Starting phenix.real_space_refine (version: dev) on Tue Apr 5 04:57:39 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h6e_0149/04_2022/6h6e_0149.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h6e_0149/04_2022/6h6e_0149.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h6e_0149/04_2022/6h6e_0149.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h6e_0149/04_2022/6h6e_0149.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h6e_0149/04_2022/6h6e_0149.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h6e_0149/04_2022/6h6e_0149.pdb" } resolution = 3.95 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 167": "OE1" <-> "OE2" Residue "A TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 488": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 659": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 868": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 950": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1018": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1024": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1039": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1040": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1044": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1176": "OE1" <-> "OE2" Residue "A TYR 1205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1595": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1641": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1661": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1708": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1725": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1767": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1772": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1774": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1805": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1848": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1883": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1948": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1959": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2036": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2099": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2395": "OD1" <-> "OD2" Residue "A TYR 2426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2493": "OE1" <-> "OE2" Residue "A TYR 2513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 167": "OE1" <-> "OE2" Residue "B PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 488": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 659": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 786": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 868": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1018": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1024": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1040": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1044": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1527": "OE1" <-> "OE2" Residue "B TYR 1567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1595": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1616": "NH1" <-> "NH2" Residue "B PHE 1641": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1661": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1708": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1725": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1767": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1772": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1774": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1814": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1848": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1883": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1948": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1959": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2036": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 2062": "OE1" <-> "OE2" Residue "B TYR 2099": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 2163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 2185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 2251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 2280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 2301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 2426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 2513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 167": "OE1" <-> "OE2" Residue "C PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 333": "OE1" <-> "OE2" Residue "C TYR 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 488": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 659": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 786": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 868": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1006": "OE1" <-> "OE2" Residue "C PHE 1018": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1024": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1040": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1044": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1227": "OE1" <-> "OE2" Residue "C TYR 1250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1365": "OE1" <-> "OE2" Residue "C TYR 1378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1595": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1641": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1661": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1708": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1725": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1756": "OE1" <-> "OE2" Residue "C TYR 1767": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1772": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1774": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1798": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1848": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1868": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1883": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1948": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1959": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1982": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2036": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 2099": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 2163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 2185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 2251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 2301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 2341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 2426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 2513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 167": "OE1" <-> "OE2" Residue "D PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 488": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 493": "OE1" <-> "OE2" Residue "D PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 659": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 842": "OD1" <-> "OD2" Residue "D PHE 868": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 950": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1018": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1024": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1039": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1040": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1595": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 1616": "NH1" <-> "NH2" Residue "D PHE 1641": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1661": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1708": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1725": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1767": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1772": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1798": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1805": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1814": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1848": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1883": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1982": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 2036": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 2099": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 2145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 2163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 2185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 2251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 2277": "OE1" <-> "OE2" Residue "D PHE 2291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 2301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 2318": "OE1" <-> "OE2" Residue "D PHE 2351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 2426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 2460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 2469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 2472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 2513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 488": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 659": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 786": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 868": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 950": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1018": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1024": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1039": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1040": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1044": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 1176": "OE1" <-> "OE2" Residue "E GLU 1191": "OE1" <-> "OE2" Residue "E TYR 1205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 1227": "OE1" <-> "OE2" Residue "E TYR 1250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 1527": "OE1" <-> "OE2" Residue "E TYR 1567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1595": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 1616": "NH1" <-> "NH2" Residue "E PHE 1641": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1661": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1708": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1725": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1767": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1772": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1774": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1798": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1814": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1848": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1883": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1948": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1959": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 2036": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 2099": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 2147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 2163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 2185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 2251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 2280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 2291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 2301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 2341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 2351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 2377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 2393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 2426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 2460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 2464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 2469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 2472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 2486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 2513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 135": "OE1" <-> "OE2" Residue "F PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 207": "OE1" <-> "OE2" Residue "F TYR 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 495": "OE1" <-> "OE2" Residue "F PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 720": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 738": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 772": "OD1" <-> "OD2" Residue "F PHE 832": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 835": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 839": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 861": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 887": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 906": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 941": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 952": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 963": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 1012": "OD1" <-> "OD2" Residue "F TYR 1016": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 1054": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 1074": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 1076": "OE1" <-> "OE2" Residue "F PHE 1080": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 1106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 1111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 1113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 1160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 1182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 1211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 1331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 1405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 1406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 1425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 1447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 1456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 1488": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 1559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 1701": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 1774": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 1822": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 1840": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 1872": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 1881": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 1974": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 2077": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 2078": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 2096": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 2112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 2141": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.26s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 112922 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 19161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2417, 19161 Classifications: {'peptide': 2417} Link IDs: {'PTRANS': 88, 'TRANS': 2328} Chain breaks: 2 Chain: "B" Number of atoms: 19161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2417, 19161 Classifications: {'peptide': 2417} Link IDs: {'PTRANS': 88, 'TRANS': 2328} Chain breaks: 2 Chain: "C" Number of atoms: 19161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2417, 19161 Classifications: {'peptide': 2417} Link IDs: {'PTRANS': 88, 'TRANS': 2328} Chain breaks: 2 Chain: "D" Number of atoms: 19161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2417, 19161 Classifications: {'peptide': 2417} Link IDs: {'PTRANS': 88, 'TRANS': 2328} Chain breaks: 2 Chain: "E" Number of atoms: 19161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2417, 19161 Classifications: {'peptide': 2417} Link IDs: {'PTRANS': 88, 'TRANS': 2328} Chain breaks: 2 Chain: "F" Number of atoms: 17117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2146, 17117 Classifications: {'peptide': 2146} Link IDs: {'PTRANS': 115, 'TRANS': 2030} Chain breaks: 1 Time building chain proxies: 45.90, per 1000 atoms: 0.41 Number of scatterers: 112922 At special positions: 0 Unit cell: (190.38, 189.24, 381.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 340 16.00 O 21902 8.00 N 19278 7.00 C 71402 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: 36.25 Conformation dependent library (CDL) restraints added in 12.3 seconds 28394 Ramachandran restraints generated. 14197 Oldfield, 0 Emsley, 14197 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 26878 Finding SS restraints... Secondary structure from input PDB file: 550 helices and 0 sheets defined 45.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.28 Creating SS restraints... Processing helix chain 'A' and resid 71 through 76 Processing helix chain 'A' and resid 77 through 81 Processing helix chain 'A' and resid 86 through 96 Processing helix chain 'A' and resid 98 through 102 Processing helix chain 'A' and resid 114 through 127 Processing helix chain 'A' and resid 137 through 142 Processing helix chain 'A' and resid 143 through 148 Processing helix chain 'A' and resid 151 through 157 Processing helix chain 'A' and resid 161 through 177 Processing helix chain 'A' and resid 181 through 191 removed outlier: 3.736A pdb=" N THR A 191 " --> pdb=" O GLU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 215 Processing helix chain 'A' and resid 218 through 223 Processing helix chain 'A' and resid 224 through 229 Processing helix chain 'A' and resid 232 through 241 removed outlier: 3.526A pdb=" N GLY A 238 " --> pdb=" O ALA A 234 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE A 239 " --> pdb=" O SER A 235 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASN A 240 " --> pdb=" O LEU A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 252 Processing helix chain 'A' and resid 259 through 268 Processing helix chain 'A' and resid 272 through 277 Processing helix chain 'A' and resid 278 through 286 Processing helix chain 'A' and resid 289 through 298 Processing helix chain 'A' and resid 337 through 339 No H-bonds generated for 'chain 'A' and resid 337 through 339' Processing helix chain 'A' and resid 398 through 404 Processing helix chain 'A' and resid 433 through 451 Processing helix chain 'A' and resid 453 through 465 Processing helix chain 'A' and resid 471 through 489 Processing helix chain 'A' and resid 491 through 498 Processing helix chain 'A' and resid 513 through 520 Processing helix chain 'A' and resid 523 through 527 Processing helix chain 'A' and resid 545 through 556 Processing helix chain 'A' and resid 558 through 570 Processing helix chain 'A' and resid 581 through 598 Processing helix chain 'A' and resid 601 through 613 Processing helix chain 'A' and resid 618 through 622 Processing helix chain 'A' and resid 623 through 645 Processing helix chain 'A' and resid 647 through 656 Processing helix chain 'A' and resid 664 through 678 Processing helix chain 'A' and resid 687 through 701 Proline residue: A 694 - end of helix Processing helix chain 'A' and resid 704 through 719 Processing helix chain 'A' and resid 726 through 737 Processing helix chain 'A' and resid 748 through 770 removed outlier: 3.585A pdb=" N ILE A 752 " --> pdb=" O THR A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 782 Processing helix chain 'A' and resid 783 through 787 Processing helix chain 'A' and resid 797 through 815 Processing helix chain 'A' and resid 817 through 827 Processing helix chain 'A' and resid 831 through 840 Processing helix chain 'A' and resid 842 through 856 Processing helix chain 'A' and resid 870 through 888 Processing helix chain 'A' and resid 890 through 899 Processing helix chain 'A' and resid 903 through 908 Processing helix chain 'A' and resid 911 through 924 Processing helix chain 'A' and resid 927 through 954 Processing helix chain 'A' and resid 963 through 972 Processing helix chain 'A' and resid 984 through 1002 Processing helix chain 'A' and resid 1009 through 1014 removed outlier: 3.520A pdb=" N ILE A1013 " --> pdb=" O ASN A1009 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1020 Processing helix chain 'A' and resid 1027 through 1040 removed outlier: 3.781A pdb=" N VAL A1038 " --> pdb=" O VAL A1034 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR A1039 " --> pdb=" O SER A1035 " (cutoff:3.500A) Processing helix chain 'A' and resid 1041 through 1044 Processing helix chain 'A' and resid 1054 through 1064 Processing helix chain 'A' and resid 1070 through 1090 Processing helix chain 'A' and resid 1138 through 1141 Processing helix chain 'A' and resid 1153 through 1156 Processing helix chain 'A' and resid 1217 through 1224 removed outlier: 3.715A pdb=" N LEU A1224 " --> pdb=" O LYS A1220 " (cutoff:3.500A) Processing helix chain 'A' and resid 1240 through 1243 Processing helix chain 'A' and resid 1255 through 1262 Processing helix chain 'A' and resid 1279 through 1291 Processing helix chain 'A' and resid 1292 through 1294 No H-bonds generated for 'chain 'A' and resid 1292 through 1294' Processing helix chain 'A' and resid 1326 through 1329 Processing helix chain 'A' and resid 1366 through 1379 Processing helix chain 'A' and resid 1463 through 1468 Processing helix chain 'A' and resid 1494 through 1496 No H-bonds generated for 'chain 'A' and resid 1494 through 1496' Processing helix chain 'A' and resid 1513 through 1517 Processing helix chain 'A' and resid 1608 through 1614 removed outlier: 3.857A pdb=" N VAL A1614 " --> pdb=" O ALA A1610 " (cutoff:3.500A) Processing helix chain 'A' and resid 1620 through 1625 Processing helix chain 'A' and resid 1628 through 1631 Processing helix chain 'A' and resid 1764 through 1773 Processing helix chain 'A' and resid 1773 through 1786 Processing helix chain 'A' and resid 1788 through 1798 Processing helix chain 'A' and resid 1818 through 1823 Processing helix chain 'A' and resid 1830 through 1834 Processing helix chain 'A' and resid 1836 through 1844 Processing helix chain 'A' and resid 1845 through 1870 Processing helix chain 'A' and resid 1872 through 1891 Processing helix chain 'A' and resid 1906 through 1912 Processing helix chain 'A' and resid 1912 through 1922 Processing helix chain 'A' and resid 1943 through 1947 Processing helix chain 'A' and resid 1953 through 1972 Processing helix chain 'A' and resid 2018 through 2105 Processing helix chain 'A' and resid 2108 through 2123 Processing helix chain 'A' and resid 2124 through 2139 Processing helix chain 'A' and resid 2155 through 2244 Processing helix chain 'A' and resid 2247 through 2285 Processing helix chain 'A' and resid 2298 through 2302 Processing helix chain 'A' and resid 2305 through 2324 Processing helix chain 'A' and resid 2337 through 2343 Processing helix chain 'A' and resid 2345 through 2349 Processing helix chain 'A' and resid 2352 through 2363 Processing helix chain 'A' and resid 2380 through 2384 removed outlier: 3.802A pdb=" N LYS A2384 " --> pdb=" O THR A2381 " (cutoff:3.500A) Processing helix chain 'A' and resid 2397 through 2402 removed outlier: 3.564A pdb=" N TYR A2402 " --> pdb=" O ARG A2399 " (cutoff:3.500A) Processing helix chain 'A' and resid 2403 through 2407 Processing helix chain 'A' and resid 2490 through 2494 Processing helix chain 'A' and resid 2497 through 2502 Processing helix chain 'B' and resid 71 through 76 Processing helix chain 'B' and resid 86 through 96 Processing helix chain 'B' and resid 98 through 102 Processing helix chain 'B' and resid 114 through 127 Processing helix chain 'B' and resid 137 through 142 Processing helix chain 'B' and resid 143 through 148 removed outlier: 3.556A pdb=" N SER B 147 " --> pdb=" O PRO B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 157 Processing helix chain 'B' and resid 161 through 177 Processing helix chain 'B' and resid 181 through 191 removed outlier: 3.756A pdb=" N THR B 191 " --> pdb=" O GLU B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 215 Processing helix chain 'B' and resid 218 through 223 removed outlier: 3.575A pdb=" N ASN B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 229 Processing helix chain 'B' and resid 232 through 241 removed outlier: 3.537A pdb=" N GLY B 238 " --> pdb=" O ALA B 234 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE B 239 " --> pdb=" O SER B 235 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ASN B 240 " --> pdb=" O LEU B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 252 Processing helix chain 'B' and resid 256 through 258 No H-bonds generated for 'chain 'B' and resid 256 through 258' Processing helix chain 'B' and resid 259 through 269 Processing helix chain 'B' and resid 272 through 277 Processing helix chain 'B' and resid 278 through 286 Processing helix chain 'B' and resid 289 through 298 Processing helix chain 'B' and resid 337 through 339 No H-bonds generated for 'chain 'B' and resid 337 through 339' Processing helix chain 'B' and resid 398 through 403 Processing helix chain 'B' and resid 433 through 451 Processing helix chain 'B' and resid 453 through 465 Processing helix chain 'B' and resid 471 through 489 Processing helix chain 'B' and resid 491 through 498 Processing helix chain 'B' and resid 513 through 520 Processing helix chain 'B' and resid 545 through 556 removed outlier: 3.846A pdb=" N LEU B 551 " --> pdb=" O ARG B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 570 Processing helix chain 'B' and resid 581 through 598 Processing helix chain 'B' and resid 601 through 613 Processing helix chain 'B' and resid 618 through 622 Processing helix chain 'B' and resid 623 through 645 Processing helix chain 'B' and resid 647 through 656 Processing helix chain 'B' and resid 664 through 678 Processing helix chain 'B' and resid 687 through 700 Proline residue: B 694 - end of helix removed outlier: 3.623A pdb=" N ALA B 698 " --> pdb=" O PRO B 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 704 through 719 Processing helix chain 'B' and resid 726 through 738 Processing helix chain 'B' and resid 748 through 770 removed outlier: 3.571A pdb=" N ILE B 752 " --> pdb=" O THR B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 772 through 782 Processing helix chain 'B' and resid 783 through 787 Processing helix chain 'B' and resid 797 through 815 Processing helix chain 'B' and resid 817 through 827 Processing helix chain 'B' and resid 831 through 840 Processing helix chain 'B' and resid 842 through 856 Processing helix chain 'B' and resid 870 through 888 Processing helix chain 'B' and resid 890 through 899 Processing helix chain 'B' and resid 903 through 907 Processing helix chain 'B' and resid 911 through 924 Processing helix chain 'B' and resid 927 through 954 Processing helix chain 'B' and resid 963 through 972 Processing helix chain 'B' and resid 984 through 1002 Processing helix chain 'B' and resid 1009 through 1014 Processing helix chain 'B' and resid 1015 through 1020 Processing helix chain 'B' and resid 1021 through 1023 No H-bonds generated for 'chain 'B' and resid 1021 through 1023' Processing helix chain 'B' and resid 1027 through 1037 Processing helix chain 'B' and resid 1038 through 1039 No H-bonds generated for 'chain 'B' and resid 1038 through 1039' Processing helix chain 'B' and resid 1040 through 1044 Processing helix chain 'B' and resid 1054 through 1064 Processing helix chain 'B' and resid 1070 through 1090 Processing helix chain 'B' and resid 1138 through 1141 Processing helix chain 'B' and resid 1153 through 1156 Processing helix chain 'B' and resid 1217 through 1223 Processing helix chain 'B' and resid 1240 through 1243 Processing helix chain 'B' and resid 1255 through 1262 Processing helix chain 'B' and resid 1279 through 1291 Processing helix chain 'B' and resid 1292 through 1294 No H-bonds generated for 'chain 'B' and resid 1292 through 1294' Processing helix chain 'B' and resid 1326 through 1329 Processing helix chain 'B' and resid 1366 through 1379 Processing helix chain 'B' and resid 1439 through 1442 Processing helix chain 'B' and resid 1463 through 1468 Processing helix chain 'B' and resid 1494 through 1496 No H-bonds generated for 'chain 'B' and resid 1494 through 1496' Processing helix chain 'B' and resid 1513 through 1517 Processing helix chain 'B' and resid 1544 through 1546 No H-bonds generated for 'chain 'B' and resid 1544 through 1546' Processing helix chain 'B' and resid 1608 through 1617 removed outlier: 4.586A pdb=" N ALA B1615 " --> pdb=" O ARG B1611 " (cutoff:3.500A) Processing helix chain 'B' and resid 1620 through 1625 Processing helix chain 'B' and resid 1628 through 1631 Processing helix chain 'B' and resid 1651 through 1656 Processing helix chain 'B' and resid 1764 through 1773 Processing helix chain 'B' and resid 1773 through 1786 Processing helix chain 'B' and resid 1788 through 1797 Processing helix chain 'B' and resid 1818 through 1823 Processing helix chain 'B' and resid 1830 through 1834 removed outlier: 3.685A pdb=" N ASP B1833 " --> pdb=" O ASP B1830 " (cutoff:3.500A) Processing helix chain 'B' and resid 1836 through 1844 Processing helix chain 'B' and resid 1845 through 1871 Processing helix chain 'B' and resid 1872 through 1891 Processing helix chain 'B' and resid 1906 through 1911 Processing helix chain 'B' and resid 1912 through 1922 removed outlier: 3.558A pdb=" N GLN B1916 " --> pdb=" O ASP B1912 " (cutoff:3.500A) Processing helix chain 'B' and resid 1943 through 1947 Processing helix chain 'B' and resid 1953 through 1972 Processing helix chain 'B' and resid 2018 through 2106 removed outlier: 3.590A pdb=" N ASN B2106 " --> pdb=" O LEU B2102 " (cutoff:3.500A) Processing helix chain 'B' and resid 2108 through 2123 Processing helix chain 'B' and resid 2124 through 2140 Processing helix chain 'B' and resid 2155 through 2244 Processing helix chain 'B' and resid 2247 through 2285 Processing helix chain 'B' and resid 2298 through 2302 Processing helix chain 'B' and resid 2305 through 2323 Processing helix chain 'B' and resid 2337 through 2343 Processing helix chain 'B' and resid 2352 through 2363 Processing helix chain 'B' and resid 2380 through 2384 Processing helix chain 'B' and resid 2393 through 2397 Processing helix chain 'B' and resid 2398 through 2402 Processing helix chain 'B' and resid 2403 through 2407 Processing helix chain 'B' and resid 2490 through 2494 Processing helix chain 'B' and resid 2497 through 2502 Processing helix chain 'C' and resid 71 through 76 Processing helix chain 'C' and resid 77 through 81 Processing helix chain 'C' and resid 86 through 96 Processing helix chain 'C' and resid 98 through 102 Processing helix chain 'C' and resid 116 through 127 Processing helix chain 'C' and resid 137 through 142 Processing helix chain 'C' and resid 142 through 147 removed outlier: 4.086A pdb=" N LYS C 146 " --> pdb=" O ARG C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 157 Processing helix chain 'C' and resid 161 through 177 Processing helix chain 'C' and resid 181 through 191 removed outlier: 4.023A pdb=" N THR C 191 " --> pdb=" O GLU C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 215 Processing helix chain 'C' and resid 218 through 224 Processing helix chain 'C' and resid 224 through 229 Processing helix chain 'C' and resid 232 through 241 removed outlier: 3.608A pdb=" N GLY C 238 " --> pdb=" O ALA C 234 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE C 239 " --> pdb=" O SER C 235 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ASN C 240 " --> pdb=" O LEU C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 252 Processing helix chain 'C' and resid 259 through 268 Processing helix chain 'C' and resid 272 through 277 Processing helix chain 'C' and resid 278 through 286 Processing helix chain 'C' and resid 289 through 298 removed outlier: 3.972A pdb=" N PHE C 296 " --> pdb=" O GLU C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 339 No H-bonds generated for 'chain 'C' and resid 337 through 339' Processing helix chain 'C' and resid 398 through 403 Processing helix chain 'C' and resid 433 through 451 Processing helix chain 'C' and resid 453 through 465 Processing helix chain 'C' and resid 471 through 489 Processing helix chain 'C' and resid 491 through 498 Processing helix chain 'C' and resid 513 through 520 Processing helix chain 'C' and resid 523 through 527 Processing helix chain 'C' and resid 545 through 556 Processing helix chain 'C' and resid 558 through 570 Processing helix chain 'C' and resid 581 through 598 Processing helix chain 'C' and resid 601 through 613 Processing helix chain 'C' and resid 618 through 622 Processing helix chain 'C' and resid 623 through 645 Processing helix chain 'C' and resid 647 through 656 Processing helix chain 'C' and resid 664 through 678 Processing helix chain 'C' and resid 688 through 701 Proline residue: C 694 - end of helix Processing helix chain 'C' and resid 704 through 719 Processing helix chain 'C' and resid 726 through 737 Processing helix chain 'C' and resid 748 through 770 removed outlier: 3.562A pdb=" N ILE C 752 " --> pdb=" O THR C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 772 through 782 Processing helix chain 'C' and resid 783 through 787 Processing helix chain 'C' and resid 797 through 815 Processing helix chain 'C' and resid 817 through 827 Processing helix chain 'C' and resid 831 through 840 Processing helix chain 'C' and resid 842 through 856 removed outlier: 3.515A pdb=" N LEU C 846 " --> pdb=" O ASP C 842 " (cutoff:3.500A) Processing helix chain 'C' and resid 870 through 888 Processing helix chain 'C' and resid 890 through 899 Processing helix chain 'C' and resid 903 through 908 Processing helix chain 'C' and resid 911 through 924 Processing helix chain 'C' and resid 927 through 954 Processing helix chain 'C' and resid 963 through 972 Processing helix chain 'C' and resid 984 through 1002 Processing helix chain 'C' and resid 1009 through 1014 Processing helix chain 'C' and resid 1015 through 1020 Processing helix chain 'C' and resid 1021 through 1023 No H-bonds generated for 'chain 'C' and resid 1021 through 1023' Processing helix chain 'C' and resid 1027 through 1040 removed outlier: 3.829A pdb=" N GLY C1033 " --> pdb=" O SER C1029 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TYR C1039 " --> pdb=" O SER C1035 " (cutoff:3.500A) Processing helix chain 'C' and resid 1041 through 1044 Processing helix chain 'C' and resid 1054 through 1064 Processing helix chain 'C' and resid 1070 through 1090 Processing helix chain 'C' and resid 1138 through 1141 Processing helix chain 'C' and resid 1153 through 1156 Processing helix chain 'C' and resid 1217 through 1223 Processing helix chain 'C' and resid 1240 through 1244 removed outlier: 3.916A pdb=" N THR C1244 " --> pdb=" O GLY C1241 " (cutoff:3.500A) Processing helix chain 'C' and resid 1255 through 1260 removed outlier: 3.566A pdb=" N TYR C1259 " --> pdb=" O THR C1255 " (cutoff:3.500A) Processing helix chain 'C' and resid 1279 through 1291 Processing helix chain 'C' and resid 1292 through 1294 No H-bonds generated for 'chain 'C' and resid 1292 through 1294' Processing helix chain 'C' and resid 1326 through 1329 Processing helix chain 'C' and resid 1366 through 1379 Processing helix chain 'C' and resid 1463 through 1468 Processing helix chain 'C' and resid 1494 through 1496 No H-bonds generated for 'chain 'C' and resid 1494 through 1496' Processing helix chain 'C' and resid 1513 through 1517 Processing helix chain 'C' and resid 1608 through 1618 removed outlier: 3.682A pdb=" N GLN C1612 " --> pdb=" O LEU C1608 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL C1614 " --> pdb=" O ALA C1610 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N ALA C1615 " --> pdb=" O ARG C1611 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ARG C1616 " --> pdb=" O GLN C1612 " (cutoff:3.500A) Processing helix chain 'C' and resid 1620 through 1625 Processing helix chain 'C' and resid 1628 through 1631 Processing helix chain 'C' and resid 1651 through 1656 Processing helix chain 'C' and resid 1764 through 1773 Processing helix chain 'C' and resid 1773 through 1786 Processing helix chain 'C' and resid 1788 through 1798 Processing helix chain 'C' and resid 1818 through 1823 Processing helix chain 'C' and resid 1830 through 1834 removed outlier: 3.643A pdb=" N SER C1834 " --> pdb=" O PRO C1831 " (cutoff:3.500A) Processing helix chain 'C' and resid 1836 through 1844 Processing helix chain 'C' and resid 1845 through 1871 Processing helix chain 'C' and resid 1872 through 1891 Processing helix chain 'C' and resid 1906 through 1912 Processing helix chain 'C' and resid 1912 through 1922 Processing helix chain 'C' and resid 1943 through 1947 Processing helix chain 'C' and resid 1953 through 1972 Processing helix chain 'C' and resid 2018 through 2105 Processing helix chain 'C' and resid 2108 through 2123 Processing helix chain 'C' and resid 2124 through 2140 Processing helix chain 'C' and resid 2155 through 2244 Processing helix chain 'C' and resid 2247 through 2285 Processing helix chain 'C' and resid 2305 through 2325 Processing helix chain 'C' and resid 2337 through 2343 Processing helix chain 'C' and resid 2345 through 2349 Processing helix chain 'C' and resid 2352 through 2363 Processing helix chain 'C' and resid 2380 through 2384 Processing helix chain 'C' and resid 2394 through 2402 removed outlier: 5.977A pdb=" N ILE C2398 " --> pdb=" O ASP C2395 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N ARG C2399 " --> pdb=" O LEU C2396 " (cutoff:3.500A) Processing helix chain 'C' and resid 2403 through 2407 Processing helix chain 'C' and resid 2437 through 2441 removed outlier: 4.246A pdb=" N GLY C2440 " --> pdb=" O ASP C2437 " (cutoff:3.500A) Processing helix chain 'C' and resid 2490 through 2494 Processing helix chain 'C' and resid 2499 through 2504 Processing helix chain 'D' and resid 71 through 77 Processing helix chain 'D' and resid 78 through 81 Processing helix chain 'D' and resid 86 through 96 Processing helix chain 'D' and resid 98 through 102 Processing helix chain 'D' and resid 114 through 127 Processing helix chain 'D' and resid 137 through 142 Processing helix chain 'D' and resid 142 through 148 removed outlier: 4.265A pdb=" N LYS D 146 " --> pdb=" O ARG D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 157 Processing helix chain 'D' and resid 161 through 177 Processing helix chain 'D' and resid 181 through 192 removed outlier: 3.759A pdb=" N THR D 191 " --> pdb=" O GLU D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 215 Processing helix chain 'D' and resid 218 through 223 Processing helix chain 'D' and resid 224 through 229 Processing helix chain 'D' and resid 232 through 241 removed outlier: 3.626A pdb=" N GLY D 238 " --> pdb=" O ALA D 234 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE D 239 " --> pdb=" O SER D 235 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASN D 240 " --> pdb=" O LEU D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 252 Processing helix chain 'D' and resid 259 through 269 Processing helix chain 'D' and resid 272 through 277 Processing helix chain 'D' and resid 278 through 286 Processing helix chain 'D' and resid 289 through 298 removed outlier: 3.550A pdb=" N PHE D 296 " --> pdb=" O GLU D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 339 No H-bonds generated for 'chain 'D' and resid 337 through 339' Processing helix chain 'D' and resid 398 through 403 Processing helix chain 'D' and resid 433 through 451 Processing helix chain 'D' and resid 453 through 465 Processing helix chain 'D' and resid 471 through 489 Processing helix chain 'D' and resid 491 through 498 Processing helix chain 'D' and resid 513 through 520 Processing helix chain 'D' and resid 523 through 527 Processing helix chain 'D' and resid 545 through 556 Processing helix chain 'D' and resid 558 through 570 Processing helix chain 'D' and resid 581 through 598 Processing helix chain 'D' and resid 601 through 613 Processing helix chain 'D' and resid 618 through 622 Processing helix chain 'D' and resid 623 through 645 Processing helix chain 'D' and resid 647 through 655 Processing helix chain 'D' and resid 664 through 678 Processing helix chain 'D' and resid 687 through 692 Processing helix chain 'D' and resid 692 through 701 removed outlier: 5.395A pdb=" N ALA D 698 " --> pdb=" O PRO D 694 " (cutoff:3.500A) Processing helix chain 'D' and resid 704 through 719 Processing helix chain 'D' and resid 726 through 737 Processing helix chain 'D' and resid 748 through 770 Processing helix chain 'D' and resid 772 through 782 Processing helix chain 'D' and resid 783 through 787 Processing helix chain 'D' and resid 797 through 815 Processing helix chain 'D' and resid 817 through 827 Processing helix chain 'D' and resid 831 through 839 Processing helix chain 'D' and resid 842 through 856 Processing helix chain 'D' and resid 870 through 888 Processing helix chain 'D' and resid 890 through 899 Processing helix chain 'D' and resid 903 through 908 Processing helix chain 'D' and resid 911 through 924 Processing helix chain 'D' and resid 927 through 954 Processing helix chain 'D' and resid 963 through 972 Processing helix chain 'D' and resid 985 through 1002 Processing helix chain 'D' and resid 1009 through 1014 removed outlier: 3.862A pdb=" N ILE D1013 " --> pdb=" O ASN D1009 " (cutoff:3.500A) Processing helix chain 'D' and resid 1015 through 1020 Processing helix chain 'D' and resid 1027 through 1040 removed outlier: 3.733A pdb=" N VAL D1038 " --> pdb=" O VAL D1034 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR D1039 " --> pdb=" O SER D1035 " (cutoff:3.500A) Processing helix chain 'D' and resid 1041 through 1045 Processing helix chain 'D' and resid 1054 through 1064 Processing helix chain 'D' and resid 1070 through 1090 Processing helix chain 'D' and resid 1138 through 1141 Processing helix chain 'D' and resid 1153 through 1156 Processing helix chain 'D' and resid 1217 through 1222 Processing helix chain 'D' and resid 1240 through 1243 Processing helix chain 'D' and resid 1255 through 1262 removed outlier: 3.988A pdb=" N ASN D1261 " --> pdb=" O SER D1258 " (cutoff:3.500A) Processing helix chain 'D' and resid 1279 through 1289 Processing helix chain 'D' and resid 1290 through 1294 Processing helix chain 'D' and resid 1326 through 1329 Processing helix chain 'D' and resid 1366 through 1379 Processing helix chain 'D' and resid 1463 through 1468 Processing helix chain 'D' and resid 1494 through 1496 No H-bonds generated for 'chain 'D' and resid 1494 through 1496' Processing helix chain 'D' and resid 1513 through 1517 Processing helix chain 'D' and resid 1608 through 1618 removed outlier: 3.739A pdb=" N VAL D1614 " --> pdb=" O ALA D1610 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N ALA D1615 " --> pdb=" O ARG D1611 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ARG D1616 " --> pdb=" O GLN D1612 " (cutoff:3.500A) Processing helix chain 'D' and resid 1620 through 1625 Processing helix chain 'D' and resid 1626 through 1631 Processing helix chain 'D' and resid 1651 through 1656 Processing helix chain 'D' and resid 1764 through 1773 Processing helix chain 'D' and resid 1773 through 1786 Processing helix chain 'D' and resid 1788 through 1798 Processing helix chain 'D' and resid 1818 through 1823 Processing helix chain 'D' and resid 1830 through 1834 Processing helix chain 'D' and resid 1836 through 1844 Processing helix chain 'D' and resid 1845 through 1871 Processing helix chain 'D' and resid 1872 through 1891 Processing helix chain 'D' and resid 1906 through 1912 Processing helix chain 'D' and resid 1912 through 1922 Processing helix chain 'D' and resid 1943 through 1947 Processing helix chain 'D' and resid 1953 through 1972 Processing helix chain 'D' and resid 2018 through 2106 Processing helix chain 'D' and resid 2108 through 2123 Processing helix chain 'D' and resid 2124 through 2139 Processing helix chain 'D' and resid 2155 through 2244 Processing helix chain 'D' and resid 2247 through 2285 Processing helix chain 'D' and resid 2298 through 2302 Processing helix chain 'D' and resid 2305 through 2325 Processing helix chain 'D' and resid 2337 through 2343 Processing helix chain 'D' and resid 2345 through 2349 Processing helix chain 'D' and resid 2352 through 2363 Processing helix chain 'D' and resid 2393 through 2397 Processing helix chain 'D' and resid 2398 through 2402 Processing helix chain 'D' and resid 2403 through 2407 Processing helix chain 'D' and resid 2437 through 2441 Processing helix chain 'D' and resid 2490 through 2494 Processing helix chain 'D' and resid 2496 through 2501 removed outlier: 3.536A pdb=" N MET D2500 " --> pdb=" O LYS D2496 " (cutoff:3.500A) Processing helix chain 'D' and resid 2502 through 2504 No H-bonds generated for 'chain 'D' and resid 2502 through 2504' Processing helix chain 'E' and resid 71 through 76 Processing helix chain 'E' and resid 77 through 81 Processing helix chain 'E' and resid 86 through 96 Processing helix chain 'E' and resid 98 through 102 Processing helix chain 'E' and resid 114 through 127 Processing helix chain 'E' and resid 137 through 142 Processing helix chain 'E' and resid 143 through 148 Processing helix chain 'E' and resid 151 through 157 Processing helix chain 'E' and resid 161 through 177 Processing helix chain 'E' and resid 181 through 191 removed outlier: 3.823A pdb=" N THR E 191 " --> pdb=" O GLU E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 215 Processing helix chain 'E' and resid 218 through 223 Processing helix chain 'E' and resid 224 through 229 Processing helix chain 'E' and resid 232 through 241 removed outlier: 4.266A pdb=" N GLY E 238 " --> pdb=" O ALA E 234 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ILE E 239 " --> pdb=" O SER E 235 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ASN E 240 " --> pdb=" O LEU E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 252 Processing helix chain 'E' and resid 256 through 258 No H-bonds generated for 'chain 'E' and resid 256 through 258' Processing helix chain 'E' and resid 259 through 266 Processing helix chain 'E' and resid 272 through 277 Processing helix chain 'E' and resid 278 through 286 Processing helix chain 'E' and resid 289 through 298 Processing helix chain 'E' and resid 398 through 403 Processing helix chain 'E' and resid 433 through 451 Processing helix chain 'E' and resid 453 through 465 Processing helix chain 'E' and resid 471 through 489 Processing helix chain 'E' and resid 491 through 498 Processing helix chain 'E' and resid 513 through 520 Processing helix chain 'E' and resid 523 through 527 Processing helix chain 'E' and resid 545 through 556 Processing helix chain 'E' and resid 558 through 570 Processing helix chain 'E' and resid 581 through 598 Processing helix chain 'E' and resid 601 through 613 Processing helix chain 'E' and resid 618 through 622 Processing helix chain 'E' and resid 623 through 645 Processing helix chain 'E' and resid 647 through 656 Processing helix chain 'E' and resid 664 through 678 Processing helix chain 'E' and resid 687 through 701 Proline residue: E 694 - end of helix Processing helix chain 'E' and resid 704 through 719 Processing helix chain 'E' and resid 726 through 737 Processing helix chain 'E' and resid 748 through 770 removed outlier: 3.594A pdb=" N ILE E 752 " --> pdb=" O THR E 748 " (cutoff:3.500A) Processing helix chain 'E' and resid 772 through 782 Processing helix chain 'E' and resid 783 through 787 Processing helix chain 'E' and resid 797 through 814 Processing helix chain 'E' and resid 817 through 827 Processing helix chain 'E' and resid 831 through 839 Processing helix chain 'E' and resid 842 through 856 removed outlier: 3.688A pdb=" N LEU E 846 " --> pdb=" O ASP E 842 " (cutoff:3.500A) Processing helix chain 'E' and resid 863 through 867 Processing helix chain 'E' and resid 870 through 888 Processing helix chain 'E' and resid 890 through 899 Processing helix chain 'E' and resid 903 through 907 Processing helix chain 'E' and resid 911 through 924 Processing helix chain 'E' and resid 927 through 954 Processing helix chain 'E' and resid 963 through 972 Processing helix chain 'E' and resid 985 through 1002 Processing helix chain 'E' and resid 1009 through 1014 removed outlier: 3.531A pdb=" N ILE E1013 " --> pdb=" O ASN E1009 " (cutoff:3.500A) Processing helix chain 'E' and resid 1015 through 1020 Processing helix chain 'E' and resid 1027 through 1040 removed outlier: 4.121A pdb=" N VAL E1038 " --> pdb=" O VAL E1034 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR E1039 " --> pdb=" O SER E1035 " (cutoff:3.500A) Processing helix chain 'E' and resid 1041 through 1044 Processing helix chain 'E' and resid 1054 through 1064 Processing helix chain 'E' and resid 1070 through 1090 Processing helix chain 'E' and resid 1138 through 1141 Processing helix chain 'E' and resid 1153 through 1156 Processing helix chain 'E' and resid 1217 through 1224 Processing helix chain 'E' and resid 1240 through 1243 Processing helix chain 'E' and resid 1255 through 1262 removed outlier: 3.582A pdb=" N ASN E1261 " --> pdb=" O SER E1258 " (cutoff:3.500A) Processing helix chain 'E' and resid 1279 through 1291 Processing helix chain 'E' and resid 1292 through 1294 No H-bonds generated for 'chain 'E' and resid 1292 through 1294' Processing helix chain 'E' and resid 1326 through 1329 Processing helix chain 'E' and resid 1366 through 1379 Processing helix chain 'E' and resid 1463 through 1468 Processing helix chain 'E' and resid 1494 through 1496 No H-bonds generated for 'chain 'E' and resid 1494 through 1496' Processing helix chain 'E' and resid 1513 through 1517 Processing helix chain 'E' and resid 1608 through 1618 removed outlier: 3.610A pdb=" N VAL E1614 " --> pdb=" O ALA E1610 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ALA E1615 " --> pdb=" O ARG E1611 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG E1616 " --> pdb=" O GLN E1612 " (cutoff:3.500A) Processing helix chain 'E' and resid 1626 through 1631 Processing helix chain 'E' and resid 1651 through 1656 Processing helix chain 'E' and resid 1764 through 1772 Processing helix chain 'E' and resid 1773 through 1786 Processing helix chain 'E' and resid 1788 through 1797 Processing helix chain 'E' and resid 1818 through 1823 Processing helix chain 'E' and resid 1830 through 1834 removed outlier: 3.577A pdb=" N ASP E1833 " --> pdb=" O ASP E1830 " (cutoff:3.500A) Processing helix chain 'E' and resid 1836 through 1844 Processing helix chain 'E' and resid 1845 through 1871 Processing helix chain 'E' and resid 1872 through 1891 Processing helix chain 'E' and resid 1906 through 1912 Processing helix chain 'E' and resid 1912 through 1922 Processing helix chain 'E' and resid 1943 through 1947 Processing helix chain 'E' and resid 1953 through 1972 Processing helix chain 'E' and resid 2018 through 2105 Processing helix chain 'E' and resid 2108 through 2123 Processing helix chain 'E' and resid 2124 through 2140 Processing helix chain 'E' and resid 2155 through 2244 Processing helix chain 'E' and resid 2247 through 2284 Processing helix chain 'E' and resid 2298 through 2302 Processing helix chain 'E' and resid 2305 through 2325 Processing helix chain 'E' and resid 2337 through 2343 Processing helix chain 'E' and resid 2345 through 2349 Processing helix chain 'E' and resid 2352 through 2363 Processing helix chain 'E' and resid 2394 through 2397 Processing helix chain 'E' and resid 2398 through 2402 Processing helix chain 'E' and resid 2403 through 2407 Processing helix chain 'E' and resid 2490 through 2494 Processing helix chain 'E' and resid 2497 through 2502 Processing helix chain 'F' and resid 170 through 172 No H-bonds generated for 'chain 'F' and resid 170 through 172' Processing helix chain 'F' and resid 213 through 220 Processing helix chain 'F' and resid 252 through 254 No H-bonds generated for 'chain 'F' and resid 252 through 254' Processing helix chain 'F' and resid 313 through 319 Processing helix chain 'F' and resid 374 through 379 Processing helix chain 'F' and resid 385 through 388 Processing helix chain 'F' and resid 495 through 498 Processing helix chain 'F' and resid 606 through 608 No H-bonds generated for 'chain 'F' and resid 606 through 608' Processing helix chain 'F' and resid 717 through 732 Processing helix chain 'F' and resid 814 through 819 Processing helix chain 'F' and resid 820 through 825 Processing helix chain 'F' and resid 854 through 864 Processing helix chain 'F' and resid 880 through 885 removed outlier: 3.564A pdb=" N HIS F 884 " --> pdb=" O THR F 881 " (cutoff:3.500A) Processing helix chain 'F' and resid 969 through 974 Processing helix chain 'F' and resid 975 through 976 No H-bonds generated for 'chain 'F' and resid 975 through 976' Processing helix chain 'F' and resid 977 through 981 Processing helix chain 'F' and resid 1017 through 1021 Processing helix chain 'F' and resid 1027 through 1032 Processing helix chain 'F' and resid 1081 through 1087 Processing helix chain 'F' and resid 1093 through 1104 Processing helix chain 'F' and resid 1133 through 1137 Processing helix chain 'F' and resid 1235 through 1241 Processing helix chain 'F' and resid 1264 through 1282 removed outlier: 4.944A pdb=" N GLN F1274 " --> pdb=" O ARG F1270 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N GLN F1277 " --> pdb=" O GLU F1273 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N LYS F1278 " --> pdb=" O GLN F1274 " (cutoff:3.500A) Processing helix chain 'F' and resid 1292 through 1302 Processing helix chain 'F' and resid 1306 through 1316 Processing helix chain 'F' and resid 1414 through 1421 Processing helix chain 'F' and resid 1461 through 1466 Processing helix chain 'F' and resid 1467 through 1470 Processing helix chain 'F' and resid 1484 through 1489 Processing helix chain 'F' and resid 1538 through 1546 Processing helix chain 'F' and resid 1635 through 1641 removed outlier: 3.675A pdb=" N HIS F1641 " --> pdb=" O ALA F1637 " (cutoff:3.500A) Processing helix chain 'F' and resid 1688 through 1694 Processing helix chain 'F' and resid 1865 through 1869 Processing helix chain 'F' and resid 1918 through 1920 No H-bonds generated for 'chain 'F' and resid 1918 through 1920' Processing helix chain 'F' and resid 1922 through 1927 removed outlier: 4.180A pdb=" N ASP F1927 " --> pdb=" O PRO F1923 " (cutoff:3.500A) Processing helix chain 'F' and resid 1928 through 1930 No H-bonds generated for 'chain 'F' and resid 1928 through 1930' Processing helix chain 'F' and resid 2090 through 2095 Processing helix chain 'F' and resid 2100 through 2104 Processing helix chain 'F' and resid 2143 through 2147 4297 hydrogen bonds defined for protein. 12204 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: 45.78 Time building geometry restraints manager: 40.38 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: 20131 1.30 - 1.44: 34463 1.44 - 1.58: 60015 1.58 - 1.71: 179 1.71 - 1.85: 620 Bond restraints: 115408 Sorted by residual: bond pdb=" CB HIS B1847 " pdb=" CG HIS B1847 " ideal model delta sigma weight residual 1.497 1.394 0.103 1.40e-02 5.10e+03 5.37e+01 bond pdb=" CB HIS E1847 " pdb=" CG HIS E1847 " ideal model delta sigma weight residual 1.497 1.400 0.097 1.40e-02 5.10e+03 4.79e+01 bond pdb=" CB HIS B1145 " pdb=" CG HIS B1145 " ideal model delta sigma weight residual 1.497 1.400 0.097 1.40e-02 5.10e+03 4.76e+01 bond pdb=" NE1 TRP E1800 " pdb=" CE2 TRP E1800 " ideal model delta sigma weight residual 1.370 1.295 0.075 1.10e-02 8.26e+03 4.64e+01 bond pdb=" CB HIS C1724 " pdb=" CG HIS C1724 " ideal model delta sigma weight residual 1.497 1.402 0.095 1.40e-02 5.10e+03 4.61e+01 ... (remaining 115403 not shown) Histogram of bond angle deviations from ideal: 94.22 - 102.23: 537 102.23 - 110.24: 32137 110.24 - 118.26: 57948 118.26 - 126.27: 64748 126.27 - 134.29: 1484 Bond angle restraints: 156854 Sorted by residual: angle pdb=" N LYS E1738 " pdb=" CA LYS E1738 " pdb=" C LYS E1738 " ideal model delta sigma weight residual 114.31 100.40 13.91 1.29e+00 6.01e-01 1.16e+02 angle pdb=" C ASP A1844 " pdb=" N PRO A1845 " pdb=" CA PRO A1845 " ideal model delta sigma weight residual 119.56 129.46 -9.90 1.02e+00 9.61e-01 9.42e+01 angle pdb=" C SER C1354 " pdb=" N PRO C1355 " pdb=" CA PRO C1355 " ideal model delta sigma weight residual 120.31 129.76 -9.45 9.80e-01 1.04e+00 9.31e+01 angle pdb=" N GLY A1011 " pdb=" CA GLY A1011 " pdb=" C GLY A1011 " ideal model delta sigma weight residual 112.66 97.18 15.48 1.62e+00 3.81e-01 9.13e+01 angle pdb=" N VAL C1004 " pdb=" CA VAL C1004 " pdb=" C VAL C1004 " ideal model delta sigma weight residual 110.72 101.22 9.50 1.01e+00 9.80e-01 8.85e+01 ... (remaining 156849 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.12: 66626 18.12 - 36.24: 1636 36.24 - 54.36: 408 54.36 - 72.48: 319 72.48 - 90.60: 76 Dihedral angle restraints: 69065 sinusoidal: 27262 harmonic: 41803 Sorted by residual: dihedral pdb=" C PHE D1525 " pdb=" N PHE D1525 " pdb=" CA PHE D1525 " pdb=" CB PHE D1525 " ideal model delta harmonic sigma weight residual -122.60 -111.08 -11.52 0 2.50e+00 1.60e-01 2.13e+01 dihedral pdb=" C THR F1780 " pdb=" N THR F1780 " pdb=" CA THR F1780 " pdb=" CB THR F1780 " ideal model delta harmonic sigma weight residual -122.00 -112.00 -10.00 0 2.50e+00 1.60e-01 1.60e+01 dihedral pdb=" C ASN C1025 " pdb=" N ASN C1025 " pdb=" CA ASN C1025 " pdb=" CB ASN C1025 " ideal model delta harmonic sigma weight residual -122.60 -132.45 9.85 0 2.50e+00 1.60e-01 1.55e+01 ... (remaining 69062 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 11664 0.091 - 0.181: 4560 0.181 - 0.272: 980 0.272 - 0.363: 106 0.363 - 0.453: 14 Chirality restraints: 17324 Sorted by residual: chirality pdb=" CA THR F1442 " pdb=" N THR F1442 " pdb=" C THR F1442 " pdb=" CB THR F1442 " both_signs ideal model delta sigma weight residual False 2.53 2.07 0.45 2.00e-01 2.50e+01 5.13e+00 chirality pdb=" CA THR E 198 " pdb=" N THR E 198 " pdb=" C THR E 198 " pdb=" CB THR E 198 " both_signs ideal model delta sigma weight residual False 2.53 2.07 0.45 2.00e-01 2.50e+01 5.12e+00 chirality pdb=" CA ASN C1025 " pdb=" N ASN C1025 " pdb=" C ASN C1025 " pdb=" CB ASN C1025 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.44 2.00e-01 2.50e+01 4.73e+00 ... (remaining 17321 not shown) Planarity restraints: 20447 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 859 " -0.124 5.00e-02 4.00e+02 1.90e-01 5.76e+01 pdb=" N PRO D 860 " 0.328 5.00e-02 4.00e+02 pdb=" CA PRO D 860 " -0.111 5.00e-02 4.00e+02 pdb=" CD PRO D 860 " -0.093 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 859 " -0.123 5.00e-02 4.00e+02 1.88e-01 5.68e+01 pdb=" N PRO B 860 " 0.326 5.00e-02 4.00e+02 pdb=" CA PRO B 860 " -0.110 5.00e-02 4.00e+02 pdb=" CD PRO B 860 " -0.093 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 859 " 0.123 5.00e-02 4.00e+02 1.87e-01 5.62e+01 pdb=" N PRO E 860 " -0.324 5.00e-02 4.00e+02 pdb=" CA PRO E 860 " 0.109 5.00e-02 4.00e+02 pdb=" CD PRO E 860 " 0.092 5.00e-02 4.00e+02 ... (remaining 20444 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.45: 129 2.45 - 3.06: 84096 3.06 - 3.67: 184378 3.67 - 4.29: 289329 4.29 - 4.90: 449994 Nonbonded interactions: 1007926 Sorted by model distance: nonbonded pdb=" CD1 PHE D2147 " pdb=" CE2 PHE E2147 " model vdw 1.834 3.640 nonbonded pdb=" OG1 THR A1211 " pdb=" OG1 THR B1116 " model vdw 2.188 2.440 nonbonded pdb=" N GLY A1011 " pdb=" O GLY A1011 " model vdw 2.224 2.496 nonbonded pdb=" N GLY E1011 " pdb=" O GLY E1011 " model vdw 2.242 2.496 nonbonded pdb=" OG1 THR A1116 " pdb=" OG1 THR E1211 " model vdw 2.252 2.440 ... (remaining 1007921 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 340 5.16 5 C 71402 2.51 5 N 19278 2.21 5 O 21902 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.170 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: 0.100 Extract box with map and model: 29.320 Check model and map are aligned: 1.230 Convert atoms to be neutral: 0.760 Process input model: 231.180 Find NCS groups from input model: 6.510 Set up NCS constraints: 0.570 Set refine NCS operators: 0.000 Set scattering table: 0.040 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 277.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 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 : 0.021 0.164 115408 Z= 1.372 Angle : 1.744 18.083 156854 Z= 1.189 Chirality : 0.096 0.453 17324 Planarity : 0.012 0.190 20447 Dihedral : 10.965 90.602 42187 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 1.60 Ramachandran Plot: Outliers : 0.26 % Allowed : 1.88 % Favored : 97.86 % Rotamer Outliers : 0.01 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.06), residues: 14197 helix: 0.07 (0.06), residues: 5662 sheet: 0.89 (0.10), residues: 2581 loop : 0.55 (0.08), residues: 5954 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 28394 Ramachandran restraints generated. 14197 Oldfield, 0 Emsley, 14197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 28394 Ramachandran restraints generated. 14197 Oldfield, 0 Emsley, 14197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 4584 residues out of total 12188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 4583 time to evaluate : 9.890 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: 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: 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: 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: 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: 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: 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 outliers start: 1 outliers final: 1 residues processed: 4583 average time/residue: 1.0209 time to fit residues: 8100.1848 Evaluate side-chains 2392 residues out of total 12188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 2391 time to evaluate : 9.825 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.7771 time to fit residues: 15.0017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1419 random chunks: chunk 1198 optimal weight: 0.9990 chunk 1075 optimal weight: 0.9990 chunk 596 optimal weight: 1.9990 chunk 367 optimal weight: 6.9990 chunk 725 optimal weight: 3.9990 chunk 574 optimal weight: 0.8980 chunk 1112 optimal weight: 3.9990 chunk 430 optimal weight: 1.9990 chunk 676 optimal weight: 0.9980 chunk 827 optimal weight: 1.9990 chunk 1288 optimal weight: 4.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN A 222 ASN A 312 GLN A 337 ASN ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 467 GLN A 514 GLN ** A 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 679 GLN A 706 ASN A 757 GLN A 767 HIS ** A 858 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 953 GLN A1053 GLN A1068 GLN A1229 ASN ** A1292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1588 HIS A1671 ASN A1781 GLN A2041 GLN A2252 ASN B 130 HIS B 222 ASN B 433 GLN B 505 GLN B 844 ASN B 932 ASN B1043 ASN B1413 ASN B1462 ASN ** B1469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1547 ASN B1671 ASN ** B1813 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1817 ASN ** B1877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2021 HIS ** B2071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2230 GLN B2248 GLN ** B2414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 79 HIS C 130 HIS C 153 GLN C 220 GLN C 222 ASN C 520 ASN C 626 GLN C 767 HIS ** C1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1090 ASN C1265 GLN C1413 ASN C1752 ASN ** C1877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1888 HIS C1969 ASN ** C2129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 491 HIS D 709 HIS D 751 HIS D 953 GLN D1068 GLN D1087 GLN D1090 ASN D1252 GLN ** D1447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1543 ASN D1680 GLN D1748 ASN D1752 ASN ** D1828 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1847 HIS ** D1888 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1958 ASN D2021 HIS ** D2025 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2205 GLN D2321 HIS ** E 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 302 ASN E 505 GLN E 525 ASN E 527 GLN E 848 GLN E 875 ASN ** E 932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 935 HIS E 953 GLN E1087 GLN E1240 GLN E1303 ASN E1397 ASN E1655 HIS E1817 ASN E1965 GLN E2021 HIS E2181 GLN ** E2230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E2427 GLN E2459 GLN E2505 ASN F 203 GLN F 230 HIS F 336 ASN ** F 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 974 ASN ** F 980 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 989 GLN F1126 HIS F1216 ASN F1252 GLN F1337 GLN F1359 HIS F1564 ASN ** F1798 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 96 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.3636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.094 115408 Z= 0.273 Angle : 0.713 14.193 156854 Z= 0.374 Chirality : 0.044 0.334 17324 Planarity : 0.006 0.127 20447 Dihedral : 4.868 38.729 15540 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.85 % Favored : 98.02 % Rotamer Outliers : 3.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.72 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.07), residues: 14197 helix: 1.57 (0.07), residues: 5623 sheet: 0.65 (0.10), residues: 2729 loop : 0.35 (0.08), residues: 5845 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 28394 Ramachandran restraints generated. 14197 Oldfield, 0 Emsley, 14197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 28394 Ramachandran restraints generated. 14197 Oldfield, 0 Emsley, 14197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3254 residues out of total 12188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 387 poor density : 2867 time to evaluate : 11.223 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 387 outliers final: 204 residues processed: 3106 average time/residue: 1.0194 time to fit residues: 5653.4877 Evaluate side-chains 2370 residues out of total 12188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 2166 time to evaluate : 9.710 Switching outliers to nearest non-outliers outliers start: 204 outliers final: 0 residues processed: 204 average time/residue: 0.8570 time to fit residues: 350.2481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1419 random chunks: chunk 716 optimal weight: 4.9990 chunk 399 optimal weight: 6.9990 chunk 1072 optimal weight: 0.0980 chunk 877 optimal weight: 1.9990 chunk 355 optimal weight: 0.8980 chunk 1290 optimal weight: 6.9990 chunk 1394 optimal weight: 8.9990 chunk 1149 optimal weight: 0.9980 chunk 1280 optimal weight: 6.9990 chunk 440 optimal weight: 7.9990 chunk 1035 optimal weight: 0.0870 overall best weight: 0.8160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 GLN ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 514 GLN ** A 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 875 ASN ** A1292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1376 ASN ** A1447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1520 GLN ** A1582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1651 ASN A1785 HIS A2021 HIS A2205 GLN A2363 GLN B 222 ASN ** B 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 767 HIS B 932 ASN B1068 GLN ** B1090 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1520 GLN ** B1813 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2235 GLN ** B2252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2488 ASN ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 222 ASN C 240 ASN ** C 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 932 ASN C 994 GLN C 998 ASN ** C1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1764 ASN C1877 ASN ** C1888 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2479 GLN ** D 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 599 GLN ** D 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 886 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 932 ASN ** D1447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1752 ASN ** D1828 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1888 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1972 HIS ** D2025 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2285 ASN ** E 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 302 ASN ** E 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 505 GLN E 669 ASN E 767 HIS ** E 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E2181 GLN E2223 GLN ** E2230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E2242 GLN ** E2252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 219 HIS ** F 663 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 895 GLN ** F 900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 980 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 989 GLN F1143 GLN F1716 GLN F1733 GLN ** F1912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F2031 GLN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.4350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.137 115408 Z= 0.215 Angle : 0.633 23.732 156854 Z= 0.324 Chirality : 0.042 0.291 17324 Planarity : 0.005 0.192 20447 Dihedral : 4.617 45.574 15540 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.11 % Favored : 97.79 % Rotamer Outliers : 2.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.07), residues: 14197 helix: 1.78 (0.07), residues: 5589 sheet: 0.62 (0.10), residues: 2762 loop : 0.22 (0.08), residues: 5846 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 28394 Ramachandran restraints generated. 14197 Oldfield, 0 Emsley, 14197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 28394 Ramachandran restraints generated. 14197 Oldfield, 0 Emsley, 14197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2696 residues out of total 12188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 257 poor density : 2439 time to evaluate : 9.944 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash outliers start: 257 outliers final: 111 residues processed: 2589 average time/residue: 1.0291 time to fit residues: 4785.8307 Evaluate side-chains 2165 residues out of total 12188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 2054 time to evaluate : 9.873 Switching outliers to nearest non-outliers outliers start: 111 outliers final: 0 residues processed: 111 average time/residue: 0.8482 time to fit residues: 191.8197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1419 random chunks: chunk 1275 optimal weight: 0.9980 chunk 970 optimal weight: 0.7980 chunk 669 optimal weight: 0.0170 chunk 142 optimal weight: 0.0870 chunk 616 optimal weight: 1.9990 chunk 866 optimal weight: 0.3980 chunk 1295 optimal weight: 3.9990 chunk 1371 optimal weight: 4.9990 chunk 676 optimal weight: 2.9990 chunk 1227 optimal weight: 6.9990 chunk 369 optimal weight: 8.9990 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 GLN ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 514 GLN ** A 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 848 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 GLN ** A1292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 ASN B 388 ASN B 650 GLN B 767 HIS B 932 ASN ** B1090 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1813 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1817 ASN ** B1877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2414 GLN ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 93 ASN ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 520 ASN ** C 932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 994 GLN C1087 GLN C1252 GLN ** C1877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1888 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2059 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 812 ASN D1007 ASN ** D1447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1793 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1817 ASN ** D1888 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2041 GLN D2452 HIS ** E 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 222 ASN E 312 GLN E 364 ASN E 719 GLN ** E 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 914 GLN ** E1062 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1370 ASN ** E1509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E2230 GLN ** E2252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 222 GLN ** F 663 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 900 GLN ** F 980 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 989 GLN F1216 ASN ** F1322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1733 GLN ** F1912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2003 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.4751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.141 115408 Z= 0.187 Angle : 0.604 22.675 156854 Z= 0.304 Chirality : 0.042 0.296 17324 Planarity : 0.005 0.151 20447 Dihedral : 4.467 43.784 15540 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.08 % Favored : 97.82 % Rotamer Outliers : 1.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.72 % Twisted General : 0.01 % 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: 1.28 (0.07), residues: 14197 helix: 1.81 (0.07), residues: 5574 sheet: 0.66 (0.10), residues: 2616 loop : 0.11 (0.08), residues: 6007 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 28394 Ramachandran restraints generated. 14197 Oldfield, 0 Emsley, 14197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 28394 Ramachandran restraints generated. 14197 Oldfield, 0 Emsley, 14197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2628 residues out of total 12188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 228 poor density : 2400 time to evaluate : 9.524 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 228 outliers final: 104 residues processed: 2515 average time/residue: 0.9998 time to fit residues: 4513.9842 Evaluate side-chains 2136 residues out of total 12188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 2032 time to evaluate : 9.536 Switching outliers to nearest non-outliers outliers start: 104 outliers final: 0 residues processed: 104 average time/residue: 0.8663 time to fit residues: 185.5676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1419 random chunks: chunk 1142 optimal weight: 3.9990 chunk 778 optimal weight: 8.9990 chunk 19 optimal weight: 0.8980 chunk 1021 optimal weight: 0.5980 chunk 565 optimal weight: 0.2980 chunk 1170 optimal weight: 0.6980 chunk 948 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 700 optimal weight: 5.9990 chunk 1231 optimal weight: 8.9990 chunk 346 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 514 GLN ** A 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 848 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1667 HIS A1671 ASN A1785 HIS ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 520 ASN ** B 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 767 HIS B 932 ASN ** B1090 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1462 ASN ** B1469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1813 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2230 GLN ** B2237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 525 ASN C 709 HIS C 796 HIS ** C 932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 994 GLN ** C1062 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1282 GLN C1877 ASN ** C1888 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2059 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2181 GLN ** C2452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 767 HIS ** D 886 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1361 HIS ** D1447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1888 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2129 GLN ** D2197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 ASN ** E 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 581 ASN E 669 ASN E 751 HIS ** E 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 914 GLN ** E1062 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1667 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E2181 GLN ** E2252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 663 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 980 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1301 GLN F1308 GLN ** F1322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1597 GLN ** F1856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F2010 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.5012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.145 115408 Z= 0.194 Angle : 0.610 28.157 156854 Z= 0.303 Chirality : 0.041 0.275 17324 Planarity : 0.005 0.213 20447 Dihedral : 4.378 45.103 15540 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.23 % Favored : 97.65 % Rotamer Outliers : 1.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.90 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.07), residues: 14197 helix: 1.85 (0.07), residues: 5604 sheet: 0.65 (0.10), residues: 2676 loop : 0.06 (0.08), residues: 5917 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 28394 Ramachandran restraints generated. 14197 Oldfield, 0 Emsley, 14197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 28394 Ramachandran restraints generated. 14197 Oldfield, 0 Emsley, 14197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2388 residues out of total 12188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 2216 time to evaluate : 9.931 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 172 outliers final: 82 residues processed: 2297 average time/residue: 0.9633 time to fit residues: 3972.8458 Evaluate side-chains 2060 residues out of total 12188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 1978 time to evaluate : 10.119 Switching outliers to nearest non-outliers outliers start: 82 outliers final: 0 residues processed: 82 average time/residue: 0.8479 time to fit residues: 147.7976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1419 random chunks: chunk 461 optimal weight: 3.9990 chunk 1235 optimal weight: 7.9990 chunk 271 optimal weight: 7.9990 chunk 805 optimal weight: 2.9990 chunk 338 optimal weight: 1.9990 chunk 1372 optimal weight: 2.9990 chunk 1139 optimal weight: 6.9990 chunk 635 optimal weight: 0.9990 chunk 114 optimal weight: 2.9990 chunk 454 optimal weight: 2.9990 chunk 720 optimal weight: 0.3980 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 848 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1053 GLN ** A1447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1785 HIS ** A1958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2059 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 166 ASN ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 767 HIS B 932 ASN B1376 ASN ** B1469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2230 GLN ** B2237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2427 GLN C 556 ASN ** C 932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 994 GLN ** C 998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1062 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1533 ASN C1588 HIS C1752 ASN ** C1877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1888 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2059 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2252 ASN ** C2452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 505 GLN ** D 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 679 GLN ** D 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 886 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1888 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1969 ASN ** D2197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 669 ASN ** E 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1667 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E2181 GLN E2230 GLN E2285 ASN ** E2355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E2479 GLN F 163 GLN ** F 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 336 ASN ** F 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 895 GLN ** F 980 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1089 ASN ** F1250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.5319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.141 115408 Z= 0.289 Angle : 0.634 13.790 156854 Z= 0.323 Chirality : 0.043 0.291 17324 Planarity : 0.005 0.138 20447 Dihedral : 4.504 58.071 15540 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.74 % Favored : 97.16 % Rotamer Outliers : 1.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.90 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.07), residues: 14197 helix: 1.64 (0.07), residues: 5703 sheet: 0.55 (0.10), residues: 2665 loop : -0.07 (0.08), residues: 5829 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 28394 Ramachandran restraints generated. 14197 Oldfield, 0 Emsley, 14197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 28394 Ramachandran restraints generated. 14197 Oldfield, 0 Emsley, 14197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2314 residues out of total 12188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 222 poor density : 2092 time to evaluate : 9.926 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: 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: 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: 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: 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 outliers start: 222 outliers final: 137 residues processed: 2196 average time/residue: 0.9942 time to fit residues: 3925.4131 Evaluate side-chains 2012 residues out of total 12188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 1875 time to evaluate : 9.127 Switching outliers to nearest non-outliers outliers start: 137 outliers final: 0 residues processed: 137 average time/residue: 0.7673 time to fit residues: 214.7106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1419 random chunks: chunk 1323 optimal weight: 7.9990 chunk 154 optimal weight: 0.9980 chunk 782 optimal weight: 0.8980 chunk 1002 optimal weight: 2.9990 chunk 776 optimal weight: 0.9990 chunk 1155 optimal weight: 0.9990 chunk 766 optimal weight: 5.9990 chunk 1367 optimal weight: 10.0000 chunk 855 optimal weight: 3.9990 chunk 833 optimal weight: 3.9990 chunk 631 optimal weight: 0.8980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 520 ASN ** A 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 848 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1087 GLN ** A1447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1785 HIS A1812 GLN A1817 ASN A1958 ASN ** A1965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2021 HIS ** A2233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2230 GLN ** B2237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2278 GLN ** B2414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 166 ASN C 932 ASN C 994 GLN ** C1062 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1752 ASN ** C1877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1888 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2041 GLN ** C2059 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 222 ASN D 305 GLN ** D 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 812 ASN ** D 886 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1361 HIS ** D1447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1888 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2197 ASN ** D2505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 669 ASN ** E 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1062 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1240 GLN ** E1304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1667 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 668 GLN ** F 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 980 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.5510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.145 115408 Z= 0.202 Angle : 0.610 13.696 156854 Z= 0.306 Chirality : 0.042 0.322 17324 Planarity : 0.004 0.130 20447 Dihedral : 4.415 56.080 15540 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.59 % Favored : 97.31 % Rotamer Outliers : 1.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.90 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.07), residues: 14197 helix: 1.72 (0.07), residues: 5628 sheet: 0.54 (0.10), residues: 2643 loop : -0.07 (0.08), residues: 5926 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 28394 Ramachandran restraints generated. 14197 Oldfield, 0 Emsley, 14197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 28394 Ramachandran restraints generated. 14197 Oldfield, 0 Emsley, 14197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2222 residues out of total 12188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 2096 time to evaluate : 9.817 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 126 outliers final: 49 residues processed: 2167 average time/residue: 0.9635 time to fit residues: 3746.1771 Evaluate side-chains 1962 residues out of total 12188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 1913 time to evaluate : 9.948 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 0 residues processed: 49 average time/residue: 0.8116 time to fit residues: 90.8301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1419 random chunks: chunk 846 optimal weight: 0.8980 chunk 546 optimal weight: 0.8980 chunk 816 optimal weight: 4.9990 chunk 411 optimal weight: 0.8980 chunk 268 optimal weight: 4.9990 chunk 264 optimal weight: 1.9990 chunk 869 optimal weight: 0.0070 chunk 931 optimal weight: 0.7980 chunk 676 optimal weight: 0.8980 chunk 127 optimal weight: 0.0570 chunk 1075 optimal weight: 1.9990 overall best weight: 0.5316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN A 398 ASN ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 599 GLN ** A 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 848 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 858 HIS A1087 GLN ** A1965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2004 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1087 GLN ** B1469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 857 GLN C 875 ASN C 994 GLN C1062 GLN ** C1877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1958 ASN ** C2059 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2181 GLN ** C2452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 220 GLN ** D 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 525 ASN ** D 886 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1888 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2430 GLN ** D2505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 ASN ** E 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1667 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1961 GLN ** E2248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 862 ASN ** F 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 980 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1912 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.5700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.157 115408 Z= 0.183 Angle : 0.621 24.255 156854 Z= 0.308 Chirality : 0.042 0.275 17324 Planarity : 0.005 0.187 20447 Dihedral : 4.359 53.914 15540 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.59 % Favored : 97.32 % Rotamer Outliers : 0.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.90 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.07), residues: 14197 helix: 1.70 (0.07), residues: 5633 sheet: 0.59 (0.10), residues: 2639 loop : -0.08 (0.08), residues: 5925 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 28394 Ramachandran restraints generated. 14197 Oldfield, 0 Emsley, 14197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 28394 Ramachandran restraints generated. 14197 Oldfield, 0 Emsley, 14197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2195 residues out of total 12188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 2107 time to evaluate : 10.036 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 88 outliers final: 40 residues processed: 2147 average time/residue: 0.9741 time to fit residues: 3753.8980 Evaluate side-chains 1988 residues out of total 12188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 1948 time to evaluate : 9.837 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 0 residues processed: 40 average time/residue: 0.8676 time to fit residues: 79.0837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1419 random chunks: chunk 1244 optimal weight: 0.5980 chunk 1310 optimal weight: 9.9990 chunk 1195 optimal weight: 5.9990 chunk 1274 optimal weight: 6.9990 chunk 1309 optimal weight: 0.9980 chunk 767 optimal weight: 1.9990 chunk 555 optimal weight: 0.7980 chunk 1000 optimal weight: 6.9990 chunk 391 optimal weight: 6.9990 chunk 1151 optimal weight: 6.9990 chunk 1205 optimal weight: 0.3980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 848 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 858 HIS A 914 GLN A1087 GLN A1612 GLN ** A1965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2004 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1292 GLN ** B1469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2237 GLN ** B2252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 994 GLN ** C1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1888 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2059 GLN ** C2129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 295 GLN ** D1139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1361 HIS ** D1888 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2181 GLN ** D2505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 669 ASN ** E 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1282 GLN ** E1304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1667 HIS ** E2248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 895 GLN ** F 980 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2003 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.5845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.222 115408 Z= 0.217 Angle : 0.642 13.988 156854 Z= 0.319 Chirality : 0.042 0.306 17324 Planarity : 0.005 0.191 20447 Dihedral : 4.367 58.747 15540 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.82 % Favored : 97.09 % Rotamer Outliers : 0.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.01 % 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: 1.01 (0.07), residues: 14197 helix: 1.65 (0.07), residues: 5653 sheet: 0.53 (0.10), residues: 2579 loop : -0.14 (0.08), residues: 5965 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 28394 Ramachandran restraints generated. 14197 Oldfield, 0 Emsley, 14197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 28394 Ramachandran restraints generated. 14197 Oldfield, 0 Emsley, 14197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2081 residues out of total 12188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 2014 time to evaluate : 9.918 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 67 outliers final: 35 residues processed: 2047 average time/residue: 1.0051 time to fit residues: 3710.3878 Evaluate side-chains 1932 residues out of total 12188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 1897 time to evaluate : 9.960 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.8516 time to fit residues: 71.6294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1419 random chunks: chunk 1270 optimal weight: 1.9990 chunk 836 optimal weight: 0.3980 chunk 1347 optimal weight: 2.9990 chunk 822 optimal weight: 2.9990 chunk 639 optimal weight: 10.0000 chunk 936 optimal weight: 0.9980 chunk 1413 optimal weight: 5.9990 chunk 1301 optimal weight: 2.9990 chunk 1125 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 869 optimal weight: 10.0000 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 240 ASN ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 848 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 GLN A1087 GLN B 222 ASN B 306 GLN ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 914 GLN C 994 GLN ** C1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1743 HIS ** C1877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1888 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1870 GLN ** D1888 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2181 GLN ** D2505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 166 ASN ** E 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 706 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 980 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1125 HIS ** F1250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1526 GLN ** F1530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2003 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.5996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.187 115408 Z= 0.294 Angle : 0.681 15.862 156854 Z= 0.345 Chirality : 0.043 0.326 17324 Planarity : 0.005 0.173 20447 Dihedral : 4.526 51.536 15540 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 16.16 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.25 % Favored : 96.66 % Rotamer Outliers : 0.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.07), residues: 14197 helix: 1.53 (0.07), residues: 5643 sheet: 0.55 (0.10), residues: 2576 loop : -0.25 (0.08), residues: 5978 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 28394 Ramachandran restraints generated. 14197 Oldfield, 0 Emsley, 14197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 28394 Ramachandran restraints generated. 14197 Oldfield, 0 Emsley, 14197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1984 residues out of total 12188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 1928 time to evaluate : 10.004 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: 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: 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: 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 outliers start: 56 outliers final: 39 residues processed: 1956 average time/residue: 0.9939 time to fit residues: 3491.9164 Evaluate side-chains 1868 residues out of total 12188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 1829 time to evaluate : 9.829 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 0 residues processed: 39 average time/residue: 0.8518 time to fit residues: 78.0138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1419 random chunks: chunk 690 optimal weight: 0.9990 chunk 894 optimal weight: 0.6980 chunk 1199 optimal weight: 5.9990 chunk 344 optimal weight: 6.9990 chunk 1037 optimal weight: 1.9990 chunk 166 optimal weight: 8.9990 chunk 312 optimal weight: 0.7980 chunk 1127 optimal weight: 0.6980 chunk 471 optimal weight: 0.7980 chunk 1157 optimal weight: 3.9990 chunk 142 optimal weight: 7.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 ASN ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 635 ASN ** A 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 848 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1087 GLN ** A1965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 ASN ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1847 HIS ** B1877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2230 GLN ** B2252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 994 GLN ** C1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1888 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2233 GLN ** D 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 626 GLN ** D1007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1888 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1958 ASN D2181 GLN ** D2414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 166 ASN ** E 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 751 HIS ** E 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1003 ASN ** E1103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 980 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 989 GLN ** F1250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2003 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.089472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.075884 restraints weight = 349735.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.078078 restraints weight = 182278.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.079542 restraints weight = 113521.811| |-----------------------------------------------------------------------------| r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.6117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.202 115408 Z= 0.210 Angle : 0.662 16.374 156854 Z= 0.329 Chirality : 0.043 0.302 17324 Planarity : 0.005 0.159 20447 Dihedral : 4.445 50.632 15540 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.98 % Favored : 96.94 % Rotamer Outliers : 0.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.07), residues: 14197 helix: 1.58 (0.07), residues: 5623 sheet: 0.52 (0.10), residues: 2528 loop : -0.21 (0.08), residues: 6046 =============================================================================== Job complete usr+sys time: 54665.36 seconds wall clock time: 930 minutes 24.80 seconds (55824.80 seconds total)