Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 22 12:35:33 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h6e_0149/04_2023/6h6e_0149.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h6e_0149/04_2023/6h6e_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_2023/6h6e_0149.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h6e_0149/04_2023/6h6e_0149.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h6e_0149/04_2023/6h6e_0149.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h6e_0149/04_2023/6h6e_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 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. 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: 0.25s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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: 40.28, per 1000 atoms: 0.36 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: 33.42 Conformation dependent library (CDL) restraints added in 11.9 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: 4.19 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: 38.33 Time building geometry restraints manager: 36.76 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 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: 6.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.130 Extract box with map and model: 27.360 Check model and map are aligned: 1.200 Set scattering table: 0.740 Process input model: 209.880 Find NCS groups from input model: 6.110 Set up NCS constraints: 0.520 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:2.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 255.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 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 : 1.64 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 : 9.555 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: 1.0127 time to fit residues: 7943.0943 Evaluate side-chains 2397 residues out of total 12188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 2396 time to evaluate : 9.561 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.7736 time to fit residues: 14.5958 ------------------------------------------------------------------------------- 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: 0.0270 chunk 676 optimal weight: 0.9980 chunk 827 optimal weight: 1.9990 chunk 1288 optimal weight: 4.9990 overall best weight: 0.7842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 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 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 A1785 HIS A2041 GLN A2252 ASN 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 B2021 HIS ** B2071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2230 GLN B2248 GLN ** B2414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2427 GLN 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 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 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 E1152 ASN 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 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 974 ASN ** F 980 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 989 GLN F1064 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: 95 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.3625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.078 115408 Z= 0.227 Angle : 0.695 14.315 156854 Z= 0.364 Chirality : 0.044 0.321 17324 Planarity : 0.005 0.129 20447 Dihedral : 4.858 38.743 15540 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.83 % Favored : 98.04 % Rotamer Outliers : 3.01 % 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: 5569 sheet: 0.66 (0.10), residues: 2733 loop : 0.36 (0.08), residues: 5895 *********************** 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 3315 residues out of total 12188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 367 poor density : 2948 time to evaluate : 9.836 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 outliers start: 367 outliers final: 184 residues processed: 3174 average time/residue: 1.0015 time to fit residues: 5606.4145 Evaluate side-chains 2346 residues out of total 12188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 2162 time to evaluate : 8.569 Switching outliers to nearest non-outliers outliers start: 184 outliers final: 0 residues processed: 184 average time/residue: 0.8060 time to fit residues: 295.4214 ------------------------------------------------------------------------------- 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: 0.8980 chunk 399 optimal weight: 6.9990 chunk 1072 optimal weight: 6.9990 chunk 877 optimal weight: 1.9990 chunk 355 optimal weight: 2.9990 chunk 1290 optimal weight: 6.9990 chunk 1394 optimal weight: 0.9990 chunk 1149 optimal weight: 1.9990 chunk 1280 optimal weight: 6.9990 chunk 440 optimal weight: 7.9990 chunk 1035 optimal weight: 0.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 GLN ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 511 GLN ** 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 679 GLN A 761 GLN A 848 GLN ** A 858 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1376 ASN A1520 GLN ** A1533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1651 ASN A2021 HIS A2205 GLN B 130 HIS B 222 ASN B 388 ASN B 441 ASN ** B 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 767 HIS B 932 ASN B1036 GLN 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** ** B2173 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** 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 520 ASN C 856 HIS C 932 ASN C 994 GLN C 998 ASN ** C1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1265 GLN C1764 ASN C1877 ASN ** C1888 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2059 GLN C2455 ASN C2479 GLN ** D 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 386 GLN D 599 GLN D 679 GLN D 709 HIS D 812 ASN ** D 886 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 932 ASN D1367 GLN ** 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 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1062 GLN ** E1103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1265 GLN ** 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 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 222 GLN ** F 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 336 ASN ** F 663 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 895 GLN F 900 GLN ** F 980 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1716 GLN F1733 GLN ** F1912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F2031 GLN Total number of N/Q/H flips: 58 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.4419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.069 115408 Z= 0.253 Angle : 0.637 13.210 156854 Z= 0.330 Chirality : 0.043 0.248 17324 Planarity : 0.005 0.157 20447 Dihedral : 4.642 41.885 15540 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.23 % Favored : 97.66 % Rotamer Outliers : 2.44 % 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: 1.19 (0.07), residues: 14197 helix: 1.64 (0.07), residues: 5705 sheet: 0.60 (0.10), residues: 2733 loop : 0.14 (0.08), residues: 5759 *********************** 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 2664 residues out of total 12188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 297 poor density : 2367 time to evaluate : 9.617 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 outliers start: 297 outliers final: 141 residues processed: 2542 average time/residue: 0.9763 time to fit residues: 4414.4749 Evaluate side-chains 2135 residues out of total 12188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 1994 time to evaluate : 9.491 Switching outliers to nearest non-outliers outliers start: 141 outliers final: 0 residues processed: 141 average time/residue: 0.7839 time to fit residues: 222.8929 ------------------------------------------------------------------------------- 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: 10.0000 chunk 970 optimal weight: 0.9990 chunk 669 optimal weight: 0.0010 chunk 142 optimal weight: 0.0770 chunk 616 optimal weight: 3.9990 chunk 866 optimal weight: 0.9990 chunk 1295 optimal weight: 0.9980 chunk 1371 optimal weight: 6.9990 chunk 676 optimal weight: 2.9990 chunk 1227 optimal weight: 9.9990 chunk 369 optimal weight: 0.7980 overall best weight: 0.5746 ------------------------------------------------------------------------------- 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 511 GLN ** 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 A1036 GLN ** 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 A2205 GLN A2363 GLN B 222 ASN B 635 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 B2173 ASN ** B2252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2414 GLN ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 93 ASN ** C 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** C2252 ASN ** 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 232 HIS ** D1139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1817 ASN ** D1888 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1965 GLN D2041 GLN D2129 GLN D2452 HIS ** E 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 222 ASN E 312 GLN E 364 ASN E 669 ASN E 719 GLN E 767 HIS ** E 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 914 GLN ** E 932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1062 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1370 ASN ** E1509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1667 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E2459 GLN F 145 GLN ** 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** F 989 GLN F1143 GLN F1216 ASN F1301 GLN ** 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** F2010 GLN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.4801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.074 115408 Z= 0.184 Angle : 0.601 24.127 156854 Z= 0.303 Chirality : 0.042 0.289 17324 Planarity : 0.004 0.140 20447 Dihedral : 4.459 40.087 15540 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.09 % Favored : 97.80 % Rotamer Outliers : 1.83 % 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: 1.31 (0.07), residues: 14197 helix: 1.82 (0.07), residues: 5565 sheet: 0.67 (0.10), residues: 2671 loop : 0.14 (0.08), residues: 5961 *********************** 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 2554 residues out of total 12188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 223 poor density : 2331 time to evaluate : 9.591 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: 223 outliers final: 109 residues processed: 2449 average time/residue: 0.9511 time to fit residues: 4130.4770 Evaluate side-chains 2096 residues out of total 12188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 1987 time to evaluate : 9.543 Switching outliers to nearest non-outliers outliers start: 109 outliers final: 0 residues processed: 109 average time/residue: 0.7956 time to fit residues: 178.9447 ------------------------------------------------------------------------------- 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: 4.9990 chunk 778 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 1021 optimal weight: 0.9980 chunk 565 optimal weight: 2.9990 chunk 1170 optimal weight: 0.6980 chunk 948 optimal weight: 4.9990 chunk 1 optimal weight: 0.0040 chunk 700 optimal weight: 6.9990 chunk 1231 optimal weight: 0.9990 chunk 346 optimal weight: 3.9990 overall best weight: 1.1396 ------------------------------------------------------------------------------- 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 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 520 ASN ** A 669 ASN ** 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** ** A1888 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 ASN ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 520 ASN ** 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** B1843 HIS B2173 ASN B2230 GLN B2252 ASN ** B2414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 796 HIS ** C 932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 994 GLN C1282 GLN 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** ** C2452 HIS ** 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 232 HIS D 767 HIS ** D 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 886 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1007 ASN ** D1139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1361 HIS ** D1397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 76 ASN ** E 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 669 ASN ** 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** E1174 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** ** E1888 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E2479 GLN ** F 236 ASN ** 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** F 989 GLN ** F1250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1308 GLN ** F1322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1597 GLN ** F1724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2003 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F2120 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.5110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.087 115408 Z= 0.224 Angle : 0.599 11.624 156854 Z= 0.304 Chirality : 0.042 0.283 17324 Planarity : 0.004 0.135 20447 Dihedral : 4.365 38.451 15540 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.47 % Favored : 97.41 % Rotamer Outliers : 1.62 % 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: 1.22 (0.07), residues: 14197 helix: 1.74 (0.07), residues: 5689 sheet: 0.71 (0.10), residues: 2659 loop : 0.01 (0.08), residues: 5849 *********************** 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 2351 residues out of total 12188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 2154 time to evaluate : 9.558 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: 197 outliers final: 108 residues processed: 2249 average time/residue: 0.9699 time to fit residues: 3894.7391 Evaluate side-chains 2047 residues out of total 12188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 1939 time to evaluate : 9.545 Switching outliers to nearest non-outliers outliers start: 108 outliers final: 0 residues processed: 108 average time/residue: 0.8292 time to fit residues: 184.2983 ------------------------------------------------------------------------------- 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: 10.0000 chunk 271 optimal weight: 7.9990 chunk 805 optimal weight: 0.5980 chunk 338 optimal weight: 0.9990 chunk 1372 optimal weight: 6.9990 chunk 1139 optimal weight: 0.7980 chunk 635 optimal weight: 0.6980 chunk 114 optimal weight: 2.9990 chunk 454 optimal weight: 6.9990 chunk 720 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 GLN ** A1447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1462 ASN ** A1965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2209 GLN B 306 GLN ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 767 HIS B 932 ASN B1087 GLN B1229 ASN ** B1469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1961 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2230 GLN B2278 GLN ** B2414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 556 ASN ** C 932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 994 GLN C1533 ASN C1752 ASN ** C1877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 222 ASN ** D 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** D1961 GLN D2181 GLN ** D2505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 581 ASN ** E 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1003 ASN E1043 ASN ** 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** E1888 HIS E2181 GLN ** 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 895 GLN ** F 980 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1089 ASN F1125 HIS ** F1250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.5351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.083 115408 Z= 0.216 Angle : 0.599 13.286 156854 Z= 0.302 Chirality : 0.042 0.296 17324 Planarity : 0.004 0.134 20447 Dihedral : 4.343 37.143 15540 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.51 % Favored : 97.38 % Rotamer Outliers : 1.66 % 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: 1.19 (0.07), residues: 14197 helix: 1.73 (0.07), residues: 5709 sheet: 0.65 (0.10), residues: 2706 loop : 0.00 (0.08), residues: 5782 *********************** 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 2317 residues out of total 12188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 2115 time to evaluate : 9.559 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 outliers start: 202 outliers final: 95 residues processed: 2219 average time/residue: 0.9384 time to fit residues: 3694.8139 Evaluate side-chains 2008 residues out of total 12188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 1913 time to evaluate : 9.568 Switching outliers to nearest non-outliers outliers start: 95 outliers final: 0 residues processed: 95 average time/residue: 0.8057 time to fit residues: 158.9396 ------------------------------------------------------------------------------- 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: 4.9990 chunk 154 optimal weight: 0.8980 chunk 782 optimal weight: 2.9990 chunk 1002 optimal weight: 1.9990 chunk 776 optimal weight: 0.9990 chunk 1155 optimal weight: 0.9990 chunk 766 optimal weight: 5.9990 chunk 1367 optimal weight: 0.0770 chunk 855 optimal weight: 7.9990 chunk 833 optimal weight: 10.0000 chunk 631 optimal weight: 1.9990 overall best weight: 0.9944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN A 312 GLN A 398 ASN ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 599 GLN ** A 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1785 HIS A1812 GLN A1817 ASN ** A1888 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 166 ASN ** B 701 GLN ** 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 B1229 ASN ** B1469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1961 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2285 ASN ** B2414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 914 GLN C 932 ASN C 994 GLN ** C1877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2181 GLN ** C2452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 305 GLN ** D 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 886 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1007 ASN ** 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** D2430 GLN ** D2505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 669 ASN ** E 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1043 ASN ** 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** ** E1842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1888 HIS E1961 GLN E2181 GLN ** E2388 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 862 ASN ** 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** ** F1912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2003 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.5562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.086 115408 Z= 0.204 Angle : 0.601 12.984 156854 Z= 0.301 Chirality : 0.042 0.263 17324 Planarity : 0.004 0.134 20447 Dihedral : 4.288 36.376 15540 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.63 % Favored : 97.25 % Rotamer Outliers : 1.12 % 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: 1.20 (0.07), residues: 14197 helix: 1.77 (0.07), residues: 5643 sheet: 0.65 (0.10), residues: 2718 loop : -0.03 (0.08), residues: 5836 *********************** 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 2230 residues out of total 12188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 2094 time to evaluate : 9.600 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 outliers start: 136 outliers final: 59 residues processed: 2166 average time/residue: 0.9578 time to fit residues: 3690.4407 Evaluate side-chains 1970 residues out of total 12188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 1911 time to evaluate : 9.569 Switching outliers to nearest non-outliers outliers start: 59 outliers final: 0 residues processed: 59 average time/residue: 0.8319 time to fit residues: 106.0785 ------------------------------------------------------------------------------- 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: 0.0000 chunk 546 optimal weight: 0.9980 chunk 816 optimal weight: 4.9990 chunk 411 optimal weight: 1.9990 chunk 268 optimal weight: 2.9990 chunk 264 optimal weight: 0.7980 chunk 869 optimal weight: 10.0000 chunk 931 optimal weight: 0.9980 chunk 676 optimal weight: 0.9990 chunk 127 optimal weight: 2.9990 chunk 1075 optimal weight: 0.7980 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1612 GLN ** A1817 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1888 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1958 ASN ** A1965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2004 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 701 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B1292 GLN ** B1469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1817 ASN B1847 HIS ** B1888 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2285 ASN ** B2414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 994 GLN ** C1667 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2181 GLN ** C2452 HIS ** 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 886 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1361 HIS ** D1888 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** E1282 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** ** E1842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E2181 GLN ** E2233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 389 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** ** F1250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1912 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.5734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.089 115408 Z= 0.188 Angle : 0.611 13.705 156854 Z= 0.303 Chirality : 0.041 0.318 17324 Planarity : 0.004 0.134 20447 Dihedral : 4.257 35.771 15540 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.61 % Favored : 97.27 % Rotamer Outliers : 0.70 % 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: 1.22 (0.07), residues: 14197 helix: 1.79 (0.07), residues: 5618 sheet: 0.71 (0.10), residues: 2696 loop : -0.01 (0.08), residues: 5883 *********************** 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 2164 residues out of total 12188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 2079 time to evaluate : 9.651 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 outliers start: 85 outliers final: 39 residues processed: 2119 average time/residue: 0.9507 time to fit residues: 3599.0985 Evaluate side-chains 1954 residues out of total 12188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 1915 time to evaluate : 9.678 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 0 residues processed: 39 average time/residue: 0.8212 time to fit residues: 74.3330 ------------------------------------------------------------------------------- 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: 0.8980 chunk 1310 optimal weight: 10.0000 chunk 1195 optimal weight: 0.9990 chunk 1274 optimal weight: 4.9990 chunk 1309 optimal weight: 0.9990 chunk 767 optimal weight: 5.9990 chunk 555 optimal weight: 0.7980 chunk 1000 optimal weight: 2.9990 chunk 391 optimal weight: 7.9990 chunk 1151 optimal weight: 3.9990 chunk 1205 optimal weight: 7.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 GLN A1793 ASN ** A1817 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1888 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2021 HIS ** B 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1036 GLN ** B1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1817 ASN ** B2414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 857 GLN C 994 GLN ** C1667 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1788 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** C2041 GLN ** D 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 886 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1361 HIS D1870 GLN ** D1888 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2041 GLN ** D2505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 ASN ** E 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 669 ASN ** E 706 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** E1304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1667 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E2181 GLN ** E2233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 389 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** ** F1250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.5888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.088 115408 Z= 0.234 Angle : 0.635 13.901 156854 Z= 0.317 Chirality : 0.042 0.292 17324 Planarity : 0.004 0.135 20447 Dihedral : 4.304 35.237 15540 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.92 % Favored : 96.96 % Rotamer Outliers : 0.71 % 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: 1.14 (0.07), residues: 14197 helix: 1.70 (0.07), residues: 5633 sheet: 0.71 (0.10), residues: 2680 loop : -0.07 (0.08), residues: 5884 *********************** 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 2068 residues out of total 12188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 1982 time to evaluate : 9.640 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 outliers start: 86 outliers final: 47 residues processed: 2025 average time/residue: 0.9746 time to fit residues: 3516.3711 Evaluate side-chains 1899 residues out of total 12188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 1852 time to evaluate : 9.596 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 0 residues processed: 47 average time/residue: 0.8200 time to fit residues: 87.0179 ------------------------------------------------------------------------------- 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: 0.4980 chunk 836 optimal weight: 0.8980 chunk 1347 optimal weight: 8.9990 chunk 822 optimal weight: 0.9980 chunk 639 optimal weight: 9.9990 chunk 936 optimal weight: 0.8980 chunk 1413 optimal weight: 7.9990 chunk 1301 optimal weight: 0.0670 chunk 1125 optimal weight: 0.3980 chunk 116 optimal weight: 2.9990 chunk 869 optimal weight: 9.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- 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 310 ASN ** A 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 398 ASN ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 511 GLN ** 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 914 GLN A1612 GLN ** A1817 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1888 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1817 ASN ** B1973 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2235 GLN B2414 GLN ** C 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 HIS C 875 ASN C 994 GLN ** C1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1667 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2233 GLN ** D 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 295 GLN ** D 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 886 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1053 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1361 HIS ** D1888 HIS ** 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 ** 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** ** 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** ** E1842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 389 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** ** F1250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.6024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.092 115408 Z= 0.187 Angle : 0.647 14.162 156854 Z= 0.318 Chirality : 0.043 0.420 17324 Planarity : 0.004 0.135 20447 Dihedral : 4.282 35.071 15540 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.72 % Favored : 97.16 % Rotamer Outliers : 0.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.90 % 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: 1.12 (0.07), residues: 14197 helix: 1.64 (0.07), residues: 5647 sheet: 0.77 (0.10), residues: 2683 loop : -0.07 (0.08), residues: 5867 ********************** 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 2084 residues out of total 12188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 2050 time to evaluate : 9.578 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 outliers start: 34 outliers final: 14 residues processed: 2063 average time/residue: 0.9822 time to fit residues: 3616.3042 Evaluate side-chains 1926 residues out of total 12188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 1912 time to evaluate : 9.615 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.8044 time to fit residues: 34.7139 ------------------------------------------------------------------------------- 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: 2.9990 chunk 894 optimal weight: 2.9990 chunk 1199 optimal weight: 4.9990 chunk 344 optimal weight: 6.9990 chunk 1037 optimal weight: 0.9990 chunk 166 optimal weight: 6.9990 chunk 312 optimal weight: 3.9990 chunk 1127 optimal weight: 0.8980 chunk 471 optimal weight: 0.9980 chunk 1157 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 310 ASN ** A 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 635 ASN ** A 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 858 HIS ** A 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1105 GLN A1547 ASN ** A1817 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1888 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 ASN ** B 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1817 ASN ** B2414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 709 HIS C 856 HIS C 994 GLN ** C1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1588 HIS ** C1667 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1877 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** ** D 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 626 GLN ** D 886 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1361 HIS ** D1888 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1958 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 166 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** ** E1667 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2248 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 389 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** ** F1187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1526 GLN ** F1530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.089067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.075434 restraints weight = 348392.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.077588 restraints weight = 183676.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.079027 restraints weight = 115736.900| |-----------------------------------------------------------------------------| r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.6152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.090 115408 Z= 0.285 Angle : 0.683 14.149 156854 Z= 0.342 Chirality : 0.044 0.338 17324 Planarity : 0.005 0.137 20447 Dihedral : 4.385 34.596 15540 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 16.29 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.21 % Favored : 96.67 % Rotamer Outliers : 0.43 % 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: 0.97 (0.07), residues: 14197 helix: 1.55 (0.07), residues: 5638 sheet: 0.68 (0.10), residues: 2616 loop : -0.18 (0.08), residues: 5943 =============================================================================== Job complete usr+sys time: 52146.57 seconds wall clock time: 899 minutes 8.70 seconds (53948.70 seconds total)