' and resid 1161 through 1164 removed outlier: 7.261A pdb=" N SER A1161 " --> pdb=" O ILE A1155 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N ILE A1155 " --> pdb=" O SER A1161 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N THR A1163 " --> pdb=" O SER A1153 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N SER A1153 " --> pdb=" O ARG A1288 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N ASN A1290 " --> pdb=" O SER A1153 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILE A1155 " --> pdb=" O ASN A1290 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ILE A1334 " --> pdb=" O ASN A1390 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N TYR A1392 " --> pdb=" O ILE A1334 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N LEU A1336 " --> pdb=" O TYR A1392 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1179 through 1181 removed outlier: 6.638A pdb=" N ASP A1185 " --> pdb=" O PHE A1267 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N ILE A1275 " --> pdb=" O GLY A1235 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N GLY A1235 " --> pdb=" O ILE A1275 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N LYS A1277 " --> pdb=" O GLU A1233 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASN A1227 " --> pdb=" O GLU A1283 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N GLU A1168 " --> pdb=" O PHE A1230 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N TYR A1232 " --> pdb=" O GLU A1168 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1171 through 1173 Processing sheet with id=AB6, first strand: chain 'A' and resid 1219 through 1221 removed outlier: 6.945A pdb=" N TYR A1323 " --> pdb=" O VAL A1345 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N ASP A1347 " --> pdb=" O TYR A1323 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LEU A1325 " --> pdb=" O ASP A1347 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N TRP A1344 " --> pdb=" O SER A1403 " (cutoff:3.500A) removed outlier: 8.895A pdb=" N THR A1405 " --> pdb=" O TRP A1344 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N ILE A1346 " --> pdb=" O THR A1405 " (cutoff:3.500A) removed outlier: 9.321A pdb=" N SER A1407 " --> pdb=" O ILE A1346 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ILE A1412 " --> pdb=" O ILE A1408 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1353 through 1358 removed outlier: 4.659A pdb=" N ASN A1354 " --> pdb=" O GLY A1365 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1459 through 1466 Processing sheet with id=AB9, first strand: chain 'A' and resid 1675 through 1678 removed outlier: 6.362A pdb=" N ILE A1675 " --> pdb=" O ASN A1704 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N THR A1706 " --> pdb=" O ILE A1675 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N PHE A1677 " --> pdb=" O THR A1706 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1815 through 1819 Processing sheet with id=AC2, first strand: chain 'A' and resid 1835 through 1838 removed outlier: 3.697A pdb=" N LYS A1847 " --> pdb=" O ASN A1852 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASN A1852 " --> pdb=" O LYS A1847 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 1856 through 1860 Processing sheet with id=AC4, first strand: chain 'A' and resid 1878 through 1882 Processing sheet with id=AC5, first strand: chain 'A' and resid 1898 through 1902 removed outlier: 3.626A pdb=" N GLU A1922 " --> pdb=" O ALA A1910 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 1928 through 1932 Processing sheet with id=AC7, first strand: chain 'A' and resid 1949 through 1952 Processing sheet with id=AC8, first strand: chain 'A' and resid 1969 through 1973 Processing sheet with id=AC9, first strand: chain 'A' and resid 1989 through 1993 Processing sheet with id=AD1, first strand: chain 'A' and resid 2010 through 2013 Processing sheet with id=AD2, first strand: chain 'A' and resid 2029 through 2033 Processing sheet with id=AD3, first strand: chain 'A' and resid 2059 through 2063 Processing sheet with id=AD4, first strand: chain 'A' and resid 2079 through 2082 Processing sheet with id=AD5, first strand: chain 'A' and resid 2101 through 2105 removed outlier: 4.008A pdb=" N TYR A2111 " --> pdb=" O GLN A2119 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 2121 through 2125 Processing sheet with id=AD7, first strand: chain 'A' and resid 2141 through 2145 removed outlier: 4.608A pdb=" N GLY A2141 " --> pdb=" O ILE A2152 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ILE A2152 " --> pdb=" O GLY A2141 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 2161 through 2163 removed outlier: 4.016A pdb=" N TYR A2171 " --> pdb=" O VAL A2187 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 2191 through 2195 removed outlier: 4.755A pdb=" N TYR A2201 " --> pdb=" O GLU A2209 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 2211 through 2215 Processing sheet with id=AE2, first strand: chain 'A' and resid 2232 through 2236 Processing sheet with id=AE3, first strand: chain 'A' and resid 2252 through 2256 Processing sheet with id=AE4, first strand: chain 'A' and resid 2272 through 2276 Processing sheet with id=AE5, first strand: chain 'A' and resid 2292 through 2296 Processing sheet with id=AE6, first strand: chain 'A' and resid 2322 through 2326 Processing sheet with id=AE7, first strand: chain 'A' and resid 2343 through 2346 removed outlier: 4.515A pdb=" N TYR A2352 " --> pdb=" O VAL A2361 " (cutoff:3.500A) 714 hydrogen bonds defined for protein. 1914 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: 11.87 Time building geometry restraints manager: 8.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 3338 1.30 - 1.43: 5027 1.43 - 1.56: 11022 1.56 - 1.69: 0 1.69 - 1.82: 84 Bond restraints: 19471 Sorted by residual: bond pdb=" C TYR A1683 " pdb=" N GLY A1684 " ideal model delta sigma weight residual 1.331 1.252 0.078 1.46e-02 4.69e+03 2.86e+01 bond pdb=" C TYR A1683 " pdb=" O TYR A1683 " ideal model delta sigma weight residual 1.234 1.173 0.061 1.17e-02 7.31e+03 2.71e+01 bond pdb=" CA TYR A1683 " pdb=" CB TYR A1683 " ideal model delta sigma weight residual 1.530 1.500 0.031 1.62e-02 3.81e+03 3.62e+00 bond pdb=" CB TYR A1683 " pdb=" CG TYR A1683 " ideal model delta sigma weight residual 1.512 1.476 0.036 2.20e-02 2.07e+03 2.67e+00 bond pdb=" CA TYR A1683 " pdb=" C TYR A1683 " ideal model delta sigma weight residual 1.523 1.504 0.019 1.23e-02 6.61e+03 2.29e+00 ... (remaining 19466 not shown) Histogram of bond angle deviations from ideal: 85.50 - 95.24: 1 95.24 - 104.97: 200 104.97 - 114.70: 11347 114.70 - 124.43: 14552 124.43 - 134.16: 243 Bond angle restraints: 26343 Sorted by residual: angle pdb=" C TYR A1683 " pdb=" CA TYR A1683 " pdb=" CB TYR A1683 " ideal model delta sigma weight residual 109.70 85.50 24.20 1.61e+00 3.86e-01 2.26e+02 angle pdb=" C VAL A1650 " pdb=" CA VAL A1650 " pdb=" CB VAL A1650 " ideal model delta sigma weight residual 110.88 103.75 7.13 1.09e+00 8.42e-01 4.28e+01 angle pdb=" CA TYR A1683 " pdb=" C TYR A1683 " pdb=" O TYR A1683 " ideal model delta sigma weight residual 121.15 128.07 -6.92 1.10e+00 8.26e-01 3.95e+01 angle pdb=" N VAL A 121 " pdb=" CA VAL A 121 " pdb=" C VAL A 121 " ideal model delta sigma weight residual 113.71 109.10 4.61 9.50e-01 1.11e+00 2.36e+01 angle pdb=" C TYR A 538 " pdb=" N PHE A 539 " pdb=" CA PHE A 539 " ideal model delta sigma weight residual 121.54 130.05 -8.51 1.91e+00 2.74e-01 1.98e+01 ... (remaining 26338 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.01: 9616 18.01 - 36.03: 1402 36.03 - 54.04: 477 54.04 - 72.05: 126 72.05 - 90.07: 36 Dihedral angle restraints: 11657 sinusoidal: 4688 harmonic: 6969 Sorted by residual: dihedral pdb=" CA SER A1774 " pdb=" C SER A1774 " pdb=" N ASP A1775 " pdb=" CA ASP A1775 " ideal model delta harmonic sigma weight residual 180.00 121.80 58.20 0 5.00e+00 4.00e-02 1.35e+02 dihedral pdb=" C TYR A1683 " pdb=" N TYR A1683 " pdb=" CA TYR A1683 " pdb=" CB TYR A1683 " ideal model delta harmonic sigma weight residual -122.60 -96.04 -26.56 0 2.50e+00 1.60e-01 1.13e+02 dihedral pdb=" CA ALA A1068 " pdb=" C ALA A1068 " pdb=" N VAL A1069 " pdb=" CA VAL A1069 " ideal model delta harmonic sigma weight residual -180.00 -147.47 -32.53 0 5.00e+00 4.00e-02 4.23e+01 ... (remaining 11654 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 2061 0.049 - 0.098: 645 0.098 - 0.147: 185 0.147 - 0.197: 12 0.197 - 0.246: 2 Chirality restraints: 2905 Sorted by residual: chirality pdb=" CA TYR A1683 " pdb=" N TYR A1683 " pdb=" C TYR A1683 " pdb=" CB TYR A1683 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CA ILE A 606 " pdb=" N ILE A 606 " pdb=" C ILE A 606 " pdb=" CB ILE A 606 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" CA ILE A1637 " pdb=" N ILE A1637 " pdb=" C ILE A1637 " pdb=" CB ILE A1637 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 8.02e-01 ... (remaining 2902 not shown) Planarity restraints: 3406 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 369 " 0.045 5.00e-02 4.00e+02 6.90e-02 7.61e+00 pdb=" N PRO A 370 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO A 370 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 370 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A1710 " -0.039 5.00e-02 4.00e+02 5.83e-02 5.44e+00 pdb=" N PRO A1711 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO A1711 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A1711 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A1029 " 0.038 5.00e-02 4.00e+02 5.82e-02 5.43e+00 pdb=" N PRO A1030 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO A1030 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A1030 " 0.031 5.00e-02 4.00e+02 ... (remaining 3403 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 307 2.61 - 3.18: 16759 3.18 - 3.75: 28844 3.75 - 4.33: 41204 4.33 - 4.90: 66285 Nonbonded interactions: 153399 Sorted by model distance: nonbonded pdb=" OH TYR A 125 " pdb=" O LEU A 363 " model vdw 2.037 3.040 nonbonded pdb=" ND2 ASN A2307 " pdb=" O ASN A2312 " model vdw 2.053 3.120 nonbonded pdb=" O ASN A 58 " pdb=" OG1 THR A 62 " model vdw 2.087 3.040 nonbonded pdb=" O SER A 90 " pdb=" OG SER A 90 " model vdw 2.096 3.040 nonbonded pdb=" O THR A1547 " pdb=" ND2 ASN A1597 " model vdw 2.097 3.120 ... (remaining 153394 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: 3.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.770 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 60.400 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5644 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 : 0.005 0.078 19471 Z= 0.291 Angle : 0.846 24.195 26343 Z= 0.489 Chirality : 0.051 0.246 2905 Planarity : 0.005 0.069 3406 Dihedral : 20.155 90.067 7195 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 16.30 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.73 % Favored : 91.11 % Rotamer: Outliers : 13.38 % Allowed : 28.73 % Favored : 57.88 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.79 % 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: -4.22 (0.14), residues: 2361 helix: -3.22 (0.15), residues: 622 sheet: -2.63 (0.22), residues: 411 loop : -2.68 (0.14), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A1743 HIS 0.007 0.001 HIS A1178 PHE 0.034 0.002 PHE A 539 TYR 0.026 0.002 TYR A1531 ARG 0.009 0.001 ARG A1241 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 2137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 286 poor density : 212 time to evaluate : 2.176 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 MET cc_start: 0.6133 (mtm) cc_final: 0.5802 (mtm) REVERT: A 68 ARG cc_start: 0.5450 (OUTLIER) cc_final: 0.4885 (ptm160) REVERT: A 81 MET cc_start: 0.5487 (OUTLIER) cc_final: 0.5149 (ttt) REVERT: A 141 LEU cc_start: 0.6303 (OUTLIER) cc_final: 0.5998 (tp) REVERT: A 190 TYR cc_start: 0.4713 (OUTLIER) cc_final: 0.3729 (t80) REVERT: A 191 LYS cc_start: 0.7047 (mttt) cc_final: 0.6692 (mttt) REVERT: A 213 GLU cc_start: 0.6342 (OUTLIER) cc_final: 0.4129 (mp0) REVERT: A 262 ARG cc_start: 0.7438 (OUTLIER) cc_final: 0.6628 (mmt90) REVERT: A 278 LYS cc_start: 0.6833 (OUTLIER) cc_final: 0.6459 (ttpt) REVERT: A 318 GLU cc_start: 0.4735 (OUTLIER) cc_final: 0.4389 (mt-10) REVERT: A 530 GLN cc_start: 0.5728 (OUTLIER) cc_final: 0.5276 (tp40) REVERT: A 573 ARG cc_start: 0.1339 (OUTLIER) cc_final: 0.0610 (ptt180) REVERT: A 576 GLU cc_start: 0.4972 (OUTLIER) cc_final: 0.3525 (pm20) REVERT: A 579 HIS cc_start: 0.1234 (OUTLIER) cc_final: 0.0692 (t-170) REVERT: A 642 ASN cc_start: 0.4202 (OUTLIER) cc_final: 0.3991 (p0) REVERT: A 769 ILE cc_start: 0.6363 (OUTLIER) cc_final: 0.6040 (mp) REVERT: A 820 MET cc_start: 0.4651 (tmm) cc_final: 0.4151 (tmm) REVERT: A 974 THR cc_start: 0.4437 (OUTLIER) cc_final: 0.3778 (p) REVERT: A 1019 ILE cc_start: 0.4792 (OUTLIER) cc_final: 0.4531 (tt) REVERT: A 1314 TYR cc_start: 0.5245 (OUTLIER) cc_final: 0.3407 (m-80) REVERT: A 1334 ILE cc_start: 0.3183 (OUTLIER) cc_final: 0.2386 (mp) REVERT: A 1342 ASP cc_start: 0.5625 (OUTLIER) cc_final: 0.5401 (t70) REVERT: A 1530 ASN cc_start: 0.6463 (OUTLIER) cc_final: 0.5601 (p0) REVERT: A 1663 HIS cc_start: 0.5846 (OUTLIER) cc_final: 0.4050 (p-80) REVERT: A 1735 ASN cc_start: 0.4117 (OUTLIER) cc_final: 0.3787 (m110) REVERT: A 1810 PHE cc_start: 0.4995 (p90) cc_final: 0.4738 (p90) REVERT: A 1822 ASP cc_start: 0.6502 (m-30) cc_final: 0.6131 (m-30) REVERT: A 1853 LEU cc_start: 0.7338 (OUTLIER) cc_final: 0.7057 (tp) REVERT: A 1854 ILE cc_start: 0.5978 (OUTLIER) cc_final: 0.5731 (mt) REVERT: A 2003 ASP cc_start: 0.2102 (OUTLIER) cc_final: 0.1374 (m-30) REVERT: A 2265 GLU cc_start: 0.2446 (OUTLIER) cc_final: 0.2166 (tp30) REVERT: A 2273 TYR cc_start: 0.2225 (OUTLIER) cc_final: 0.1966 (t80) REVERT: A 2329 LYS cc_start: 0.3461 (OUTLIER) cc_final: 0.2514 (tptp) outliers start: 286 outliers final: 124 residues processed: 469 average time/residue: 0.8562 time to fit residues: 479.5189 Evaluate side-chains 309 residues out of total 2137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 157 time to evaluate : 2.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 5 ASN Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 190 TYR Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 384 ASN Chi-restraints excluded: chain A residue 402 GLN Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 509 SER Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 530 GLN Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 573 ARG Chi-restraints excluded: chain A residue 576 GLU Chi-restraints excluded: chain A residue 579 HIS Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 619 TYR Chi-restraints excluded: chain A residue 636 ILE Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 642 ASN Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 690 TYR Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 769 ILE Chi-restraints excluded: chain A residue 789 VAL Chi-restraints excluded: chain A residue 798 SER Chi-restraints excluded: chain A residue 799 THR Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain A residue 864 SER Chi-restraints excluded: chain A residue 875 GLN Chi-restraints excluded: chain A residue 885 SER Chi-restraints excluded: chain A residue 892 THR Chi-restraints excluded: chain A residue 926 SER Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 939 ASN Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 961 SER Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 1019 ILE Chi-restraints excluded: chain A residue 1045 ILE Chi-restraints excluded: chain A residue 1085 ILE Chi-restraints excluded: chain A residue 1149 ASP Chi-restraints excluded: chain A residue 1152 LEU Chi-restraints excluded: chain A residue 1155 ILE Chi-restraints excluded: chain A residue 1161 SER Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain A residue 1221 VAL Chi-restraints excluded: chain A residue 1281 ARG Chi-restraints excluded: chain A residue 1282 TYR Chi-restraints excluded: chain A residue 1314 TYR Chi-restraints excluded: chain A residue 1322 SER Chi-restraints excluded: chain A residue 1334 ILE Chi-restraints excluded: chain A residue 1342 ASP Chi-restraints excluded: chain A residue 1383 ILE Chi-restraints excluded: chain A residue 1388 THR Chi-restraints excluded: chain A residue 1405 THR Chi-restraints excluded: chain A residue 1418 ILE Chi-restraints excluded: chain A residue 1436 LEU Chi-restraints excluded: chain A residue 1467 ASN Chi-restraints excluded: chain A residue 1472 ASN Chi-restraints excluded: chain A residue 1483 LEU Chi-restraints excluded: chain A residue 1485 THR Chi-restraints excluded: chain A residue 1530 ASN Chi-restraints excluded: chain A residue 1531 TYR Chi-restraints excluded: chain A residue 1549 THR Chi-restraints excluded: chain A residue 1552 LEU Chi-restraints excluded: chain A residue 1606 ILE Chi-restraints excluded: chain A residue 1613 ILE Chi-restraints excluded: chain A residue 1618 SER Chi-restraints excluded: chain A residue 1623 GLU Chi-restraints excluded: chain A residue 1624 LEU Chi-restraints excluded: chain A residue 1641 ILE Chi-restraints excluded: chain A residue 1644 THR Chi-restraints excluded: chain A residue 1645 SER Chi-restraints excluded: chain A residue 1663 HIS Chi-restraints excluded: chain A residue 1671 SER Chi-restraints excluded: chain A residue 1698 LEU Chi-restraints excluded: chain A residue 1702 GLU Chi-restraints excluded: chain A residue 1706 THR Chi-restraints excluded: chain A residue 1715 CYS Chi-restraints excluded: chain A residue 1735 ASN Chi-restraints excluded: chain A residue 1736 ASP Chi-restraints excluded: chain A residue 1739 ILE Chi-restraints excluded: chain A residue 1748 SER Chi-restraints excluded: chain A residue 1774 SER Chi-restraints excluded: chain A residue 1780 LYS Chi-restraints excluded: chain A residue 1792 SER Chi-restraints excluded: chain A residue 1833 VAL Chi-restraints excluded: chain A residue 1837 ILE Chi-restraints excluded: chain A residue 1843 LEU Chi-restraints excluded: chain A residue 1853 LEU Chi-restraints excluded: chain A residue 1854 ILE Chi-restraints excluded: chain A residue 1858 THR Chi-restraints excluded: chain A residue 1872 SER Chi-restraints excluded: chain A residue 1902 THR Chi-restraints excluded: chain A residue 1947 VAL Chi-restraints excluded: chain A residue 1948 GLU Chi-restraints excluded: chain A residue 1960 ASN Chi-restraints excluded: chain A residue 1970 LEU Chi-restraints excluded: chain A residue 1985 ILE Chi-restraints excluded: chain A residue 2003 ASP Chi-restraints excluded: chain A residue 2013 VAL Chi-restraints excluded: chain A residue 2028 LEU Chi-restraints excluded: chain A residue 2087 SER Chi-restraints excluded: chain A residue 2088 THR Chi-restraints excluded: chain A residue 2144 ASN Chi-restraints excluded: chain A residue 2165 THR Chi-restraints excluded: chain A residue 2194 ARG Chi-restraints excluded: chain A residue 2230 TYR Chi-restraints excluded: chain A residue 2236 VAL Chi-restraints excluded: chain A residue 2251 THR Chi-restraints excluded: chain A residue 2265 GLU Chi-restraints excluded: chain A residue 2270 GLN Chi-restraints excluded: chain A residue 2273 TYR Chi-restraints excluded: chain A residue 2280 MET Chi-restraints excluded: chain A residue 2321 THR Chi-restraints excluded: chain A residue 2329 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 199 optimal weight: 0.8980 chunk 178 optimal weight: 0.1980 chunk 99 optimal weight: 2.9990 chunk 61 optimal weight: 10.0000 chunk 120 optimal weight: 0.6980 chunk 95 optimal weight: 0.6980 chunk 184 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 chunk 112 optimal weight: 3.9990 chunk 137 optimal weight: 0.9990 chunk 214 optimal weight: 3.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 GLN A 10 GLN A 20 GLN A 35 HIS A 36 ASN A 212 ASN A 294 GLN A 343 GLN A 379 ASN A 405 ASN A 479 GLN A 510 GLN A 553 GLN A 579 HIS ** A 583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 596 ASN A 639 GLN A 659 ASN A 846 ASN A 853 ASN ** A1052 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1058 GLN A1294 ASN ** A1307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1370 ASN A1456 HIS A1504 ASN A1520 ASN A1530 ASN A1735 ASN A1763 GLN A1840 ASN ** A1851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1925 ASN A2058 ASN A2176 ASN A2196 ASN A2234 ASN A2312 ASN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5546 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19471 Z= 0.194 Angle : 0.687 10.104 26343 Z= 0.364 Chirality : 0.048 0.192 2905 Planarity : 0.004 0.056 3406 Dihedral : 11.487 64.019 2832 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.07 % Favored : 92.84 % Rotamer: Outliers : 9.45 % Allowed : 30.60 % Favored : 59.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.12 (0.15), residues: 2361 helix: -1.81 (0.18), residues: 634 sheet: -2.16 (0.23), residues: 416 loop : -2.19 (0.15), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1743 HIS 0.005 0.001 HIS A1178 PHE 0.029 0.002 PHE A 539 TYR 0.020 0.001 TYR A1531 ARG 0.004 0.001 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 168 time to evaluate : 2.153 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 GLN cc_start: 0.7349 (OUTLIER) cc_final: 0.7037 (mt0) REVERT: A 68 ARG cc_start: 0.5421 (OUTLIER) cc_final: 0.4734 (ptp-170) REVERT: A 134 ASN cc_start: 0.7172 (OUTLIER) cc_final: 0.6941 (t0) REVERT: A 190 TYR cc_start: 0.4707 (OUTLIER) cc_final: 0.4015 (t80) REVERT: A 278 LYS cc_start: 0.7024 (OUTLIER) cc_final: 0.6593 (ttpt) REVERT: A 318 GLU cc_start: 0.4286 (OUTLIER) cc_final: 0.4059 (mp0) REVERT: A 573 ARG cc_start: 0.1009 (OUTLIER) cc_final: -0.0469 (ptt180) REVERT: A 579 HIS cc_start: 0.0754 (OUTLIER) cc_final: 0.0422 (t-90) REVERT: A 820 MET cc_start: 0.4350 (tmm) cc_final: 0.3979 (tmm) REVERT: A 832 ILE cc_start: 0.5338 (OUTLIER) cc_final: 0.4882 (pt) REVERT: A 1019 ILE cc_start: 0.4615 (OUTLIER) cc_final: 0.4341 (tt) REVERT: A 1058 GLN cc_start: 0.6972 (pt0) cc_final: 0.6530 (mm-40) REVERT: A 1145 MET cc_start: 0.5628 (ttp) cc_final: 0.5364 (ttt) REVERT: A 1270 ILE cc_start: 0.5435 (OUTLIER) cc_final: 0.5193 (pp) REVERT: A 1342 ASP cc_start: 0.5732 (OUTLIER) cc_final: 0.5131 (t70) REVERT: A 1472 ASN cc_start: 0.5835 (OUTLIER) cc_final: 0.5473 (m-40) REVERT: A 1483 LEU cc_start: 0.6143 (OUTLIER) cc_final: 0.5891 (tp) REVERT: A 1613 ILE cc_start: 0.6645 (OUTLIER) cc_final: 0.6266 (tt) REVERT: A 1663 HIS cc_start: 0.5599 (OUTLIER) cc_final: 0.3641 (p-80) REVERT: A 1703 ILE cc_start: 0.6023 (OUTLIER) cc_final: 0.5685 (mt) REVERT: A 1822 ASP cc_start: 0.5868 (m-30) cc_final: 0.5311 (m-30) REVERT: A 1988 THR cc_start: 0.3870 (OUTLIER) cc_final: 0.3615 (t) REVERT: A 2265 GLU cc_start: 0.2731 (OUTLIER) cc_final: 0.2343 (tp30) REVERT: A 2329 LYS cc_start: 0.3355 (OUTLIER) cc_final: 0.2426 (tptp) outliers start: 202 outliers final: 79 residues processed: 346 average time/residue: 0.8990 time to fit residues: 369.0536 Evaluate side-chains 245 residues out of total 2137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 146 time to evaluate : 2.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 8 GLN Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 190 TYR Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 402 GLN Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 573 ARG Chi-restraints excluded: chain A residue 579 HIS Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 636 ILE Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 690 TYR Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 731 SER Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain A residue 849 SER Chi-restraints excluded: chain A residue 887 GLU Chi-restraints excluded: chain A residue 892 THR Chi-restraints excluded: chain A residue 936 ILE Chi-restraints excluded: chain A residue 939 ASN Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain A residue 1019 ILE Chi-restraints excluded: chain A residue 1045 ILE Chi-restraints excluded: chain A residue 1085 ILE Chi-restraints excluded: chain A residue 1118 THR Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain A residue 1167 CYS Chi-restraints excluded: chain A residue 1181 THR Chi-restraints excluded: chain A residue 1205 VAL Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain A residue 1281 ARG Chi-restraints excluded: chain A residue 1282 TYR Chi-restraints excluded: chain A residue 1342 ASP Chi-restraints excluded: chain A residue 1383 ILE Chi-restraints excluded: chain A residue 1394 ASP Chi-restraints excluded: chain A residue 1418 ILE Chi-restraints excluded: chain A residue 1467 ASN Chi-restraints excluded: chain A residue 1472 ASN Chi-restraints excluded: chain A residue 1483 LEU Chi-restraints excluded: chain A residue 1485 THR Chi-restraints excluded: chain A residue 1530 ASN Chi-restraints excluded: chain A residue 1549 THR Chi-restraints excluded: chain A residue 1552 LEU Chi-restraints excluded: chain A residue 1603 ILE Chi-restraints excluded: chain A residue 1606 ILE Chi-restraints excluded: chain A residue 1613 ILE Chi-restraints excluded: chain A residue 1617 ASN Chi-restraints excluded: chain A residue 1624 LEU Chi-restraints excluded: chain A residue 1663 HIS Chi-restraints excluded: chain A residue 1671 SER Chi-restraints excluded: chain A residue 1698 LEU Chi-restraints excluded: chain A residue 1703 ILE Chi-restraints excluded: chain A residue 1706 THR Chi-restraints excluded: chain A residue 1715 CYS Chi-restraints excluded: chain A residue 1739 ILE Chi-restraints excluded: chain A residue 1748 SER Chi-restraints excluded: chain A residue 1774 SER Chi-restraints excluded: chain A residue 1858 THR Chi-restraints excluded: chain A residue 1860 ILE Chi-restraints excluded: chain A residue 1899 VAL Chi-restraints excluded: chain A residue 1902 THR Chi-restraints excluded: chain A residue 1932 ILE Chi-restraints excluded: chain A residue 1947 VAL Chi-restraints excluded: chain A residue 1948 GLU Chi-restraints excluded: chain A residue 1970 LEU Chi-restraints excluded: chain A residue 1988 THR Chi-restraints excluded: chain A residue 2013 VAL Chi-restraints excluded: chain A residue 2088 THR Chi-restraints excluded: chain A residue 2104 VAL Chi-restraints excluded: chain A residue 2165 THR Chi-restraints excluded: chain A residue 2194 ARG Chi-restraints excluded: chain A residue 2230 TYR Chi-restraints excluded: chain A residue 2265 GLU Chi-restraints excluded: chain A residue 2270 GLN Chi-restraints excluded: chain A residue 2273 TYR Chi-restraints excluded: chain A residue 2280 MET Chi-restraints excluded: chain A residue 2329 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 119 optimal weight: 0.9990 chunk 66 optimal weight: 8.9990 chunk 178 optimal weight: 0.5980 chunk 145 optimal weight: 4.9990 chunk 59 optimal weight: 9.9990 chunk 214 optimal weight: 8.9990 chunk 231 optimal weight: 9.9990 chunk 191 optimal weight: 0.0770 chunk 212 optimal weight: 9.9990 chunk 73 optimal weight: 1.9990 chunk 172 optimal weight: 0.9990 overall best weight: 0.9344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 GLN A 20 GLN A 113 ASN ** A 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 553 GLN A 583 GLN A 642 ASN A 874 HIS ** A1052 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1453 ASN A1763 GLN ** A1851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5563 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19471 Z= 0.210 Angle : 0.670 12.271 26343 Z= 0.354 Chirality : 0.047 0.169 2905 Planarity : 0.004 0.053 3406 Dihedral : 9.539 59.893 2692 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.37 % Favored : 92.55 % Rotamer: Outliers : 8.33 % Allowed : 31.68 % Favored : 59.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: -2.59 (0.16), residues: 2361 helix: -1.25 (0.19), residues: 639 sheet: -1.84 (0.24), residues: 417 loop : -1.92 (0.16), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1743 HIS 0.004 0.001 HIS A1178 PHE 0.030 0.002 PHE A 539 TYR 0.019 0.001 TYR A1531 ARG 0.003 0.000 ARG A 173 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 160 time to evaluate : 2.086 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: symmetry clash REVERT: A 10 GLN cc_start: 0.7943 (OUTLIER) cc_final: 0.7732 (tt0) REVERT: A 18 ARG cc_start: 0.6587 (OUTLIER) cc_final: 0.6346 (mtt-85) REVERT: A 68 ARG cc_start: 0.5419 (OUTLIER) cc_final: 0.4755 (ptp-110) REVERT: A 159 GLU cc_start: 0.5688 (OUTLIER) cc_final: 0.5171 (pm20) REVERT: A 190 TYR cc_start: 0.4964 (OUTLIER) cc_final: 0.4090 (t80) REVERT: A 573 ARG cc_start: 0.1310 (OUTLIER) cc_final: -0.0008 (ptt180) REVERT: A 579 HIS cc_start: 0.0859 (OUTLIER) cc_final: 0.0251 (m90) REVERT: A 599 SER cc_start: 0.5087 (OUTLIER) cc_final: 0.4824 (t) REVERT: A 616 GLU cc_start: 0.5760 (OUTLIER) cc_final: 0.5554 (tp30) REVERT: A 820 MET cc_start: 0.4292 (tmm) cc_final: 0.3986 (tmm) REVERT: A 832 ILE cc_start: 0.5363 (OUTLIER) cc_final: 0.4907 (pt) REVERT: A 974 THR cc_start: 0.3612 (OUTLIER) cc_final: 0.3245 (m) REVERT: A 1020 ASP cc_start: 0.5085 (OUTLIER) cc_final: 0.4841 (m-30) REVERT: A 1050 GLU cc_start: 0.7521 (tm-30) cc_final: 0.7087 (tt0) REVERT: A 1058 GLN cc_start: 0.6954 (pt0) cc_final: 0.6544 (mm-40) REVERT: A 1129 LEU cc_start: 0.6672 (OUTLIER) cc_final: 0.6427 (tp) REVERT: A 1164 LEU cc_start: 0.6431 (OUTLIER) cc_final: 0.6105 (pp) REVERT: A 1342 ASP cc_start: 0.6030 (OUTLIER) cc_final: 0.5409 (t70) REVERT: A 1364 LYS cc_start: 0.3036 (OUTLIER) cc_final: 0.2509 (mttt) REVERT: A 1421 VAL cc_start: 0.6211 (t) cc_final: 0.5815 (t) REVERT: A 1472 ASN cc_start: 0.5995 (OUTLIER) cc_final: 0.5672 (m-40) REVERT: A 1474 PHE cc_start: 0.6228 (m-80) cc_final: 0.5877 (m-80) REVERT: A 1483 LEU cc_start: 0.6237 (OUTLIER) cc_final: 0.5954 (tp) REVERT: A 1613 ILE cc_start: 0.6594 (OUTLIER) cc_final: 0.6172 (tt) REVERT: A 1663 HIS cc_start: 0.5994 (OUTLIER) cc_final: 0.3928 (p-80) REVERT: A 1702 GLU cc_start: 0.6696 (OUTLIER) cc_final: 0.5443 (tp30) REVERT: A 1715 CYS cc_start: 0.6643 (OUTLIER) cc_final: 0.6275 (t) REVERT: A 1822 ASP cc_start: 0.5967 (m-30) cc_final: 0.5502 (m-30) REVERT: A 1854 ILE cc_start: 0.5995 (OUTLIER) cc_final: 0.5735 (mt) REVERT: A 1930 LEU cc_start: 0.3092 (OUTLIER) cc_final: 0.2331 (tp) REVERT: A 2265 GLU cc_start: 0.2847 (OUTLIER) cc_final: 0.2407 (tp30) outliers start: 178 outliers final: 75 residues processed: 316 average time/residue: 0.9013 time to fit residues: 341.6549 Evaluate side-chains 242 residues out of total 2137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 142 time to evaluate : 1.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 GLN Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 190 TYR Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 402 GLN Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 573 ARG Chi-restraints excluded: chain A residue 579 HIS Chi-restraints excluded: chain A residue 599 SER Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 619 TYR Chi-restraints excluded: chain A residue 636 ILE Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 690 TYR Chi-restraints excluded: chain A residue 731 SER Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 767 SER Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain A residue 849 SER Chi-restraints excluded: chain A residue 887 GLU Chi-restraints excluded: chain A residue 892 THR Chi-restraints excluded: chain A residue 936 ILE Chi-restraints excluded: chain A residue 939 ASN Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain A residue 1020 ASP Chi-restraints excluded: chain A residue 1045 ILE Chi-restraints excluded: chain A residue 1085 ILE Chi-restraints excluded: chain A residue 1100 SER Chi-restraints excluded: chain A residue 1118 THR Chi-restraints excluded: chain A residue 1129 LEU Chi-restraints excluded: chain A residue 1162 ILE Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain A residue 1167 CYS Chi-restraints excluded: chain A residue 1181 THR Chi-restraints excluded: chain A residue 1281 ARG Chi-restraints excluded: chain A residue 1342 ASP Chi-restraints excluded: chain A residue 1364 LYS Chi-restraints excluded: chain A residue 1383 ILE Chi-restraints excluded: chain A residue 1394 ASP Chi-restraints excluded: chain A residue 1405 THR Chi-restraints excluded: chain A residue 1418 ILE Chi-restraints excluded: chain A residue 1467 ASN Chi-restraints excluded: chain A residue 1472 ASN Chi-restraints excluded: chain A residue 1483 LEU Chi-restraints excluded: chain A residue 1485 THR Chi-restraints excluded: chain A residue 1530 ASN Chi-restraints excluded: chain A residue 1549 THR Chi-restraints excluded: chain A residue 1552 LEU Chi-restraints excluded: chain A residue 1562 VAL Chi-restraints excluded: chain A residue 1606 ILE Chi-restraints excluded: chain A residue 1613 ILE Chi-restraints excluded: chain A residue 1617 ASN Chi-restraints excluded: chain A residue 1624 LEU Chi-restraints excluded: chain A residue 1663 HIS Chi-restraints excluded: chain A residue 1698 LEU Chi-restraints excluded: chain A residue 1702 GLU Chi-restraints excluded: chain A residue 1715 CYS Chi-restraints excluded: chain A residue 1717 GLU Chi-restraints excluded: chain A residue 1739 ILE Chi-restraints excluded: chain A residue 1748 SER Chi-restraints excluded: chain A residue 1774 SER Chi-restraints excluded: chain A residue 1792 SER Chi-restraints excluded: chain A residue 1854 ILE Chi-restraints excluded: chain A residue 1858 THR Chi-restraints excluded: chain A residue 1860 ILE Chi-restraints excluded: chain A residue 1872 SER Chi-restraints excluded: chain A residue 1899 VAL Chi-restraints excluded: chain A residue 1902 THR Chi-restraints excluded: chain A residue 1930 LEU Chi-restraints excluded: chain A residue 1932 ILE Chi-restraints excluded: chain A residue 1948 GLU Chi-restraints excluded: chain A residue 1970 LEU Chi-restraints excluded: chain A residue 2013 VAL Chi-restraints excluded: chain A residue 2054 LEU Chi-restraints excluded: chain A residue 2088 THR Chi-restraints excluded: chain A residue 2104 VAL Chi-restraints excluded: chain A residue 2120 LEU Chi-restraints excluded: chain A residue 2165 THR Chi-restraints excluded: chain A residue 2230 TYR Chi-restraints excluded: chain A residue 2265 GLU Chi-restraints excluded: chain A residue 2354 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 212 optimal weight: 7.9990 chunk 161 optimal weight: 0.8980 chunk 111 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 102 optimal weight: 0.9980 chunk 144 optimal weight: 0.8980 chunk 215 optimal weight: 0.0570 chunk 228 optimal weight: 9.9990 chunk 112 optimal weight: 4.9990 chunk 204 optimal weight: 3.9990 chunk 61 optimal weight: 8.9990 overall best weight: 1.3700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 GLN A 10 GLN A 152 ASN ** A 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 611 ASN ** A1052 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1257 HIS A1727 ASN ** A1851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1892 GLN A2260 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5627 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 19471 Z= 0.263 Angle : 0.708 10.496 26343 Z= 0.373 Chirality : 0.049 0.212 2905 Planarity : 0.004 0.055 3406 Dihedral : 9.012 58.948 2657 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.84 % Favored : 92.08 % Rotamer: Outliers : 8.89 % Allowed : 31.54 % Favored : 59.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: -2.55 (0.16), residues: 2361 helix: -1.29 (0.19), residues: 639 sheet: -1.72 (0.24), residues: 423 loop : -1.88 (0.16), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1743 HIS 0.004 0.001 HIS A1178 PHE 0.031 0.002 PHE A 539 TYR 0.034 0.002 TYR A 14 ARG 0.004 0.000 ARG A 68 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 154 time to evaluate : 2.122 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: symmetry clash REVERT: A 8 GLN cc_start: 0.7469 (OUTLIER) cc_final: 0.7169 (mt0) REVERT: A 18 ARG cc_start: 0.6660 (OUTLIER) cc_final: 0.6329 (mtt-85) REVERT: A 68 ARG cc_start: 0.5500 (OUTLIER) cc_final: 0.4806 (ptp-170) REVERT: A 190 TYR cc_start: 0.5168 (OUTLIER) cc_final: 0.4076 (t80) REVERT: A 318 GLU cc_start: 0.4270 (OUTLIER) cc_final: 0.3963 (mp0) REVERT: A 573 ARG cc_start: 0.1483 (OUTLIER) cc_final: 0.0142 (ptt180) REVERT: A 579 HIS cc_start: 0.1078 (OUTLIER) cc_final: 0.0700 (t-90) REVERT: A 599 SER cc_start: 0.5145 (OUTLIER) cc_final: 0.4888 (t) REVERT: A 832 ILE cc_start: 0.5383 (OUTLIER) cc_final: 0.4968 (pt) REVERT: A 974 THR cc_start: 0.3764 (OUTLIER) cc_final: 0.3314 (m) REVERT: A 1020 ASP cc_start: 0.5183 (OUTLIER) cc_final: 0.4886 (m-30) REVERT: A 1050 GLU cc_start: 0.7602 (tm-30) cc_final: 0.7290 (tt0) REVERT: A 1164 LEU cc_start: 0.6452 (OUTLIER) cc_final: 0.6212 (pp) REVERT: A 1342 ASP cc_start: 0.6177 (OUTLIER) cc_final: 0.5567 (t70) REVERT: A 1364 LYS cc_start: 0.2994 (OUTLIER) cc_final: 0.2386 (mttt) REVERT: A 1472 ASN cc_start: 0.6093 (OUTLIER) cc_final: 0.5799 (m-40) REVERT: A 1483 LEU cc_start: 0.6331 (OUTLIER) cc_final: 0.6021 (tp) REVERT: A 1702 GLU cc_start: 0.6748 (OUTLIER) cc_final: 0.5456 (tp30) REVERT: A 1703 ILE cc_start: 0.5744 (OUTLIER) cc_final: 0.5423 (mt) REVERT: A 1822 ASP cc_start: 0.6110 (OUTLIER) cc_final: 0.5769 (m-30) REVERT: A 1854 ILE cc_start: 0.6207 (OUTLIER) cc_final: 0.5939 (mt) REVERT: A 1930 LEU cc_start: 0.2877 (OUTLIER) cc_final: 0.2133 (tp) REVERT: A 1959 PHE cc_start: 0.4597 (OUTLIER) cc_final: 0.4332 (m-80) REVERT: A 2249 MET cc_start: 0.4848 (tpt) cc_final: 0.4492 (mmp) REVERT: A 2269 MET cc_start: 0.0522 (tpp) cc_final: -0.0453 (tpt) outliers start: 190 outliers final: 97 residues processed: 324 average time/residue: 0.8834 time to fit residues: 343.3450 Evaluate side-chains 256 residues out of total 2137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 137 time to evaluate : 2.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLN Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain A residue 87 LYS Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 190 TYR Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 402 GLN Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 449 LYS Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 573 ARG Chi-restraints excluded: chain A residue 579 HIS Chi-restraints excluded: chain A residue 599 SER Chi-restraints excluded: chain A residue 619 TYR Chi-restraints excluded: chain A residue 636 ILE Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 690 TYR Chi-restraints excluded: chain A residue 731 SER Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 767 SER Chi-restraints excluded: chain A residue 780 PHE Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 811 SER Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain A residue 849 SER Chi-restraints excluded: chain A residue 855 ILE Chi-restraints excluded: chain A residue 887 GLU Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 936 ILE Chi-restraints excluded: chain A residue 939 ASN Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain A residue 995 SER Chi-restraints excluded: chain A residue 1020 ASP Chi-restraints excluded: chain A residue 1034 THR Chi-restraints excluded: chain A residue 1045 ILE Chi-restraints excluded: chain A residue 1085 ILE Chi-restraints excluded: chain A residue 1089 PHE Chi-restraints excluded: chain A residue 1100 SER Chi-restraints excluded: chain A residue 1118 THR Chi-restraints excluded: chain A residue 1129 LEU Chi-restraints excluded: chain A residue 1162 ILE Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain A residue 1181 THR Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1248 THR Chi-restraints excluded: chain A residue 1342 ASP Chi-restraints excluded: chain A residue 1364 LYS Chi-restraints excluded: chain A residue 1378 GLU Chi-restraints excluded: chain A residue 1383 ILE Chi-restraints excluded: chain A residue 1394 ASP Chi-restraints excluded: chain A residue 1405 THR Chi-restraints excluded: chain A residue 1418 ILE Chi-restraints excluded: chain A residue 1467 ASN Chi-restraints excluded: chain A residue 1472 ASN Chi-restraints excluded: chain A residue 1483 LEU Chi-restraints excluded: chain A residue 1485 THR Chi-restraints excluded: chain A residue 1530 ASN Chi-restraints excluded: chain A residue 1533 LYS Chi-restraints excluded: chain A residue 1549 THR Chi-restraints excluded: chain A residue 1552 LEU Chi-restraints excluded: chain A residue 1562 VAL Chi-restraints excluded: chain A residue 1606 ILE Chi-restraints excluded: chain A residue 1613 ILE Chi-restraints excluded: chain A residue 1698 LEU Chi-restraints excluded: chain A residue 1702 GLU Chi-restraints excluded: chain A residue 1703 ILE Chi-restraints excluded: chain A residue 1717 GLU Chi-restraints excluded: chain A residue 1739 ILE Chi-restraints excluded: chain A residue 1748 SER Chi-restraints excluded: chain A residue 1774 SER Chi-restraints excluded: chain A residue 1790 ASP Chi-restraints excluded: chain A residue 1792 SER Chi-restraints excluded: chain A residue 1822 ASP Chi-restraints excluded: chain A residue 1833 VAL Chi-restraints excluded: chain A residue 1854 ILE Chi-restraints excluded: chain A residue 1858 THR Chi-restraints excluded: chain A residue 1860 ILE Chi-restraints excluded: chain A residue 1872 SER Chi-restraints excluded: chain A residue 1899 VAL Chi-restraints excluded: chain A residue 1930 LEU Chi-restraints excluded: chain A residue 1932 ILE Chi-restraints excluded: chain A residue 1947 VAL Chi-restraints excluded: chain A residue 1948 GLU Chi-restraints excluded: chain A residue 1959 PHE Chi-restraints excluded: chain A residue 1970 LEU Chi-restraints excluded: chain A residue 2013 VAL Chi-restraints excluded: chain A residue 2104 VAL Chi-restraints excluded: chain A residue 2120 LEU Chi-restraints excluded: chain A residue 2127 ASP Chi-restraints excluded: chain A residue 2165 THR Chi-restraints excluded: chain A residue 2230 TYR Chi-restraints excluded: chain A residue 2236 VAL Chi-restraints excluded: chain A residue 2354 ASP Chi-restraints excluded: chain A residue 2362 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 189 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 169 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 194 optimal weight: 1.9990 chunk 157 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 116 optimal weight: 0.7980 chunk 204 optimal weight: 0.9980 chunk 57 optimal weight: 9.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 GLN A 58 ASN A 197 ASN ** A 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 ASN A 425 ASN ** A 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 874 HIS ** A1052 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1058 GLN A1158 ASN A1727 ASN ** A1851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5598 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19471 Z= 0.225 Angle : 0.671 11.816 26343 Z= 0.353 Chirality : 0.047 0.207 2905 Planarity : 0.004 0.052 3406 Dihedral : 8.419 58.010 2638 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.37 % Favored : 92.55 % Rotamer: Outliers : 8.10 % Allowed : 32.71 % Favored : 59.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: -2.28 (0.16), residues: 2361 helix: -1.07 (0.19), residues: 640 sheet: -1.53 (0.24), residues: 434 loop : -1.73 (0.17), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1743 HIS 0.004 0.001 HIS A1178 PHE 0.030 0.002 PHE A1269 TYR 0.018 0.002 TYR A1531 ARG 0.004 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 152 time to evaluate : 2.253 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: symmetry clash REVERT: A 18 ARG cc_start: 0.6631 (OUTLIER) cc_final: 0.6305 (mtt-85) REVERT: A 68 ARG cc_start: 0.5319 (OUTLIER) cc_final: 0.4366 (ptp-170) REVERT: A 190 TYR cc_start: 0.5251 (OUTLIER) cc_final: 0.4131 (t80) REVERT: A 318 GLU cc_start: 0.4567 (OUTLIER) cc_final: 0.4218 (mp0) REVERT: A 573 ARG cc_start: 0.1419 (OUTLIER) cc_final: -0.0905 (ptt180) REVERT: A 579 HIS cc_start: 0.0998 (OUTLIER) cc_final: 0.0649 (t-90) REVERT: A 599 SER cc_start: 0.5146 (OUTLIER) cc_final: 0.4898 (t) REVERT: A 832 ILE cc_start: 0.5280 (OUTLIER) cc_final: 0.4855 (pt) REVERT: A 974 THR cc_start: 0.3638 (OUTLIER) cc_final: 0.3256 (m) REVERT: A 1020 ASP cc_start: 0.5220 (OUTLIER) cc_final: 0.4909 (m-30) REVERT: A 1050 GLU cc_start: 0.7523 (tm-30) cc_final: 0.7230 (tt0) REVERT: A 1058 GLN cc_start: 0.7007 (pt0) cc_final: 0.6535 (mm-40) REVERT: A 1129 LEU cc_start: 0.6683 (OUTLIER) cc_final: 0.6457 (tp) REVERT: A 1342 ASP cc_start: 0.6061 (OUTLIER) cc_final: 0.5438 (t70) REVERT: A 1364 LYS cc_start: 0.3220 (OUTLIER) cc_final: 0.2457 (mttt) REVERT: A 1421 VAL cc_start: 0.6260 (t) cc_final: 0.5825 (t) REVERT: A 1472 ASN cc_start: 0.6024 (OUTLIER) cc_final: 0.5527 (m-40) REVERT: A 1483 LEU cc_start: 0.6317 (OUTLIER) cc_final: 0.5993 (tp) REVERT: A 1703 ILE cc_start: 0.5770 (OUTLIER) cc_final: 0.5542 (mt) REVERT: A 1710 LYS cc_start: 0.5442 (OUTLIER) cc_final: 0.4718 (pptt) REVERT: A 1822 ASP cc_start: 0.6013 (m-30) cc_final: 0.5613 (m-30) REVERT: A 1854 ILE cc_start: 0.6239 (OUTLIER) cc_final: 0.5979 (mt) REVERT: A 1959 PHE cc_start: 0.4534 (OUTLIER) cc_final: 0.4279 (m-80) REVERT: A 2085 ASP cc_start: 0.0073 (OUTLIER) cc_final: -0.0170 (p0) REVERT: A 2249 MET cc_start: 0.4716 (tpt) cc_final: 0.4454 (mmp) REVERT: A 2269 MET cc_start: 0.0475 (tpp) cc_final: -0.0719 (tpt) outliers start: 173 outliers final: 105 residues processed: 306 average time/residue: 0.8922 time to fit residues: 328.4677 Evaluate side-chains 263 residues out of total 2137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 138 time to evaluate : 1.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 87 LYS Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 190 TYR Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 346 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 402 GLN Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 449 LYS Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 573 ARG Chi-restraints excluded: chain A residue 579 HIS Chi-restraints excluded: chain A residue 599 SER Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 619 TYR Chi-restraints excluded: chain A residue 636 ILE Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 690 TYR Chi-restraints excluded: chain A residue 731 SER Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 780 PHE Chi-restraints excluded: chain A residue 799 THR Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 811 SER Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain A residue 849 SER Chi-restraints excluded: chain A residue 855 ILE Chi-restraints excluded: chain A residue 887 GLU Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 936 ILE Chi-restraints excluded: chain A residue 939 ASN Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain A residue 995 SER Chi-restraints excluded: chain A residue 1020 ASP Chi-restraints excluded: chain A residue 1034 THR Chi-restraints excluded: chain A residue 1045 ILE Chi-restraints excluded: chain A residue 1085 ILE Chi-restraints excluded: chain A residue 1089 PHE Chi-restraints excluded: chain A residue 1100 SER Chi-restraints excluded: chain A residue 1118 THR Chi-restraints excluded: chain A residue 1129 LEU Chi-restraints excluded: chain A residue 1149 ASP Chi-restraints excluded: chain A residue 1162 ILE Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain A residue 1181 THR Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1221 VAL Chi-restraints excluded: chain A residue 1236 TRP Chi-restraints excluded: chain A residue 1248 THR Chi-restraints excluded: chain A residue 1339 VAL Chi-restraints excluded: chain A residue 1342 ASP Chi-restraints excluded: chain A residue 1364 LYS Chi-restraints excluded: chain A residue 1383 ILE Chi-restraints excluded: chain A residue 1394 ASP Chi-restraints excluded: chain A residue 1405 THR Chi-restraints excluded: chain A residue 1418 ILE Chi-restraints excluded: chain A residue 1472 ASN Chi-restraints excluded: chain A residue 1483 LEU Chi-restraints excluded: chain A residue 1485 THR Chi-restraints excluded: chain A residue 1512 ASP Chi-restraints excluded: chain A residue 1530 ASN Chi-restraints excluded: chain A residue 1549 THR Chi-restraints excluded: chain A residue 1552 LEU Chi-restraints excluded: chain A residue 1562 VAL Chi-restraints excluded: chain A residue 1606 ILE Chi-restraints excluded: chain A residue 1613 ILE Chi-restraints excluded: chain A residue 1623 GLU Chi-restraints excluded: chain A residue 1641 ILE Chi-restraints excluded: chain A residue 1698 LEU Chi-restraints excluded: chain A residue 1703 ILE Chi-restraints excluded: chain A residue 1710 LYS Chi-restraints excluded: chain A residue 1717 GLU Chi-restraints excluded: chain A residue 1739 ILE Chi-restraints excluded: chain A residue 1748 SER Chi-restraints excluded: chain A residue 1774 SER Chi-restraints excluded: chain A residue 1790 ASP Chi-restraints excluded: chain A residue 1792 SER Chi-restraints excluded: chain A residue 1833 VAL Chi-restraints excluded: chain A residue 1837 ILE Chi-restraints excluded: chain A residue 1854 ILE Chi-restraints excluded: chain A residue 1858 THR Chi-restraints excluded: chain A residue 1860 ILE Chi-restraints excluded: chain A residue 1872 SER Chi-restraints excluded: chain A residue 1899 VAL Chi-restraints excluded: chain A residue 1932 ILE Chi-restraints excluded: chain A residue 1947 VAL Chi-restraints excluded: chain A residue 1948 GLU Chi-restraints excluded: chain A residue 1959 PHE Chi-restraints excluded: chain A residue 2013 VAL Chi-restraints excluded: chain A residue 2085 ASP Chi-restraints excluded: chain A residue 2104 VAL Chi-restraints excluded: chain A residue 2120 LEU Chi-restraints excluded: chain A residue 2127 ASP Chi-restraints excluded: chain A residue 2165 THR Chi-restraints excluded: chain A residue 2230 TYR Chi-restraints excluded: chain A residue 2236 VAL Chi-restraints excluded: chain A residue 2354 ASP Chi-restraints excluded: chain A residue 2362 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 76 optimal weight: 3.9990 chunk 205 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 133 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 228 optimal weight: 9.9990 chunk 189 optimal weight: 0.0470 chunk 105 optimal weight: 0.0870 chunk 18 optimal weight: 1.9990 chunk 75 optimal weight: 8.9990 chunk 119 optimal weight: 8.9990 overall best weight: 0.7860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 GLN ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1052 ASN A1158 ASN A1727 ASN ** A2148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5558 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19471 Z= 0.191 Angle : 0.638 10.343 26343 Z= 0.337 Chirality : 0.046 0.197 2905 Planarity : 0.004 0.047 3406 Dihedral : 7.996 57.491 2634 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.90 % Favored : 93.01 % Rotamer: Outliers : 7.72 % Allowed : 33.32 % Favored : 58.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.17), residues: 2361 helix: -0.68 (0.20), residues: 641 sheet: -1.38 (0.24), residues: 426 loop : -1.57 (0.17), residues: 1294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1743 HIS 0.003 0.001 HIS A1178 PHE 0.029 0.002 PHE A1269 TYR 0.014 0.001 TYR A1531 ARG 0.010 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 148 time to evaluate : 2.080 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: symmetry clash REVERT: A 10 GLN cc_start: 0.7760 (OUTLIER) cc_final: 0.7508 (tt0) REVERT: A 17 PHE cc_start: 0.6987 (OUTLIER) cc_final: 0.6319 (m-80) REVERT: A 18 ARG cc_start: 0.6590 (OUTLIER) cc_final: 0.6231 (mtt-85) REVERT: A 68 ARG cc_start: 0.5440 (OUTLIER) cc_final: 0.4542 (ptp-170) REVERT: A 190 TYR cc_start: 0.5187 (OUTLIER) cc_final: 0.4362 (t80) REVERT: A 311 SER cc_start: 0.7304 (p) cc_final: 0.6878 (m) REVERT: A 314 MET cc_start: 0.5596 (OUTLIER) cc_final: 0.4941 (mmm) REVERT: A 318 GLU cc_start: 0.4399 (OUTLIER) cc_final: 0.4082 (mp0) REVERT: A 573 ARG cc_start: 0.1769 (OUTLIER) cc_final: -0.0580 (ptt180) REVERT: A 579 HIS cc_start: 0.0922 (OUTLIER) cc_final: 0.0610 (t-90) REVERT: A 599 SER cc_start: 0.5157 (OUTLIER) cc_final: 0.4915 (t) REVERT: A 832 ILE cc_start: 0.5159 (OUTLIER) cc_final: 0.4784 (pt) REVERT: A 974 THR cc_start: 0.3387 (OUTLIER) cc_final: 0.3122 (m) REVERT: A 1050 GLU cc_start: 0.7446 (tm-30) cc_final: 0.7129 (tt0) REVERT: A 1058 GLN cc_start: 0.6700 (pt0) cc_final: 0.6225 (mm-40) REVERT: A 1312 LEU cc_start: 0.5484 (OUTLIER) cc_final: 0.4894 (tt) REVERT: A 1332 MET cc_start: 0.7185 (tpt) cc_final: 0.6946 (mmt) REVERT: A 1342 ASP cc_start: 0.6053 (OUTLIER) cc_final: 0.5423 (t70) REVERT: A 1472 ASN cc_start: 0.6070 (OUTLIER) cc_final: 0.5620 (m-40) REVERT: A 1483 LEU cc_start: 0.6409 (OUTLIER) cc_final: 0.6085 (tp) REVERT: A 1613 ILE cc_start: 0.6587 (OUTLIER) cc_final: 0.6270 (tt) REVERT: A 1702 GLU cc_start: 0.6583 (OUTLIER) cc_final: 0.5433 (tp30) REVERT: A 1822 ASP cc_start: 0.5908 (OUTLIER) cc_final: 0.5452 (m-30) REVERT: A 1854 ILE cc_start: 0.6224 (OUTLIER) cc_final: 0.5989 (mt) REVERT: A 1930 LEU cc_start: 0.2635 (OUTLIER) cc_final: 0.1898 (tp) REVERT: A 1959 PHE cc_start: 0.4438 (OUTLIER) cc_final: 0.4210 (m-80) REVERT: A 1985 ILE cc_start: 0.5077 (OUTLIER) cc_final: 0.4782 (pt) REVERT: A 2249 MET cc_start: 0.4600 (tpt) cc_final: 0.4333 (mmp) REVERT: A 2269 MET cc_start: 0.0483 (tpp) cc_final: -0.0732 (tpt) outliers start: 165 outliers final: 85 residues processed: 291 average time/residue: 0.7592 time to fit residues: 265.0849 Evaluate side-chains 245 residues out of total 2137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 137 time to evaluate : 2.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 GLN Chi-restraints excluded: chain A residue 17 PHE Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 190 TYR Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 346 PHE Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 402 GLN Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 449 LYS Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 573 ARG Chi-restraints excluded: chain A residue 579 HIS Chi-restraints excluded: chain A residue 599 SER Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 636 ILE Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 690 TYR Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 811 SER Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain A residue 855 ILE Chi-restraints excluded: chain A residue 887 GLU Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain A residue 936 ILE Chi-restraints excluded: chain A residue 939 ASN Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain A residue 995 SER Chi-restraints excluded: chain A residue 1034 THR Chi-restraints excluded: chain A residue 1045 ILE Chi-restraints excluded: chain A residue 1085 ILE Chi-restraints excluded: chain A residue 1089 PHE Chi-restraints excluded: chain A residue 1100 SER Chi-restraints excluded: chain A residue 1118 THR Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain A residue 1236 TRP Chi-restraints excluded: chain A residue 1248 THR Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1334 ILE Chi-restraints excluded: chain A residue 1339 VAL Chi-restraints excluded: chain A residue 1342 ASP Chi-restraints excluded: chain A residue 1383 ILE Chi-restraints excluded: chain A residue 1394 ASP Chi-restraints excluded: chain A residue 1405 THR Chi-restraints excluded: chain A residue 1418 ILE Chi-restraints excluded: chain A residue 1472 ASN Chi-restraints excluded: chain A residue 1483 LEU Chi-restraints excluded: chain A residue 1512 ASP Chi-restraints excluded: chain A residue 1530 ASN Chi-restraints excluded: chain A residue 1562 VAL Chi-restraints excluded: chain A residue 1606 ILE Chi-restraints excluded: chain A residue 1613 ILE Chi-restraints excluded: chain A residue 1623 GLU Chi-restraints excluded: chain A residue 1698 LEU Chi-restraints excluded: chain A residue 1702 GLU Chi-restraints excluded: chain A residue 1717 GLU Chi-restraints excluded: chain A residue 1739 ILE Chi-restraints excluded: chain A residue 1748 SER Chi-restraints excluded: chain A residue 1774 SER Chi-restraints excluded: chain A residue 1792 SER Chi-restraints excluded: chain A residue 1822 ASP Chi-restraints excluded: chain A residue 1833 VAL Chi-restraints excluded: chain A residue 1837 ILE Chi-restraints excluded: chain A residue 1854 ILE Chi-restraints excluded: chain A residue 1858 THR Chi-restraints excluded: chain A residue 1860 ILE Chi-restraints excluded: chain A residue 1872 SER Chi-restraints excluded: chain A residue 1899 VAL Chi-restraints excluded: chain A residue 1930 LEU Chi-restraints excluded: chain A residue 1932 ILE Chi-restraints excluded: chain A residue 1947 VAL Chi-restraints excluded: chain A residue 1948 GLU Chi-restraints excluded: chain A residue 1959 PHE Chi-restraints excluded: chain A residue 1970 LEU Chi-restraints excluded: chain A residue 1985 ILE Chi-restraints excluded: chain A residue 2013 VAL Chi-restraints excluded: chain A residue 2102 LEU Chi-restraints excluded: chain A residue 2104 VAL Chi-restraints excluded: chain A residue 2120 LEU Chi-restraints excluded: chain A residue 2127 ASP Chi-restraints excluded: chain A residue 2159 LEU Chi-restraints excluded: chain A residue 2165 THR Chi-restraints excluded: chain A residue 2230 TYR Chi-restraints excluded: chain A residue 2236 VAL Chi-restraints excluded: chain A residue 2312 ASN Chi-restraints excluded: chain A residue 2354 ASP Chi-restraints excluded: chain A residue 2362 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 220 optimal weight: 20.0000 chunk 25 optimal weight: 0.6980 chunk 130 optimal weight: 2.9990 chunk 166 optimal weight: 1.9990 chunk 129 optimal weight: 0.9990 chunk 192 optimal weight: 0.2980 chunk 127 optimal weight: 10.0000 chunk 227 optimal weight: 2.9990 chunk 142 optimal weight: 5.9990 chunk 138 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1052 ASN A1158 ASN A1396 ASN A1727 ASN ** A1851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5583 moved from start: 0.3378 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: