Starting phenix.real_space_refine on Sat Jan 20 06:37:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k5b_22679/01_2024/7k5b_22679_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k5b_22679/01_2024/7k5b_22679.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k5b_22679/01_2024/7k5b_22679.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k5b_22679/01_2024/7k5b_22679.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k5b_22679/01_2024/7k5b_22679_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k5b_22679/01_2024/7k5b_22679_updated.pdb" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.029 sd= 0.189 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: 7 Type Number sf(0) Gaussians P 21 5.49 5 Mg 9 5.21 5 S 546 5.16 5 C 75784 2.51 5 N 20431 2.21 5 O 22626 1.98 5 H 156 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 579": "OE1" <-> "OE2" Residue "A PHE 587": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 603": "OE1" <-> "OE2" Residue "A ARG 611": "NH1" <-> "NH2" Residue "A PHE 614": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 641": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 651": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 652": "OE1" <-> "OE2" Residue "A PHE 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 656": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 688": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 697": "NH1" <-> "NH2" Residue "A GLU 698": "OE1" <-> "OE2" Residue "A ARG 704": "NH1" <-> "NH2" Residue "A TYR 726": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 727": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 738": "OE1" <-> "OE2" Residue "A ARG 739": "NH1" <-> "NH2" Residue "A ASP 760": "OD1" <-> "OD2" Residue "A ARG 764": "NH1" <-> "NH2" Residue "A GLU 778": "OE1" <-> "OE2" Residue "A TYR 780": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 783": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 800": "OD1" <-> "OD2" Residue "A ARG 805": "NH1" <-> "NH2" Residue "A GLU 807": "OE1" <-> "OE2" Residue "A PHE 847": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 881": "OE1" <-> "OE2" Residue "A ARG 888": "NH1" <-> "NH2" Residue "A TYR 890": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 931": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 950": "OE1" <-> "OE2" Residue "A TYR 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 985": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1048": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1105": "NH1" <-> "NH2" Residue "A ASP 1130": "OD1" <-> "OD2" Residue "A TYR 1134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1137": "OE1" <-> "OE2" Residue "A ARG 1143": "NH1" <-> "NH2" Residue "A PHE 1153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1185": "NH1" <-> "NH2" Residue "A TYR 1201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1568": "OD1" <-> "OD2" Residue "A TYR 1591": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1625": "OE1" <-> "OE2" Residue "A GLU 1628": "OE1" <-> "OE2" Residue "A GLU 1664": "OE1" <-> "OE2" Residue "A GLU 1688": "OE1" <-> "OE2" Residue "A GLU 1737": "OE1" <-> "OE2" Residue "A GLU 1740": "OE1" <-> "OE2" Residue "A ARG 1741": "NH1" <-> "NH2" Residue "A GLU 1756": "OE1" <-> "OE2" Residue "A GLU 1759": "OE1" <-> "OE2" Residue "A GLU 1782": "OE1" <-> "OE2" Residue "A GLU 1843": "OE1" <-> "OE2" Residue "A TYR 1866": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1923": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1932": "OE1" <-> "OE2" Residue "A ARG 1948": "NH1" <-> "NH2" Residue "A PHE 1955": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1959": "OE1" <-> "OE2" Residue "A GLU 1960": "OE1" <-> "OE2" Residue "A GLU 1963": "OE1" <-> "OE2" Residue "A GLU 1965": "OE1" <-> "OE2" Residue "A PHE 1973": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1983": "NH1" <-> "NH2" Residue "A ARG 2004": "NH1" <-> "NH2" Residue "A PHE 2027": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2032": "NH1" <-> "NH2" Residue "A ARG 2049": "NH1" <-> "NH2" Residue "A ASP 2100": "OD1" <-> "OD2" Residue "A GLU 2107": "OE1" <-> "OE2" Residue "A GLU 2117": "OE1" <-> "OE2" Residue "A GLU 2127": "OE1" <-> "OE2" Residue "A GLU 2145": "OE1" <-> "OE2" Residue "A ARG 2150": "NH1" <-> "NH2" Residue "A ARG 2222": "NH1" <-> "NH2" Residue "A ARG 2261": "NH1" <-> "NH2" Residue "A GLU 2266": "OE1" <-> "OE2" Residue "A PHE 2272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2273": "OE1" <-> "OE2" Residue "A TYR 2300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2305": "OE1" <-> "OE2" Residue "A GLU 2318": "OE1" <-> "OE2" Residue "A ARG 2328": "NH1" <-> "NH2" Residue "A ARG 2335": "NH1" <-> "NH2" Residue "A GLU 2346": "OE1" <-> "OE2" Residue "A PHE 2407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2465": "OD1" <-> "OD2" Residue "A PHE 2467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2470": "OE1" <-> "OE2" Residue "A PHE 2541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2580": "NH1" <-> "NH2" Residue "A TYR 2607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2627": "NH1" <-> "NH2" Residue "A PHE 2630": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2694": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2697": "NH1" <-> "NH2" Residue "A GLU 2726": "OE1" <-> "OE2" Residue "A PHE 2728": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2736": "OE1" <-> "OE2" Residue "A GLU 2738": "OE1" <-> "OE2" Residue "A ARG 2739": "NH1" <-> "NH2" Residue "A GLU 2764": "OE1" <-> "OE2" Residue "A GLU 2770": "OE1" <-> "OE2" Residue "A GLU 2772": "OE1" <-> "OE2" Residue "A GLU 2780": "OE1" <-> "OE2" Residue "A GLU 2803": "OE1" <-> "OE2" Residue "A GLU 2816": "OE1" <-> "OE2" Residue "A TYR 2828": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2854": "NH1" <-> "NH2" Residue "A ARG 2860": "NH1" <-> "NH2" Residue "A GLU 2904": "OE1" <-> "OE2" Residue "A ASP 2905": "OD1" <-> "OD2" Residue "A GLU 2933": "OE1" <-> "OE2" Residue "A GLU 2936": "OE1" <-> "OE2" Residue "A TYR 2937": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2970": "OE1" <-> "OE2" Residue "A ASP 2977": "OD1" <-> "OD2" Residue "A GLU 2982": "OE1" <-> "OE2" Residue "A TYR 2986": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2987": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 3013": "NH1" <-> "NH2" Residue "A GLU 3021": "OE1" <-> "OE2" Residue "A GLU 3032": "OE1" <-> "OE2" Residue "A GLU 3033": "OE1" <-> "OE2" Residue "A GLU 3040": "OE1" <-> "OE2" Residue "A PHE 3046": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 3054": "OE1" <-> "OE2" Residue "A GLU 3076": "OE1" <-> "OE2" Residue "A TYR 3099": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 3109": "OE1" <-> "OE2" Residue "A GLU 3197": "OE1" <-> "OE2" Residue "A PHE 3243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 3244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 3258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 3268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 3274": "OD1" <-> "OD2" Residue "A PHE 3286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 3293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 3294": "OE1" <-> "OE2" Residue "A GLU 3307": "OE1" <-> "OE2" Residue "A TYR 3342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 3416": "NH1" <-> "NH2" Residue "A GLU 3425": "OE1" <-> "OE2" Residue "A ARG 3428": "NH1" <-> "NH2" Residue "A PHE 3453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 3502": "OE1" <-> "OE2" Residue "A ARG 3542": "NH1" <-> "NH2" Residue "A PHE 3567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 3586": "OE1" <-> "OE2" Residue "A GLU 3620": "OE1" <-> "OE2" Residue "A PHE 3621": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 3628": "NH1" <-> "NH2" Residue "A GLU 3637": "OE1" <-> "OE2" Residue "A PHE 3647": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 3671": "OE1" <-> "OE2" Residue "A ASP 3680": "OD1" <-> "OD2" Residue "A GLU 3697": "OE1" <-> "OE2" Residue "A ARG 3698": "NH1" <-> "NH2" Residue "A GLU 3711": "OE1" <-> "OE2" Residue "A GLU 3745": "OE1" <-> "OE2" Residue "A TYR 3747": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 3790": "OE1" <-> "OE2" Residue "A ARG 3798": "NH1" <-> "NH2" Residue "A GLU 3820": "OE1" <-> "OE2" Residue "A GLU 3870": "OE1" <-> "OE2" Residue "A PHE 3919": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 3944": "NH1" <-> "NH2" Residue "A GLU 3981": "OE1" <-> "OE2" Residue "A ARG 4028": "NH1" <-> "NH2" Residue "A GLU 4055": "OE1" <-> "OE2" Residue "A ARG 4071": "NH1" <-> "NH2" Residue "A GLU 4077": "OE1" <-> "OE2" Residue "A PHE 4109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 4116": "OE1" <-> "OE2" Residue "A PHE 4131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 4143": "NH1" <-> "NH2" Residue "A TYR 4159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 4172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 4236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 4264": "OE1" <-> "OE2" Residue "A GLU 4292": "OE1" <-> "OE2" Residue "A GLU 4317": "OE1" <-> "OE2" Residue "A GLU 4318": "OE1" <-> "OE2" Residue "A ARG 4341": "NH1" <-> "NH2" Residue "A ARG 4358": "NH1" <-> "NH2" Residue "A ARG 4377": "NH1" <-> "NH2" Residue "A PHE 4462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 4480": "OE1" <-> "OE2" Residue "A GLU 4494": "OE1" <-> "OE2" Residue "A ARG 4510": "NH1" <-> "NH2" Residue "A GLU 4513": "OE1" <-> "OE2" Residue "A GLU 4522": "OE1" <-> "OE2" Residue "A ASP 4552": "OD1" <-> "OD2" Residue "A ARG 4586": "NH1" <-> "NH2" Residue "A PHE 4593": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 443": "OE1" <-> "OE2" Residue "B GLU 464": "OE1" <-> "OE2" Residue "B PHE 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 518": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 533": "NH1" <-> "NH2" Residue "B GLU 549": "OE1" <-> "OE2" Residue "B ARG 596": "NH1" <-> "NH2" Residue "B ARG 616": "NH1" <-> "NH2" Residue "B GLU 618": "OE1" <-> "OE2" Residue "B GLU 693": "OE1" <-> "OE2" Residue "B ARG 709": "NH1" <-> "NH2" Residue "B ARG 756": "NH1" <-> "NH2" Residue "B GLU 803": "OE1" <-> "OE2" Residue "B ARG 804": "NH1" <-> "NH2" Residue "B ARG 807": "NH1" <-> "NH2" Residue "B TYR 814": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 869": "OE1" <-> "OE2" Residue "B GLU 916": "OE1" <-> "OE2" Residue "B ARG 931": "NH1" <-> "NH2" Residue "B PHE 955": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 960": "NH1" <-> "NH2" Residue "B GLU 977": "OE1" <-> "OE2" Residue "B ASP 991": "OD1" <-> "OD2" Residue "B PHE 1101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1203": "NH1" <-> "NH2" Residue "B ARG 1500": "NH1" <-> "NH2" Residue "B GLU 1502": "OE1" <-> "OE2" Residue "B GLU 1571": "OE1" <-> "OE2" Residue "B GLU 1576": "OE1" <-> "OE2" Residue "B ARG 1577": "NH1" <-> "NH2" Residue "B ARG 1578": "NH1" <-> "NH2" Residue "B ARG 1608": "NH1" <-> "NH2" Residue "B GLU 1632": "OE1" <-> "OE2" Residue "B GLU 1654": "OE1" <-> "OE2" Residue "B PHE 1676": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1690": "OE1" <-> "OE2" Residue "B GLU 1699": "OE1" <-> "OE2" Residue "B GLU 1702": "OE1" <-> "OE2" Residue "B GLU 1723": "OE1" <-> "OE2" Residue "B GLU 1740": "OE1" <-> "OE2" Residue "B ARG 1744": "NH1" <-> "NH2" Residue "B GLU 1769": "OE1" <-> "OE2" Residue "B ARG 1784": "NH1" <-> "NH2" Residue "B GLU 1802": "OE1" <-> "OE2" Residue "B GLU 1813": "OE1" <-> "OE2" Residue "B GLU 1826": "OE1" <-> "OE2" Residue "B ARG 1840": "NH1" <-> "NH2" Residue "B ARG 1873": "NH1" <-> "NH2" Residue "B ARG 1882": "NH1" <-> "NH2" Residue "B PHE 1925": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1954": "OE1" <-> "OE2" Residue "B GLU 1961": "OE1" <-> "OE2" Residue "B GLU 1979": "OE1" <-> "OE2" Residue "B PHE 1986": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1988": "OE1" <-> "OE2" Residue "B GLU 1991": "OE1" <-> "OE2" Residue "B PHE 2001": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 2011": "NH1" <-> "NH2" Residue "B ARG 2049": "NH1" <-> "NH2" Residue "B PHE 2055": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 2077": "NH1" <-> "NH2" Residue "B ARG 2091": "NH1" <-> "NH2" Residue "B ASP 2099": "OD1" <-> "OD2" Residue "B ARG 2104": "NH1" <-> "NH2" Residue "B ARG 2107": "NH1" <-> "NH2" Residue "B ARG 2124": "NH1" <-> "NH2" Residue "B GLU 2222": "OE1" <-> "OE2" Residue "B PHE 2224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 2252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 2273": "OE1" <-> "OE2" Residue "B PHE 2294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 2304": "OE1" <-> "OE2" Residue "B PHE 2323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 2341": "NH1" <-> "NH2" Residue "B TYR 2359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 2425": "OE1" <-> "OE2" Residue "B GLU 2428": "OE1" <-> "OE2" Residue "B GLU 2433": "OE1" <-> "OE2" Residue "B PHE 2436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 2480": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 2483": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 2488": "OE1" <-> "OE2" Residue "B PHE 2507": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 2531": "NH1" <-> "NH2" Residue "B PHE 2570": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 2592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2650": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 2666": "NH1" <-> "NH2" Residue "B PHE 2716": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2728": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2735": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 2737": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 2746": "NH1" <-> "NH2" Residue "B GLU 2749": "OE1" <-> "OE2" Residue "B ARG 2753": "NH1" <-> "NH2" Residue "B TYR 2759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 2769": "NH1" <-> "NH2" Residue "B GLU 2774": "OE1" <-> "OE2" Residue "B GLU 2787": "OE1" <-> "OE2" Residue "B PHE 2791": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 2794": "NH1" <-> "NH2" Residue "B GLU 2806": "OE1" <-> "OE2" Residue "B GLU 2816": "OE1" <-> "OE2" Residue "B TYR 2834": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 2844": "NH1" <-> "NH2" Residue "B GLU 2855": "OE1" <-> "OE2" Residue "B GLU 2870": "OE1" <-> "OE2" Residue "B ARG 2877": "NH1" <-> "NH2" Residue "B PHE 2920": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 2956": "OE1" <-> "OE2" Residue "B PHE 2975": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 3030": "NH1" <-> "NH2" Residue "B PHE 3036": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 3062": "NH1" <-> "NH2" Residue "B GLU 3072": "OE1" <-> "OE2" Residue "B GLU 3094": "OE1" <-> "OE2" Residue "B GLU 3100": "OE1" <-> "OE2" Residue "B TYR 3103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 3111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 3117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 3124": "OE1" <-> "OE2" Residue "B ARG 3135": "NH1" <-> "NH2" Residue "B TYR 3136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 3155": "OE1" <-> "OE2" Residue "B GLU 3308": "OE1" <-> "OE2" Residue "B PHE 3346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 3350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 3406": "OE1" <-> "OE2" Residue "B GLU 3490": "OE1" <-> "OE2" Residue "B GLU 3493": "OE1" <-> "OE2" Residue "B ARG 3530": "NH1" <-> "NH2" Residue "B GLU 3585": "OE1" <-> "OE2" Residue "B ARG 3596": "NH1" <-> "NH2" Residue "B TYR 3616": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 3620": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 3654": "OE1" <-> "OE2" Residue "B GLU 3665": "OE1" <-> "OE2" Residue "B GLU 3670": "OE1" <-> "OE2" Residue "B GLU 3682": "OE1" <-> "OE2" Residue "B TYR 3747": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 3782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 3792": "NH1" <-> "NH2" Residue "B ARG 3831": "NH1" <-> "NH2" Residue "B ARG 3856": "NH1" <-> "NH2" Residue "B PHE 3886": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 3893": "OE1" <-> "OE2" Residue "B ARG 3897": "NH1" <-> "NH2" Residue "B GLU 3908": "OE1" <-> "OE2" Residue "B ARG 3918": "NH1" <-> "NH2" Residue "B PHE 3924": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 3931": "NH1" <-> "NH2" Residue "B ARG 3947": "NH1" <-> "NH2" Residue "B GLU 3967": "OE1" <-> "OE2" Residue "B PHE 3985": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 3996": "OE1" <-> "OE2" Residue "B GLU 3998": "OE1" <-> "OE2" Residue "B PHE 4013": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 4031": "OE1" <-> "OE2" Residue "B GLU 4035": "OE1" <-> "OE2" Residue "B GLU 4055": "OE1" <-> "OE2" Residue "B GLU 4064": "OE1" <-> "OE2" Residue "B PHE 4075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 4079": "OE1" <-> "OE2" Residue "B GLU 4117": "OE1" <-> "OE2" Residue "B GLU 4118": "OE1" <-> "OE2" Residue "B PHE 4136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 4144": "NH1" <-> "NH2" Residue "B PHE 4146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 4171": "NH1" <-> "NH2" Residue "B TYR 4172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 4195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 4206": "NH1" <-> "NH2" Residue "B GLU 4231": "OE1" <-> "OE2" Residue "B TYR 4248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 4253": "OE1" <-> "OE2" Residue "B GLU 4319": "OE1" <-> "OE2" Residue "B GLU 4322": "OE1" <-> "OE2" Residue "B GLU 4331": "OE1" <-> "OE2" Residue "B PHE 4349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 4362": "OE1" <-> "OE2" Residue "B GLU 4368": "OE1" <-> "OE2" Residue "B ARG 4395": "NH1" <-> "NH2" Residue "B ARG 4421": "NH1" <-> "NH2" Residue "B PHE 4444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 4460": "NH1" <-> "NH2" Residue "B GLU 4482": "OE1" <-> "OE2" Residue "B GLU 4489": "OE1" <-> "OE2" Residue "B TYR 4492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 4494": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 4499": "OE1" <-> "OE2" Residue "B ARG 4502": "NH1" <-> "NH2" Residue "B TYR 4505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 4512": "OE1" <-> "OE2" Residue "B TYR 4548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 4553": "NH1" <-> "NH2" Residue "B ARG 4570": "NH1" <-> "NH2" Residue "B GLU 4584": "OE1" <-> "OE2" Residue "C PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 68": "OE1" <-> "OE2" Residue "C TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 110": "OD1" <-> "OD2" Residue "C TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 137": "OE1" <-> "OE2" Residue "C TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 186": "OE1" <-> "OE2" Residue "C ARG 189": "NH1" <-> "NH2" Residue "C ARG 200": "NH1" <-> "NH2" Residue "C PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 233": "OD1" <-> "OD2" Residue "C ASP 241": "OD1" <-> "OD2" Residue "C PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 309": "OD1" <-> "OD2" Residue "C ARG 319": "NH1" <-> "NH2" Residue "C PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 840": "NH1" <-> "NH2" Residue "C GLU 842": "OE1" <-> "OE2" Residue "C GLU 865": "OE1" <-> "OE2" Residue "C PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 893": "OE1" <-> "OE2" Residue "C TYR 951": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 978": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 984": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1025": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1056": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1061": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1069": "NH1" <-> "NH2" Residue "C GLU 1070": "OE1" <-> "OE2" Residue "C GLU 1122": "OE1" <-> "OE2" Residue "C GLU 1127": "OE1" <-> "OE2" Residue "C ARG 1134": "NH1" <-> "NH2" Residue "C PHE 1141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1172": "OD1" <-> "OD2" Residue "C ARG 1184": "NH1" <-> "NH2" Residue "C GLU 1212": "OE1" <-> "OE2" Residue "C TYR 1214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1244": "OE1" <-> "OE2" Residue "C GLU 1267": "OE1" <-> "OE2" Residue "C GLU 1287": "OE1" <-> "OE2" Residue "C ARG 1308": "NH1" <-> "NH2" Residue "C ARG 1322": "NH1" <-> "NH2" Residue "C GLU 1337": "OE1" <-> "OE2" Residue "C PHE 1339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1432": "OE1" <-> "OE2" Residue "C TYR 1435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1436": "OE1" <-> "OE2" Residue "C ARG 1459": "NH1" <-> "NH2" Residue "C PHE 1486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1534": "OE1" <-> "OE2" Residue "C ASP 1565": "OD1" <-> "OD2" Residue "C PHE 1623": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1631": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1654": "OE1" <-> "OE2" Residue "C ARG 1677": "NH1" <-> "NH2" Residue "C TYR 1726": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1743": "NH1" <-> "NH2" Residue "C TYR 1818": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1825": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1844": "OE1" <-> "OE2" Residue "C TYR 1900": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1916": "OE1" <-> "OE2" Residue "C PHE 1940": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1950": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1962": "OE1" <-> "OE2" Residue "C GLU 1988": "OE1" <-> "OE2" Residue "C GLU 2033": "OE1" <-> "OE2" Residue "C TYR 2045": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 2050": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 2172": "NH1" <-> "NH2" Residue "C GLU 2179": "OE1" <-> "OE2" Residue "C ARG 2186": "NH1" <-> "NH2" Residue "C ARG 2200": "NH1" <-> "NH2" Residue "C PHE 2206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 2232": "OE1" <-> "OE2" Residue "C ARG 2246": "NH1" <-> "NH2" Residue "C PHE 2278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 2302": "NH1" <-> "NH2" Residue "C TYR 2304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 2344": "NH1" <-> "NH2" Residue "C ARG 2347": "NH1" <-> "NH2" Residue "C TYR 2390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 2403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 2411": "OE1" <-> "OE2" Residue "C ARG 2426": "NH1" <-> "NH2" Residue "C ARG 2457": "NH1" <-> "NH2" Residue "C ARG 2469": "NH1" <-> "NH2" Residue "C PHE 2476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 2521": "OE1" <-> "OE2" Residue "C PHE 2524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2530": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 2543": "OE1" <-> "OE2" Residue "C PHE 2548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 2565": "OE1" <-> "OE2" Residue "C GLU 2567": "OE1" <-> "OE2" Residue "C ARG 2568": "NH1" <-> "NH2" Residue "C ARG 2569": "NH1" <-> "NH2" Residue "C TYR 2570": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2585": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 2593": "NH1" <-> "NH2" Residue "C ASP 2705": "OD1" <-> "OD2" Residue "C PHE 2706": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2712": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 2721": "OE1" <-> "OE2" Residue "C TYR 2728": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 2736": "OE1" <-> "OE2" Residue "C GLU 2763": "OE1" <-> "OE2" Residue "C PHE 2764": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2771": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 2792": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 2834": "NH1" <-> "NH2" Residue "C PHE 2934": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2941": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 3007": "NH1" <-> "NH2" Residue "C GLU 3050": "OE1" <-> "OE2" Residue "C TYR 3053": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 3058": "OE1" <-> "OE2" Residue "C ARG 3142": "NH1" <-> "NH2" Residue "C ARG 3144": "NH1" <-> "NH2" Residue "C TYR 3174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 3205": "OE1" <-> "OE2" Residue "C GLU 3219": "OE1" <-> "OE2" Residue "C GLU 3222": "OE1" <-> "OE2" Residue "C ARG 3261": "NH1" <-> "NH2" Residue "C ARG 3388": "NH1" <-> "NH2" Residue "C GLU 3391": "OE1" <-> "OE2" Residue "C ARG 3405": "NH1" <-> "NH2" Residue "C GLU 3410": "OE1" <-> "OE2" Residue "C ARG 3427": "NH1" <-> "NH2" Residue "C GLU 3435": "OE1" <-> "OE2" Residue "C PHE 3476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 3479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 3494": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 3496": "OE1" <-> "OE2" Residue "C GLU 3497": "OE1" <-> "OE2" Residue "C GLU 3500": "OE1" <-> "OE2" Residue "C ARG 3524": "NH1" <-> "NH2" Residue "C ARG 3527": "NH1" <-> "NH2" Residue "C GLU 3542": "OE1" <-> "OE2" Residue "C GLU 3546": "OE1" <-> "OE2" Residue "C PHE 3550": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 3554": "OE1" <-> "OE2" Residue "C PHE 3566": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 3570": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 3580": "OE1" <-> "OE2" Residue "C PHE 3586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 3594": "NH1" <-> "NH2" Residue "C PHE 3595": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 3607": "NH1" <-> "NH2" Residue "C GLU 3664": "OE1" <-> "OE2" Residue "C GLU 3678": "OE1" <-> "OE2" Residue "C GLU 3709": "OE1" <-> "OE2" Residue "C PHE 3710": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 3720": "OE1" <-> "OE2" Residue "C ARG 3748": "NH1" <-> "NH2" Residue "C TYR 3765": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 3771": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 3780": "NH1" <-> "NH2" Residue "C GLU 3785": "OE1" <-> "OE2" Residue "C TYR 3804": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 3812": "OE1" <-> "OE2" Residue "C ASP 3833": "OD1" <-> "OD2" Residue "C TYR 3837": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 3840": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 3842": "OE1" <-> "OE2" Residue "C GLU 3848": "OE1" <-> "OE2" Residue "C GLU 3877": "OE1" <-> "OE2" Residue "C PHE 3901": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 3950": "NH1" <-> "NH2" Residue "C PHE 3985": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 3994": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 3999": "OE1" <-> "OE2" Residue "C TYR 4092": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 4100": "OE1" <-> "OE2" Residue "C TYR 4129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 4147": "OE1" <-> "OE2" Residue "D GLU 65": "OE1" <-> "OE2" Residue "D ARG 94": "NH1" <-> "NH2" Residue "D GLU 100": "OE1" <-> "OE2" Residue "D GLU 122": "OE1" <-> "OE2" Residue "D GLU 148": "OE1" <-> "OE2" Residue "D GLU 156": "OE1" <-> "OE2" Residue "D GLU 172": "OE1" <-> "OE2" Residue "D GLU 203": "OE1" <-> "OE2" Residue "D GLU 249": "OE1" <-> "OE2" Residue "D ARG 265": "NH1" <-> "NH2" Residue "D ARG 325": "NH1" <-> "NH2" Residue "D ARG 422": "NH1" <-> "NH2" Residue "D GLU 436": "OE1" <-> "OE2" Residue "D GLU 437": "OE1" <-> "OE2" Residue "D GLU 477": "OE1" <-> "OE2" Residue "D ARG 514": "NH1" <-> "NH2" Residue "D GLU 648": "OE1" <-> "OE2" Residue "E ARG 26": "NH1" <-> "NH2" Residue "E GLU 58": "OE1" <-> "OE2" Residue "E GLU 88": "OE1" <-> "OE2" Residue "E GLU 130": "OE1" <-> "OE2" Residue "E GLU 136": "OE1" <-> "OE2" Residue "E GLU 158": "OE1" <-> "OE2" Residue "E GLU 166": "OE1" <-> "OE2" Residue "E GLU 297": "OE1" <-> "OE2" Residue "E GLU 312": "OE1" <-> "OE2" Residue "E GLU 315": "OE1" <-> "OE2" Residue "E GLU 354": "OE1" <-> "OE2" Residue "E ARG 365": "NH1" <-> "NH2" Residue "E GLU 507": "OE1" <-> "OE2" Residue "F GLU 18": "OE1" <-> "OE2" Residue "F GLU 71": "OE1" <-> "OE2" Residue "F GLU 75": "OE1" <-> "OE2" Residue "F ARG 78": "NH1" <-> "NH2" Residue "G ARG 87": "NH1" <-> "NH2" Residue "H GLU 40": "OE1" <-> "OE2" Residue "H ARG 73": "NH1" <-> "NH2" Residue "I GLU 14": "OE1" <-> "OE2" Residue "J ARG 25": "NH1" <-> "NH2" Residue "J ARG 42": "NH1" <-> "NH2" Residue "J GLU 43": "OE1" <-> "OE2" Residue "J ARG 55": "NH1" <-> "NH2" Residue "K GLU 14": "OE1" <-> "OE2" Residue "K GLU 34": "OE1" <-> "OE2" Residue "L GLU 44": "OE1" <-> "OE2" Residue "L GLU 50": "OE1" <-> "OE2" Residue "M GLU 4": "OE1" <-> "OE2" Residue "M GLU 6": "OE1" <-> "OE2" Residue "M GLU 34": "OE1" <-> "OE2" Residue "N ARG 56": "NH1" <-> "NH2" Residue "O ARG 15": "NH1" <-> "NH2" Residue "O GLU 16": "OE1" <-> "OE2" Residue "O TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 78": "NH1" <-> "NH2" Residue "O PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 96": "NH1" <-> "NH2" Residue "O ASP 108": "OD1" <-> "OD2" Residue "Q ARG 128": "NH1" <-> "NH2" Time to flip residues: 0.25s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 119573 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 33975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4453, 33975 Classifications: {'peptide': 4453} Incomplete info: {'backbone_only': 9, 'truncation_to_alanine': 608} Link IDs: {'CIS': 1, 'PTRANS': 164, 'TRANS': 4287} Chain breaks: 27 Unresolved chain link angles: 18 Unresolved non-hydrogen bonds: 2363 Unresolved non-hydrogen angles: 2993 Unresolved non-hydrogen dihedrals: 1989 Unresolved non-hydrogen chiralities: 175 Planarities with less than four sites: {'GLN:plan1': 44, 'HIS:plan': 11, 'TYR:plan': 25, 'ASN:plan1': 47, 'TRP:plan': 11, 'ASP:plan': 44, 'PHE:plan': 32, 'GLU:plan': 58, 'ARG:plan': 28} Unresolved non-hydrogen planarities: 1344 Chain: "B" Number of atoms: 34751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4524, 34751 Classifications: {'peptide': 4524} Incomplete info: {'backbone_only': 3, 'truncation_to_alanine': 552} Link IDs: {'CIS': 2, 'PTRANS': 170, 'TRANS': 4351} Chain breaks: 8 Unresolved chain link angles: 19 Unresolved non-hydrogen bonds: 2074 Unresolved non-hydrogen angles: 2655 Unresolved non-hydrogen dihedrals: 1750 Unresolved non-hydrogen chiralities: 181 Planarities with less than four sites: {'GLN:plan1': 37, 'ARG:plan': 11, 'TYR:plan': 25, 'ASN:plan1': 43, 'TRP:plan': 11, 'HIS:plan': 12, 'PHE:plan': 31, 'GLU:plan': 38, 'ASP:plan': 36} Unresolved non-hydrogen planarities: 1112 Chain: "C" Number of atoms: 30427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3947, 30427 Classifications: {'peptide': 3947} Incomplete info: {'truncation_to_alanine': 366} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 156, 'TRANS': 3788} Chain breaks: 11 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 1281 Unresolved non-hydrogen angles: 1602 Unresolved non-hydrogen dihedrals: 1042 Unresolved non-hydrogen chiralities: 113 Planarities with less than four sites: {'GLN:plan1': 17, 'TYR:plan': 9, 'ASN:plan1': 30, 'TRP:plan': 2, 'ASP:plan': 24, 'PHE:plan': 17, 'GLU:plan': 51, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 657 Chain: "D" Number of atoms: 4680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4680 Classifications: {'peptide': 579} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 25, 'TRANS': 553} Chain breaks: 2 Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 2, 'ASN:plan1': 1, 'TYR:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 43 Chain: "E" Number of atoms: 4440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 555, 4440 Classifications: {'peptide': 555} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 26, 'TRANS': 528} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "F" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 996 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 2, 'TRANS': 125} Chain: "G" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1024 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 3, 'TRANS': 147} Unresolved non-hydrogen bonds: 205 Unresolved non-hydrogen angles: 249 Unresolved non-hydrogen dihedrals: 171 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 112 Chain: "H" Number of atoms: 750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 750 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 89} Chain: "I" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 827 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 2, 'TRANS': 103} Chain: "J" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 807 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "K" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 754 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "L" Number of atoms: 855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 855 Classifications: {'peptide': 111} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 6, 'TRANS': 104} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 18 Chain: "M" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 735 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "N" Number of atoms: 852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 852 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'TRANS': 113} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 27 Chain: "O" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 994 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "P" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 541 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 103} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 102} Chain breaks: 1 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 373 Unresolved non-hydrogen angles: 482 Unresolved non-hydrogen dihedrals: 313 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1, 'TYR:plan': 6, 'ASN:plan1': 7, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 7, 'GLU:plan': 6, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 188 Chain: "Q" Number of atoms: 1006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1006 Classifications: {'peptide': 192} Incomplete info: {'truncation_to_alanine': 165} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 182} Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 532 Unresolved non-hydrogen angles: 679 Unresolved non-hydrogen dihedrals: 421 Unresolved non-hydrogen chiralities: 64 Planarities with less than four sites: {'GLN:plan1': 6, 'TYR:plan': 3, 'ASN:plan1': 17, 'TRP:plan': 2, 'ASP:plan': 10, 'PHE:plan': 2, 'GLU:plan': 15, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 231 Chain: "R" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 895 Classifications: {'peptide': 150} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'TRANS': 149} Unresolved non-hydrogen bonds: 449 Unresolved non-hydrogen angles: 569 Unresolved non-hydrogen dihedrals: 360 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 5, 'ASN:plan1': 8, 'ASP:plan': 18, 'PHE:plan': 8, 'GLU:plan': 16, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 255 Chain: "A" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 88 Unusual residues: {' MG': 3, 'ADP': 2, 'ATP': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 88 Unusual residues: {' MG': 3, 'ADP': 2, 'ATP': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "C" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 88 Unusual residues: {' MG': 3, 'ADP': 2, 'ATP': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Time building chain proxies: 43.93, per 1000 atoms: 0.37 Number of scatterers: 119573 At special positions: 0 Unit cell: (391.902, 434.558, 354.578, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 546 16.00 P 21 15.00 Mg 9 11.99 O 22626 8.00 N 20431 7.00 C 75784 6.00 H 156 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS N 68 " - pdb=" SG CYS O 101 " distance=2.04 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 Atom "HETATMA0F2T O3A ADP C4702 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=7, symmetry=0 Number of additional bonds: simple=7, symmetry=0 Coordination: Other bonds: Time building additional restraints: 37.40 Conformation dependent library (CDL) restraints added in 15.9 seconds 30888 Ramachandran restraints generated. 15444 Oldfield, 0 Emsley, 15444 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 29688 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 541 helices and 89 sheets defined 60.8% alpha, 9.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 85.44 Creating SS restraints... Processing helix chain 'A' and resid 8 through 25 removed outlier: 4.128A pdb=" N TRP A 12 " --> pdb=" O LYS A 8 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N LEU A 21 " --> pdb=" O ILE A 17 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLN A 22 " --> pdb=" O CYS A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 41 removed outlier: 4.926A pdb=" N LYS A 36 " --> pdb=" O PHE A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 53 Processing helix chain 'A' and resid 112 through 118 removed outlier: 3.561A pdb=" N ASN A 116 " --> pdb=" O ASP A 112 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N ILE A 118 " --> pdb=" O ASN A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 150 removed outlier: 3.639A pdb=" N LEU A 131 " --> pdb=" O THR A 127 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ALA A 133 " --> pdb=" O PRO A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 182 Processing helix chain 'A' and resid 197 through 202 removed outlier: 4.748A pdb=" N SER A 201 " --> pdb=" O ILE A 197 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N GLU A 202 " --> pdb=" O SER A 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 197 through 202' Processing helix chain 'A' and resid 203 through 224 removed outlier: 3.584A pdb=" N GLN A 223 " --> pdb=" O LEU A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 262 Processing helix chain 'A' and resid 263 through 276 removed outlier: 3.576A pdb=" N LYS A 269 " --> pdb=" O PHE A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 287 removed outlier: 3.915A pdb=" N GLN A 281 " --> pdb=" O ASN A 277 " (cutoff:3.500A) Proline residue: A 283 - end of helix Processing helix chain 'A' and resid 306 through 324 Processing helix chain 'A' and resid 331 through 348 Proline residue: A 340 - end of helix removed outlier: 3.768A pdb=" N LYS A 347 " --> pdb=" O MET A 343 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N MET A 348 " --> pdb=" O ASN A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 384 Processing helix chain 'A' and resid 396 through 401 removed outlier: 5.124A pdb=" N ASP A 401 " --> pdb=" O ILE A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 438 removed outlier: 3.658A pdb=" N SER A 411 " --> pdb=" O GLU A 407 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N CYS A 412 " --> pdb=" O VAL A 408 " (cutoff:3.500A) Proline residue: A 434 - end of helix removed outlier: 3.547A pdb=" N LYS A 437 " --> pdb=" O MET A 433 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N THR A 438 " --> pdb=" O PRO A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 473 Processing helix chain 'A' and resid 478 through 503 removed outlier: 3.977A pdb=" N LEU A 502 " --> pdb=" O LYS A 498 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N LEU A 503 " --> pdb=" O GLY A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 509 Processing helix chain 'A' and resid 511 through 540 removed outlier: 3.755A pdb=" N VAL A 515 " --> pdb=" O ASP A 511 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL A 519 " --> pdb=" O VAL A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 556 removed outlier: 3.567A pdb=" N LEU A 549 " --> pdb=" O SER A 545 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N HIS A 550 " --> pdb=" O LEU A 546 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N SER A 554 " --> pdb=" O HIS A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 591 Processing helix chain 'A' and resid 602 through 625 Proline residue: A 620 - end of helix Proline residue: A 625 - end of helix Processing helix chain 'A' and resid 632 through 670 removed outlier: 3.508A pdb=" N ALA A 668 " --> pdb=" O GLU A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 706 removed outlier: 3.570A pdb=" N ASP A 703 " --> pdb=" O ALA A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 745 removed outlier: 3.636A pdb=" N ILE A 716 " --> pdb=" O SER A 712 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ASP A 721 " --> pdb=" O LEU A 717 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N LYS A 722 " --> pdb=" O LEU A 718 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N LYS A 745 " --> pdb=" O ASN A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 753 removed outlier: 4.103A pdb=" N ASN A 750 " --> pdb=" O PRO A 746 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LEU A 751 " --> pdb=" O ILE A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 769 removed outlier: 3.512A pdb=" N LEU A 759 " --> pdb=" O HIS A 755 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASP A 760 " --> pdb=" O ILE A 756 " (cutoff:3.500A) Proline residue: A 765 - end of helix Processing helix chain 'A' and resid 776 through 816 removed outlier: 3.617A pdb=" N ARG A 805 " --> pdb=" O ILE A 801 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ILE A 806 " --> pdb=" O ILE A 802 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N GLU A 807 " --> pdb=" O GLU A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 869 removed outlier: 3.605A pdb=" N SER A 850 " --> pdb=" O ASP A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 913 Processing helix chain 'A' and resid 948 through 968 removed outlier: 3.619A pdb=" N LYS A 967 " --> pdb=" O LEU A 963 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N HIS A 968 " --> pdb=" O ARG A 964 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 993 removed outlier: 4.636A pdb=" N MET A 988 " --> pdb=" O THR A 984 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N LYS A 993 " --> pdb=" O ILE A 989 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 1022 removed outlier: 3.516A pdb=" N ILE A1006 " --> pdb=" O LEU A1002 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN A1007 " --> pdb=" O THR A1003 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N PHE A1016 " --> pdb=" O LYS A1012 " (cutoff:3.500A) Processing helix chain 'A' and resid 1031 through 1042 removed outlier: 3.914A pdb=" N GLY A1042 " --> pdb=" O PHE A1038 " (cutoff:3.500A) Processing helix chain 'A' and resid 1044 through 1065 removed outlier: 4.017A pdb=" N TYR A1048 " --> pdb=" O THR A1044 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU A1049 " --> pdb=" O LEU A1045 " (cutoff:3.500A) Processing helix chain 'A' and resid 1079 through 1124 removed outlier: 3.619A pdb=" N SER A1084 " --> pdb=" O ASN A1080 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU A1107 " --> pdb=" O ARG A1103 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS A1124 " --> pdb=" O THR A1120 " (cutoff:3.500A) Processing helix chain 'A' and resid 1132 through 1137 removed outlier: 3.556A pdb=" N MET A1136 " --> pdb=" O LEU A1132 " (cutoff:3.500A) Processing helix chain 'A' and resid 1139 through 1153 removed outlier: 3.551A pdb=" N ASP A1150 " --> pdb=" O GLN A1146 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N MET A1151 " --> pdb=" O ALA A1147 " (cutoff:3.500A) Processing helix chain 'A' and resid 1159 through 1164 Processing helix chain 'A' and resid 1199 through 1212 Processing helix chain 'A' and resid 1246 through 1274 removed outlier: 4.261A pdb=" N LEU A1272 " --> pdb=" O ARG A1268 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE A1273 " --> pdb=" O GLY A1269 " (cutoff:3.500A) Processing helix chain 'A' and resid 1278 through 1317 Processing helix chain 'A' and resid 1324 through 1342 removed outlier: 5.659A pdb=" N GLU A1328 " --> pdb=" O ALA A1324 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY A1331 " --> pdb=" O GLU A1327 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY A1334 " --> pdb=" O ALA A1330 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N CYS A1337 " --> pdb=" O TYR A1333 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N LEU A1340 " --> pdb=" O GLN A1336 " (cutoff:3.500A) Proline residue: A1341 - end of helix Processing helix chain 'A' and resid 1347 through 1368 removed outlier: 4.322A pdb=" N ARG A1351 " --> pdb=" O TRP A1347 " (cutoff:3.500A) Proline residue: A1365 - end of helix Processing helix chain 'A' and resid 1377 through 1388 removed outlier: 3.537A pdb=" N THR A1387 " --> pdb=" O ILE A1383 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASN A1388 " --> pdb=" O LYS A1384 " (cutoff:3.500A) Processing helix chain 'A' and resid 1391 through 1399 Proline residue: A1396 - end of helix Processing helix chain 'A' and resid 1402 through 1408 removed outlier: 3.722A pdb=" N LYS A1408 " --> pdb=" O ILE A1404 " (cutoff:3.500A) Processing helix chain 'A' and resid 1410 through 1444 removed outlier: 5.109A pdb=" N GLN A1444 " --> pdb=" O TRP A1440 " (cutoff:3.500A) Processing helix chain 'A' and resid 1463 through 1485 removed outlier: 5.290A pdb=" N ILE A1467 " --> pdb=" O ILE A1463 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N ARG A1485 " --> pdb=" O PHE A1481 " (cutoff:3.500A) Processing helix chain 'A' and resid 1490 through 1527 removed outlier: 3.597A pdb=" N LYS A1513 " --> pdb=" O ASP A1509 " (cutoff:3.500A) Proline residue: A1523 - end of helix Processing helix chain 'A' and resid 1528 through 1535 removed outlier: 3.782A pdb=" N GLN A1533 " --> pdb=" O ASP A1529 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N MET A1534 " --> pdb=" O ILE A1530 " (cutoff:3.500A) Proline residue: A1535 - end of helix Processing helix chain 'A' and resid 1536 through 1559 removed outlier: 3.670A pdb=" N ASN A1547 " --> pdb=" O GLY A1543 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TRP A1548 " --> pdb=" O ILE A1544 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL A1556 " --> pdb=" O MET A1552 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLU A1557 " --> pdb=" O GLU A1553 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR A1558 " --> pdb=" O LYS A1554 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS A1559 " --> pdb=" O ALA A1555 " (cutoff:3.500A) Processing helix chain 'A' and resid 1560 through 1567 Processing helix chain 'A' and resid 1571 through 1600 Proline residue: A1575 - end of helix Proline residue: A1600 - end of helix Processing helix chain 'A' and resid 1601 through 1606 removed outlier: 3.902A pdb=" N VAL A1605 " --> pdb=" O ARG A1601 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N SER A1606 " --> pdb=" O PHE A1602 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1601 through 1606' Processing helix chain 'A' and resid 1607 through 1617 Processing helix chain 'A' and resid 1619 through 1628 removed outlier: 3.807A pdb=" N ILE A1623 " --> pdb=" O GLU A1619 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLN A1624 " --> pdb=" O PRO A1620 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N GLU A1625 " --> pdb=" O THR A1621 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N ASP A1626 " --> pdb=" O SER A1622 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE A1627 " --> pdb=" O ILE A1623 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N GLU A1628 " --> pdb=" O GLN A1624 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1619 through 1628' Processing helix chain 'A' and resid 1679 through 1706 removed outlier: 3.609A pdb=" N TRP A1683 " --> pdb=" O ASN A1679 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN A1692 " --> pdb=" O GLU A1688 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLN A1704 " --> pdb=" O SER A1700 " (cutoff:3.500A) Processing helix chain 'A' and resid 1710 through 1719 removed outlier: 3.574A pdb=" N SER A1716 " --> pdb=" O LYS A1712 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER A1717 " --> pdb=" O GLU A1713 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N ALA A1719 " --> pdb=" O VAL A1715 " (cutoff:3.500A) Processing helix chain 'A' and resid 1720 through 1745 Processing helix chain 'A' and resid 1748 through 1771 removed outlier: 3.674A pdb=" N LEU A1769 " --> pdb=" O SER A1765 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLU A1770 " --> pdb=" O SER A1766 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ASP A1771 " --> pdb=" O MET A1767 " (cutoff:3.500A) Processing helix chain 'A' and resid 1774 through 1798 removed outlier: 3.518A pdb=" N ARG A1778 " --> pdb=" O GLY A1774 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N HIS A1790 " --> pdb=" O THR A1786 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASP A1797 " --> pdb=" O ASP A1793 " (cutoff:3.500A) Processing helix chain 'A' and resid 1805 through 1812 removed outlier: 3.545A pdb=" N GLN A1809 " --> pdb=" O ASP A1805 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLN A1811 " --> pdb=" O GLU A1807 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N THR A1812 " --> pdb=" O TRP A1808 " (cutoff:3.500A) Processing helix chain 'A' and resid 1848 through 1865 removed outlier: 3.737A pdb=" N ILE A1856 " --> pdb=" O ASP A1852 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR A1857 " --> pdb=" O ARG A1853 " (cutoff:3.500A) Processing helix chain 'A' and resid 1877 through 1890 Processing helix chain 'A' and resid 1903 through 1918 removed outlier: 3.845A pdb=" N ILE A1910 " --> pdb=" O ASP A1906 " (cutoff:3.500A) Processing helix chain 'A' and resid 1931 through 1951 removed outlier: 3.583A pdb=" N SER A1935 " --> pdb=" O LEU A1931 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N VAL A1936 " --> pdb=" O GLU A1932 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N MET A1939 " --> pdb=" O SER A1935 " (cutoff:3.500A) Processing helix chain 'A' and resid 1987 through 1995 removed outlier: 4.298A pdb=" N VAL A1992 " --> pdb=" O GLU A1988 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU A1993 " --> pdb=" O ASN A1989 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N ARG A1995 " --> pdb=" O LYS A1991 " (cutoff:3.500A) Processing helix chain 'A' and resid 2003 through 2016 removed outlier: 3.770A pdb=" N ILE A2007 " --> pdb=" O ASP A2003 " (cutoff:3.500A) Processing helix chain 'A' and resid 2019 through 2038 removed outlier: 3.538A pdb=" N LEU A2023 " --> pdb=" O GLN A2019 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS A2025 " --> pdb=" O ASP A2021 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLU A2036 " --> pdb=" O ARG A2032 " (cutoff:3.500A) Processing helix chain 'A' and resid 2047 through 2066 removed outlier: 3.616A pdb=" N THR A2057 " --> pdb=" O SER A2053 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLN A2064 " --> pdb=" O ASN A2060 " (cutoff:3.500A) Processing helix chain 'A' and resid 2069 through 2086 removed outlier: 3.928A pdb=" N MET A2081 " --> pdb=" O SER A2077 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N SER A2084 " --> pdb=" O ASP A2080 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LYS A2085 " --> pdb=" O MET A2081 " (cutoff:3.500A) Processing helix chain 'A' and resid 2088 through 2103 Proline residue: A2092 - end of helix Proline residue: A2103 - end of helix Processing helix chain 'A' and resid 2113 through 2128 removed outlier: 3.523A pdb=" N LYS A2118 " --> pdb=" O PRO A2114 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS A2119 " --> pdb=" O ASP A2115 " (cutoff:3.500A) Proline residue: A2121 - end of helix removed outlier: 4.005A pdb=" N ALA A2126 " --> pdb=" O GLU A2122 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLU A2127 " --> pdb=" O GLU A2123 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N SER A2128 " --> pdb=" O ILE A2124 " (cutoff:3.500A) Processing helix chain 'A' and resid 2133 through 2150 removed outlier: 3.891A pdb=" N VAL A2149 " --> pdb=" O GLU A2145 " (cutoff:3.500A) Processing helix chain 'A' and resid 2162 through 2178 removed outlier: 3.797A pdb=" N LYS A2176 " --> pdb=" O GLU A2172 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLY A2178 " --> pdb=" O LEU A2174 " (cutoff:3.500A) Processing helix chain 'A' and resid 2187 through 2192 removed outlier: 3.829A pdb=" N ILE A2191 " --> pdb=" O ASN A2187 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N THR A2192 " --> pdb=" O PRO A2188 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2187 through 2192' Processing helix chain 'A' and resid 2193 through 2198 Processing helix chain 'A' and resid 2210 through 2221 removed outlier: 4.378A pdb=" N ASN A2221 " --> pdb=" O ALA A2217 " (cutoff:3.500A) Processing helix chain 'A' and resid 2237 through 2245 removed outlier: 3.762A pdb=" N ILE A2241 " --> pdb=" O ASP A2237 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLU A2242 " --> pdb=" O ALA A2238 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ASN A2243 " --> pdb=" O ILE A2239 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU A2244 " --> pdb=" O TRP A2240 " (cutoff:3.500A) Processing helix chain 'A' and resid 2281 through 2289 removed outlier: 3.646A pdb=" N VAL A2285 " --> pdb=" O SER A2281 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER A2286 " --> pdb=" O PRO A2282 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG A2287 " --> pdb=" O ALA A2283 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N CYS A2288 " --> pdb=" O THR A2284 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N GLY A2289 " --> pdb=" O VAL A2285 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2281 through 2289' Processing helix chain 'A' and resid 2294 through 2315 removed outlier: 4.311A pdb=" N LEU A2298 " --> pdb=" O SER A2294 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY A2299 " --> pdb=" O PRO A2295 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N TYR A2300 " --> pdb=" O THR A2296 " (cutoff:3.500A) removed outlier: 8.389A pdb=" N GLU A2301 " --> pdb=" O ASP A2297 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N ALA A2302 " --> pdb=" O LEU A2298 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLY A2315 " --> pdb=" O ARG A2311 " (cutoff:3.500A) Processing helix chain 'A' and resid 2316 through 2331 removed outlier: 3.595A pdb=" N SER A2320 " --> pdb=" O ARG A2316 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN A2325 " --> pdb=" O ASP A2321 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS A2329 " --> pdb=" O ASN A2325 " (cutoff:3.500A) Processing helix chain 'A' and resid 2335 through 2345 removed outlier: 3.510A pdb=" N LYS A2342 " --> pdb=" O GLU A2338 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N LYS A2345 " --> pdb=" O SER A2341 " (cutoff:3.500A) Processing helix chain 'A' and resid 2352 through 2375 removed outlier: 4.288A pdb=" N TYR A2370 " --> pdb=" O GLY A2366 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N PHE A2371 " --> pdb=" O CYS A2367 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN A2373 " --> pdb=" O GLN A2369 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR A2374 " --> pdb=" O TYR A2370 " (cutoff:3.500A) Processing helix chain 'A' and resid 2379 through 2395 Processing helix chain 'A' and resid 2400 through 2415 removed outlier: 3.527A pdb=" N VAL A2405 " --> pdb=" O ALA A2401 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG A2406 " --> pdb=" O GLN A2402 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU A2412 " --> pdb=" O HIS A2408 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA A2413 " --> pdb=" O GLU A2409 " (cutoff:3.500A) Processing helix chain 'A' and resid 2427 through 2432 removed outlier: 4.178A pdb=" N TYR A2431 " --> pdb=" O THR A2427 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N TYR A2432 " --> pdb=" O VAL A2428 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2427 through 2432' Processing helix chain 'A' and resid 2463 through 2478 removed outlier: 3.528A pdb=" N ARG A2468 " --> pdb=" O LEU A2464 " (cutoff:3.500A) Processing helix chain 'A' and resid 2498 through 2509 removed outlier: 3.525A pdb=" N SER A2502 " --> pdb=" O ALA A2498 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N LYS A2509 " --> pdb=" O LEU A2505 " (cutoff:3.500A) Processing helix chain 'A' and resid 2527 through 2540 removed outlier: 4.685A pdb=" N ASP A2540 " --> pdb=" O GLU A2536 " (cutoff:3.500A) Processing helix chain 'A' and resid 2573 through 2585 Processing helix chain 'A' and resid 2622 through 2630 removed outlier: 3.614A pdb=" N ARG A2627 " --> pdb=" O ASN A2623 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N GLN A2628 " --> pdb=" O ARG A2624 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE A2629 " --> pdb=" O LEU A2625 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N PHE A2630 " --> pdb=" O LYS A2626 " (cutoff:3.500A) Processing helix chain 'A' and resid 2640 through 2653 Proline residue: A2646 - end of helix removed outlier: 4.317A pdb=" N LYS A2653 " --> pdb=" O LYS A2649 " (cutoff:3.500A) Processing helix chain 'A' and resid 2658 through 2663 removed outlier: 3.630A pdb=" N LYS A2663 " --> pdb=" O ASP A2659 " (cutoff:3.500A) Processing helix chain 'A' and resid 2665 through 2683 removed outlier: 4.000A pdb=" N THR A2669 " --> pdb=" O ILE A2665 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N SER A2670 " --> pdb=" O GLU A2666 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ILE A2673 " --> pdb=" O THR A2669 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA A2674 " --> pdb=" O SER A2670 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR A2682 " --> pdb=" O LYS A2678 " (cutoff:3.500A) Processing helix chain 'A' and resid 2695 through 2710 removed outlier: 4.495A pdb=" N LEU A2699 " --> pdb=" O ASN A2695 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N CYS A2709 " --> pdb=" O GLY A2705 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N LYS A2710 " --> pdb=" O ILE A2706 " (cutoff:3.500A) Processing helix chain 'A' and resid 2711 through 2721 Proline residue: A2718 - end of helix Processing helix chain 'A' and resid 2724 through 2745 removed outlier: 3.711A pdb=" N VAL A2730 " --> pdb=" O GLU A2726 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ASP A2743 " --> pdb=" O ARG A2739 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N LYS A2744 " --> pdb=" O VAL A2740 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LEU A2745 " --> pdb=" O LEU A2741 " (cutoff:3.500A) Processing helix chain 'A' and resid 2747 through 2767 removed outlier: 3.739A pdb=" N LYS A2751 " --> pdb=" O ASN A2747 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER A2767 " --> pdb=" O LEU A2763 " (cutoff:3.500A) Processing helix chain 'A' and resid 2769 through 2777 removed outlier: 3.865A pdb=" N GLU A2775 " --> pdb=" O ASN A2771 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS A2776 " --> pdb=" O GLU A2772 " (cutoff:3.500A) Processing helix chain 'A' and resid 2815 through 2833 removed outlier: 3.822A pdb=" N ARG A2820 " --> pdb=" O GLU A2816 " (cutoff:3.500A) Proline residue: A2833 - end of helix Processing helix chain 'A' and resid 2842 through 2859 Proline residue: A2859 - end of helix Processing helix chain 'A' and resid 2872 through 2885 Processing helix chain 'A' and resid 2898 through 2914 Processing helix chain 'A' and resid 2925 through 2930 removed outlier: 4.920A pdb=" N LYS A2930 " --> pdb=" O ASP A2926 " (cutoff:3.500A) Processing helix chain 'A' and resid 2931 through 2944 removed outlier: 4.185A pdb=" N LEU A2935 " --> pdb=" O LYS A2931 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE A2938 " --> pdb=" O PHE A2934 " (cutoff:3.500A) Processing helix chain 'A' and resid 2954 through 2967 removed outlier: 3.752A pdb=" N VAL A2958 " --> pdb=" O ASP A2954 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASP A2962 " --> pdb=" O VAL A2958 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N GLN A2965 " --> pdb=" O GLY A2961 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ALA A2966 " --> pdb=" O ASP A2962 " (cutoff:3.500A) Processing helix chain 'A' and resid 2979 through 2995 removed outlier: 3.637A pdb=" N TRP A2984 " --> pdb=" O GLN A2980 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N THR A2985 " --> pdb=" O SER A2981 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR A2986 " --> pdb=" O GLU A2982 " (cutoff:3.500A) Processing helix chain 'A' and resid 3005 through 3015 removed outlier: 4.302A pdb=" N ARG A3009 " --> pdb=" O GLY A3005 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU A3010 " --> pdb=" O GLN A3006 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG A3013 " --> pdb=" O ARG A3009 " (cutoff:3.500A) Processing helix chain 'A' and resid 3016 through 3021 removed outlier: 6.208A pdb=" N ASN A3020 " --> pdb=" O PRO A3016 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU A3021 " --> pdb=" O ALA A3017 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3016 through 3021' Processing helix chain 'A' and resid 3031 through 3047 removed outlier: 3.600A pdb=" N THR A3041 " --> pdb=" O SER A3037 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N ASP A3047 " --> pdb=" O ILE A3043 " (cutoff:3.500A) Processing helix chain 'A' and resid 3052 through 3078 removed outlier: 3.575A pdb=" N GLN A3057 " --> pdb=" O GLU A3053 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS A3061 " --> pdb=" O GLN A3057 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N HIS A3067 " --> pdb=" O MET A3063 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP A3075 " --> pdb=" O ASN A3071 " (cutoff:3.500A) Processing helix chain 'A' and resid 3088 through 3196 Processing helix chain 'A' and resid 3211 through 3216 removed outlier: 3.927A pdb=" N GLU A3216 " --> pdb=" O VAL A3212 " (cutoff:3.500A) Processing helix chain 'A' and resid 3217 through 3227 Processing helix chain 'A' and resid 3230 through 3245 removed outlier: 3.553A pdb=" N PHE A3243 " --> pdb=" O ALA A3239 " (cutoff:3.500A) Processing helix chain 'A' and resid 3275 through 3284 removed outlier: 3.553A pdb=" N GLN A3279 " --> pdb=" O GLU A3275 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N MET A3284 " --> pdb=" O THR A3280 " (cutoff:3.500A) Processing helix chain 'A' and resid 3285 through 3293 removed outlier: 4.855A pdb=" N PHE A3293 " --> pdb=" O LYS A3289 " (cutoff:3.500A) Processing helix chain 'A' and resid 3299 through 3313 Proline residue: A3308 - end of helix Processing helix chain 'A' and resid 3318 through 3326 removed outlier: 3.553A pdb=" N SER A3326 " --> pdb=" O ALA A3322 " (cutoff:3.500A) Processing helix chain 'A' and resid 3327 through 3447 Proline residue: A3351 - end of helix Processing helix chain 'A' and resid 3461 through 3481 removed outlier: 3.671A pdb=" N GLN A3471 " --> pdb=" O LYS A3467 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ARG A3472 " --> pdb=" O LEU A3468 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N VAL A3474 " --> pdb=" O GLN A3470 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N VAL A3475 " --> pdb=" O GLN A3471 " (cutoff:3.500A) Processing helix chain 'A' and resid 3489 through 3495 removed outlier: 3.511A pdb=" N ILE A3495 " --> pdb=" O THR A3491 " (cutoff:3.500A) Processing helix chain 'A' and resid 3496 through 3507 removed outlier: 3.693A pdb=" N ILE A3500 " --> pdb=" O ASP A3496 " (cutoff:3.500A) Processing helix chain 'A' and resid 3511 through 3524 Processing helix chain 'A' and resid 3535 through 3546 removed outlier: 3.534A pdb=" N ASN A3543 " --> pdb=" O ASN A3539 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N LEU A3545 " --> pdb=" O ILE A3541 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N SER A3546 " --> pdb=" O ARG A3542 " (cutoff:3.500A) Processing helix chain 'A' and resid 3566 through 3575 removed outlier: 4.004A pdb=" N TYR A3570 " --> pdb=" O MET A3566 " (cutoff:3.500A) Processing helix chain 'A' and resid 3588 through 3597 removed outlier: 4.077A pdb=" N ASP A3592 " --> pdb=" O ASP A3588 " (cutoff:3.500A) Proline residue: A3593 - end of helix Processing helix chain 'A' and resid 3635 through 3643 removed outlier: 4.942A pdb=" N THR A3643 " --> pdb=" O SER A3639 " (cutoff:3.500A) Processing helix chain 'A' and resid 3650 through 3666 removed outlier: 3.659A pdb=" N GLN A3656 " --> pdb=" O SER A3652 " (cutoff:3.500A) Processing helix chain 'A' and resid 3667 through 3703 removed outlier: 3.514A pdb=" N GLU A3671 " --> pdb=" O GLN A3667 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLN A3703 " --> pdb=" O LEU A3699 " (cutoff:3.500A) Processing helix chain 'A' and resid 3705 through 3748 removed outlier: 5.545A pdb=" N THR A3710 " --> pdb=" O LEU A3706 " (cutoff:3.500A) removed outlier: 8.441A pdb=" N GLU A3711 " --> pdb=" O LEU A3707 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N LEU A3712 " --> pdb=" O ASP A3708 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL A3715 " --> pdb=" O GLU A3711 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS A3720 " --> pdb=" O LEU A3716 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR A3721 " --> pdb=" O ASN A3717 " (cutoff:3.500A) Processing helix chain 'A' and resid 3749 through 3769 removed outlier: 3.731A pdb=" N LEU A3766 " --> pdb=" O ILE A3762 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL A3767 " --> pdb=" O GLU A3763 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N TRP A3769 " --> pdb=" O SER A3765 " (cutoff:3.500A) Processing helix chain 'A' and resid 3774 through 3789 removed outlier: 3.596A pdb=" N PHE A3778 " --> pdb=" O SER A3774 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS A3780 " --> pdb=" O GLU A3776 " (cutoff:3.500A) Processing helix chain 'A' and resid 3794 through 3819 removed outlier: 3.790A pdb=" N PHE A3808 " --> pdb=" O SER A3804 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLY A3817 " --> pdb=" O TYR A3813 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU A3818 " --> pdb=" O VAL A3814 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N PHE A3819 " --> pdb=" O ASN A3815 " (cutoff:3.500A) Processing helix chain 'A' and resid 3820 through 3839 removed outlier: 4.474A pdb=" N ILE A3824 " --> pdb=" O GLU A3820 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N THR A3825 " --> pdb=" O LYS A3821 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE A3827 " --> pdb=" O LYS A3823 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA A3838 " --> pdb=" O ILE A3834 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N GLY A3839 " --> pdb=" O LEU A3835 " (cutoff:3.500A) Processing helix chain 'A' and resid 3842 through 3852 Processing helix chain 'A' and resid 3857 through 3862 removed outlier: 4.814A pdb=" N ARG A3862 " --> pdb=" O ILE A3858 " (cutoff:3.500A) Processing helix chain 'A' and resid 3870 through 3884 removed outlier: 3.553A pdb=" N LEU A3880 " --> pdb=" O ASN A3876 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N THR A3884 " --> pdb=" O LEU A3880 " (cutoff:3.500A) Processing helix chain 'A' and resid 3895 through 3903 removed outlier: 5.433A pdb=" N SER A3903 " --> pdb=" O LEU A3899 " (cutoff:3.500A) Processing helix chain 'A' and resid 3904 through 3913 removed outlier: 4.162A pdb=" N ARG A3908 " --> pdb=" O GLU A3904 " (cutoff:3.500A) Processing helix chain 'A' and resid 3915 through 3920 removed outlier: 3.802A pdb=" N PHE A3919 " --> pdb=" O ASP A3915 " (cutoff:3.500A) Proline residue: A3920 - end of helix No H-bonds generated for 'chain 'A' and resid 3915 through 3920' Processing helix chain 'A' and resid 3924 through 3932 removed outlier: 3.857A pdb=" N GLN A3930 " --> pdb=" O GLU A3926 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLU A3931 " --> pdb=" O SER A3927 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N LYS A3932 " --> pdb=" O ILE A3928 " (cutoff:3.500A) Processing helix chain 'A' and resid 3933 through 3947 removed outlier: 4.979A pdb=" N PHE A3937 " --> pdb=" O GLU A3933 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL A3943 " --> pdb=" O SER A3939 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ARG A3947 " --> pdb=" O VAL A3943 " (cutoff:3.500A) Processing helix chain 'A' and resid 3950 through 3963 removed outlier: 3.948A pdb=" N ALA A3954 " --> pdb=" O ARG A3950 " (cutoff:3.500A) Processing helix chain 'A' and resid 3964 through 3970 removed outlier: 4.738A pdb=" N THR A3968 " --> pdb=" O GLY A3964 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASP A3969 " --> pdb=" O LYS A3965 " (cutoff:3.500A) Proline residue: A3970 - end of helix No H-bonds generated for 'chain 'A' and resid 3964 through 3970' Processing helix chain 'A' and resid 3974 through 3983 removed outlier: 4.896A pdb=" N SER A3983 " --> pdb=" O TRP A3979 " (cutoff:3.500A) Processing helix chain 'A' and resid 3998 through 4010 removed outlier: 3.894A pdb=" N LYS A4008 " --> pdb=" O GLU A4004 " (cutoff:3.500A) Processing helix chain 'A' and resid 4022 through 4037 removed outlier: 5.054A pdb=" N VAL A4026 " --> pdb=" O GLY A4022 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLN A4029 " --> pdb=" O ARG A4025 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL A4036 " --> pdb=" O MET A4032 " (cutoff:3.500A) Processing helix chain 'A' and resid 4045 through 4050 removed outlier: 4.019A pdb=" N GLY A4049 " --> pdb=" O ASN A4045 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU A4050 " --> pdb=" O CYS A4046 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4045 through 4050' Processing helix chain 'A' and resid 4051 through 4060 removed outlier: 3.505A pdb=" N GLU A4055 " --> pdb=" O LYS A4051 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU A4057 " --> pdb=" O MET A4053 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N THR A4058 " --> pdb=" O GLU A4054 " (cutoff:3.500A) Processing helix chain 'A' and resid 4083 through 4090 removed outlier: 3.763A pdb=" N LEU A4087 " --> pdb=" O PRO A4083 " (cutoff:3.500A) Processing helix chain 'A' and resid 4100 through 4111 Processing helix chain 'A' and resid 4114 through 4121 removed outlier: 3.593A pdb=" N ASP A4119 " --> pdb=" O GLN A4115 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS A4120 " --> pdb=" O GLU A4116 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N VAL A4121 " --> pdb=" O PHE A4117 " (cutoff:3.500A) Processing helix chain 'A' and resid 4123 through 4147 removed outlier: 3.592A pdb=" N ARG A4127 " --> pdb=" O HIS A4123 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LYS A4144 " --> pdb=" O VAL A4140 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N LYS A4145 " --> pdb=" O ILE A4141 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N PHE A4146 " --> pdb=" O GLU A4142 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLY A4147 " --> pdb=" O ARG A4143 " (cutoff:3.500A) Processing helix chain 'A' and resid 4158 through 4178 removed outlier: 4.052A pdb=" N LEU A4162 " --> pdb=" O ASN A4158 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE A4169 " --> pdb=" O SER A4165 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS A4171 " --> pdb=" O LEU A4167 " (cutoff:3.500A) Processing helix chain 'A' and resid 4191 through 4205 removed outlier: 3.506A pdb=" N MET A4197 " --> pdb=" O VAL A4193 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR A4203 " --> pdb=" O CYS A4199 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY A4204 " --> pdb=" O GLU A4200 " (cutoff:3.500A) Processing helix chain 'A' and resid 4209 through 4224 Processing helix chain 'A' and resid 4258 through 4270 removed outlier: 3.763A pdb=" N TYR A4262 " --> pdb=" O GLU A4258 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS A4268 " --> pdb=" O GLU A4264 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL A4269 " --> pdb=" O TYR A4265 " (cutoff:3.500A) Proline residue: A4270 - end of helix Processing helix chain 'A' and resid 4281 through 4304 removed outlier: 4.535A pdb=" N ASP A4285 " --> pdb=" O HIS A4281 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N LEU A4286 " --> pdb=" O SER A4282 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU A4302 " --> pdb=" O ASN A4298 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR A4303 " --> pdb=" O THR A4299 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG A4304 " --> pdb=" O VAL A4300 " (cutoff:3.500A) Processing helix chain 'A' and resid 4315 through 4331 removed outlier: 3.692A pdb=" N LYS A4329 " --> pdb=" O LYS A4325 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASN A4330 " --> pdb=" O ASP A4326 " (cutoff:3.500A) Processing helix chain 'A' and resid 4336 through 4348 removed outlier: 3.745A pdb=" N LYS A4346 " --> pdb=" O GLU A4342 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU A4347 " --> pdb=" O LEU A4343 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N GLY A4348 " --> pdb=" O VAL A4344 " (cutoff:3.500A) Processing helix chain 'A' and resid 4362 through 4395 removed outlier: 3.706A pdb=" N PHE A4367 " --> pdb=" O PRO A4363 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP A4394 " --> pdb=" O ILE A4390 " (cutoff:3.500A) Processing helix chain 'A' and resid 4400 through 4413 removed outlier: 3.528A pdb=" N GLU A4405 " --> pdb=" O PRO A4401 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP A4412 " --> pdb=" O ASN A4408 " (cutoff:3.500A) Processing helix chain 'A' and resid 4416 through 4421 Processing helix chain 'A' and resid 4434 through 4455 removed outlier: 3.611A pdb=" N LYS A4447 " --> pdb=" O SER A4443 " (cutoff:3.500A) Processing helix chain 'A' and resid 4469 through 4487 removed outlier: 3.528A pdb=" N LYS A4486 " --> pdb=" O THR A4482 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N GLY A4487 " --> pdb=" O ARG A4483 " (cutoff:3.500A) Processing helix chain 'A' and resid 4587 through 4592 removed outlier: 5.699A pdb=" N ILE A4592 " --> pdb=" O ASP A4588 " (cutoff:3.500A) Processing helix chain 'A' and resid 4604 through 4612 removed outlier: 3.723A pdb=" N TRP A4608 " --> pdb=" O ASN A4604 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU A4610 " --> pdb=" O SER A4606 " (cutoff:3.500A) Processing helix chain 'A' and resid 3455 through 3460 removed outlier: 5.216A pdb=" N GLY A3458 " --> pdb=" O SER A3455 " (cutoff:3.500A) Proline residue: A3459 - end of helix No H-bonds generated for 'chain 'A' and resid 3455 through 3460' Processing helix chain 'A' and resid 4225 through 4230 removed outlier: 3.691A pdb=" N ILE A4228 " --> pdb=" O LYS A4225 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N PHE A4229 " --> pdb=" O ASP A4226 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLY A4230 " --> pdb=" O GLY A4227 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4225 through 4230' Processing helix chain 'A' and resid 4512 through 4517 removed outlier: 4.268A pdb=" N ASP A4515 " --> pdb=" O LYS A4512 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE A4516 " --> pdb=" O GLU A4513 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N GLU A4517 " --> pdb=" O LYS A4514 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4512 through 4517' Processing helix chain 'B' and resid 4 through 16 removed outlier: 3.502A pdb=" N ASP B 8 " --> pdb=" O HIS B 4 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N SER B 9 " --> pdb=" O SER B 5 " (cutoff:3.500A) Proline residue: B 10 - end of helix Processing helix chain 'B' and resid 27 through 34 Processing helix chain 'B' and resid 36 through 49 Processing helix chain 'B' and resid 117 through 137 Proline residue: B 131 - end of helix Proline residue: B 136 - end of helix Processing helix chain 'B' and resid 140 through 169 removed outlier: 6.373A pdb=" N ASP B 144 " --> pdb=" O GLN B 140 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N LEU B 145 " --> pdb=" O GLY B 141 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N VAL B 146 " --> pdb=" O TRP B 142 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N LYS B 148 " --> pdb=" O ASP B 144 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASP B 149 " --> pdb=" O LEU B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 179 removed outlier: 3.689A pdb=" N LEU B 176 " --> pdb=" O THR B 172 " (cutoff:3.500A) Proline residue: B 177 - end of helix No H-bonds generated for 'chain 'B' and resid 172 through 179' Processing helix chain 'B' and resid 190 through 220 removed outlier: 5.442A pdb=" N LYS B 212 " --> pdb=" O LYS B 208 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N LEU B 213 " --> pdb=" O ASN B 209 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N GLU B 214 " --> pdb=" O VAL B 210 " (cutoff:3.500A) Proline residue: B 215 - end of helix removed outlier: 4.215A pdb=" N LYS B 220 " --> pdb=" O GLU B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 249 Proline residue: B 227 - end of helix Processing helix chain 'B' and resid 250 through 260 removed outlier: 4.396A pdb=" N LEU B 260 " --> pdb=" O ILE B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 296 Proline residue: B 270 - end of helix Processing helix chain 'B' and resid 308 through 331 removed outlier: 6.367A pdb=" N THR B 312 " --> pdb=" O SER B 308 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N GLU B 315 " --> pdb=" O PRO B 311 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ILE B 318 " --> pdb=" O TYR B 314 " (cutoff:3.500A) Proline residue: B 319 - end of helix removed outlier: 3.861A pdb=" N ASN B 329 " --> pdb=" O LEU B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 371 removed outlier: 6.521A pdb=" N ASP B 362 " --> pdb=" O PHE B 358 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N THR B 363 " --> pdb=" O VAL B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 402 removed outlier: 4.899A pdb=" N CYS B 377 " --> pdb=" O THR B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 443 removed outlier: 3.610A pdb=" N THR B 432 " --> pdb=" O HIS B 428 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS B 438 " --> pdb=" O VAL B 434 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS B 441 " --> pdb=" O ASN B 437 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N GLU B 443 " --> pdb=" O LEU B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 473 removed outlier: 5.867A pdb=" N THR B 453 " --> pdb=" O GLY B 449 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL B 473 " --> pdb=" O ALA B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 515 removed outlier: 3.976A pdb=" N ASP B 515 " --> pdb=" O PHE B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 528 Processing helix chain 'B' and resid 534 through 566 removed outlier: 3.949A pdb=" N GLU B 539 " --> pdb=" O ILE B 535 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS B 542 " --> pdb=" O ASP B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 609 removed outlier: 3.676A pdb=" N LEU B 589 " --> pdb=" O ILE B 585 " (cutoff:3.500A) Proline residue: B 602 - end of helix removed outlier: 3.789A pdb=" N LYS B 605 " --> pdb=" O GLU B 601 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN B 608 " --> pdb=" O GLU B 604 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU B 609 " --> pdb=" O LYS B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 656 removed outlier: 3.696A pdb=" N GLN B 653 " --> pdb=" O GLU B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 674 through 691 removed outlier: 3.750A pdb=" N VAL B 678 " --> pdb=" O ASP B 674 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS B 685 " --> pdb=" O LEU B 681 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR B 686 " --> pdb=" O LYS B 682 " (cutoff:3.500A) Processing helix chain 'B' and resid 697 through 706 removed outlier: 4.832A pdb=" N ILE B 701 " --> pdb=" O THR B 697 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N GLU B 706 " --> pdb=" O TYR B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 707 through 727 removed outlier: 3.540A pdb=" N ILE B 725 " --> pdb=" O ASN B 721 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS B 726 " --> pdb=" O TYR B 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 730 through 738 Proline residue: B 735 - end of helix Processing helix chain 'B' and resid 739 through 755 Proline residue: B 750 - end of helix removed outlier: 3.556A pdb=" N GLU B 753 " --> pdb=" O LYS B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 764 through 799 removed outlier: 3.606A pdb=" N ASN B 798 " --> pdb=" O LEU B 794 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N VAL B 799 " --> pdb=" O ALA B 795 " (cutoff:3.500A) Processing helix chain 'B' and resid 812 through 848 removed outlier: 3.610A pdb=" N ALA B 820 " --> pdb=" O GLN B 816 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE B 821 " --> pdb=" O PHE B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 853 through 887 Processing helix chain 'B' and resid 888 through 895 removed outlier: 4.782A pdb=" N ASP B 895 " --> pdb=" O ILE B 891 " (cutoff:3.500A) Processing helix chain 'B' and resid 925 through 945 removed outlier: 3.789A pdb=" N PHE B 937 " --> pdb=" O TRP B 933 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ALA B 941 " --> pdb=" O PHE B 937 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N GLY B 942 " --> pdb=" O PHE B 938 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N THR B 943 " --> pdb=" O ASN B 939 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE B 944 " --> pdb=" O ILE B 940 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLN B 945 " --> pdb=" O ALA B 941 " (cutoff:3.500A) Processing helix chain 'B' and resid 955 through 962 Processing helix chain 'B' and resid 963 through 992 removed outlier: 3.943A pdb=" N PHE B 990 " --> pdb=" O PHE B 986 " (cutoff:3.500A) Processing helix chain 'B' and resid 993 through 1001 removed outlier: 5.298A pdb=" N GLU B1001 " --> pdb=" O TRP B 997 " (cutoff:3.500A) Processing helix chain 'B' and resid 1003 through 1010 removed outlier: 4.699A pdb=" N ARG B1007 " --> pdb=" O ILE B1003 " (cutoff:3.500A) Processing helix chain 'B' and resid 1046 through 1068 Processing helix chain 'B' and resid 1080 through 1122 removed outlier: 3.642A pdb=" N TYR B1098 " --> pdb=" O TRP B1094 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N LEU B1102 " --> pdb=" O TYR B1098 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N VAL B1103 " --> pdb=" O THR B1099 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN B1105 " --> pdb=" O PHE B1101 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ARG B1107 " --> pdb=" O VAL B1103 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASP B1115 " --> pdb=" O LYS B1111 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE B1116 " --> pdb=" O ASN B1112 " (cutoff:3.500A) Processing helix chain 'B' and resid 1128 through 1149 removed outlier: 3.947A pdb=" N GLU B1132 " --> pdb=" O PRO B1128 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU B1134 " --> pdb=" O ASP B1130 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS B1137 " --> pdb=" O ASN B1133 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LYS B1138 " --> pdb=" O LEU B1134 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU B1139 " --> pdb=" O HIS B1135 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N MET B1144 " --> pdb=" O LEU B1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 1150 through 1167 removed outlier: 3.664A pdb=" N GLU B1154 " --> pdb=" O VAL B1150 " (cutoff:3.500A) Proline residue: B1155 - end of helix Processing helix chain 'B' and resid 1199 through 1216 Proline residue: B1213 - end of helix Processing helix chain 'B' and resid 1253 through 1285 removed outlier: 6.045A pdb=" N ILE B1257 " --> pdb=" O GLY B1253 " (cutoff:3.500A) Processing helix chain 'B' and resid 1288 through 1332 removed outlier: 3.560A pdb=" N LYS B1292 " --> pdb=" O PHE B1288 " (cutoff:3.500A) Proline residue: B1329 - end of helix Processing helix chain 'B' and resid 1334 through 1356 Proline residue: B1353 - end of helix removed outlier: 5.491A pdb=" N ILE B1356 " --> pdb=" O LEU B1352 " (cutoff:3.500A) Processing helix chain 'B' and resid 1361 through 1384 removed outlier: 3.563A pdb=" N ILE B1365 " --> pdb=" O GLY B1361 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LYS B1368 " --> pdb=" O VAL B1364 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL B1369 " --> pdb=" O ILE B1365 " (cutoff:3.500A) Proline residue: B1377 - end of helix removed outlier: 3.532A pdb=" N ALA B1381 " --> pdb=" O PRO B1377 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU B1382 " --> pdb=" O LEU B1378 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N SER B1384 " --> pdb=" O SER B1380 " (cutoff:3.500A) Processing helix chain 'B' and resid 1388 through 1400 Processing helix chain 'B' and resid 1410 through 1419 removed outlier: 3.679A pdb=" N ASP B1414 " --> pdb=" O PHE B1410 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA B1417 " --> pdb=" O GLU B1413 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LEU B1418 " --> pdb=" O ASP B1414 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N ASN B1419 " --> pdb=" O ILE B1415 " (cutoff:3.500A) Processing helix chain 'B' and resid 1420 through 1454 removed outlier: 4.876A pdb=" N ASN B1425 " --> pdb=" O TYR B1421 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N THR B1426 " --> pdb=" O LYS B1422 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS B1439 " --> pdb=" O GLN B1435 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE B1440 " --> pdb=" O LYS B1436 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS B1453 " --> pdb=" O GLN B1449 " (cutoff:3.500A) Processing helix chain 'B' and resid 1469 through 1491 removed outlier: 3.958A pdb=" N MET B1473 " --> pdb=" O SER B1469 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER B1489 " --> pdb=" O MET B1485 " (cutoff:3.500A) Processing helix chain 'B' and resid 1492 through 1498 Processing helix chain 'B' and resid 1499 through 1533 removed outlier: 4.298A pdb=" N ASP B1503 " --> pdb=" O ASP B1499 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASP B1512 " --> pdb=" O LEU B1508 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL B1513 " --> pdb=" O GLY B1509 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL B1514 " --> pdb=" O ARG B1510 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU B1519 " --> pdb=" O VAL B1515 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ASN B1524 " --> pdb=" O LYS B1520 " (cutoff:3.500A) Processing helix chain 'B' and resid 1535 through 1543 removed outlier: 3.635A pdb=" N GLN B1541 " --> pdb=" O ASP B1537 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU B1542 " --> pdb=" O ILE B1538 " (cutoff:3.500A) Proline residue: B1543 - end of helix Processing helix chain 'B' and resid 1544 through 1567 Proline residue: B1567 - end of helix Processing helix chain 'B' and resid 1568 through 1574 Processing helix chain 'B' and resid 1575 through 1607 Proline residue: B1607 - end of helix Processing helix chain 'B' and resid 1608 through 1613 removed outlier: 5.028A pdb=" N SER B1613 " --> pdb=" O PHE B1609 " (cutoff:3.500A) Processing helix chain 'B' and resid 1614 through 1624 Processing helix chain 'B' and resid 1626 through 1638 removed outlier: 3.660A pdb=" N VAL B1630 " --> pdb=" O ASN B1626 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N TYR B1633 " --> pdb=" O LYS B1629 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU B1634 " --> pdb=" O VAL B1630 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLY B1635 " --> pdb=" O CYS B1631 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N ASP B1636 " --> pdb=" O GLU B1632 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N CYS B1637 " --> pdb=" O TYR B1633 " (cutoff:3.500A) Processing helix chain 'B' and resid 1681 through 1712 removed outlier: 3.889A pdb=" N ARG B1694 " --> pdb=" O GLU B1690 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU B1702 " --> pdb=" O GLN B1698 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLY B1703 " --> pdb=" O GLU B1699 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU B1710 " --> pdb=" O ASN B1706 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASP B1712 " --> pdb=" O ALA B1708 " (cutoff:3.500A) Processing helix chain 'B' and resid 1717 through 1726 removed outlier: 3.591A pdb=" N GLU B1723 " --> pdb=" O GLU B1719 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY B1724 " --> pdb=" O GLU B1720 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TYR B1725 " --> pdb=" O TRP B1721 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N ASN B1726 " --> pdb=" O VAL B1722 " (cutoff:3.500A) Processing helix chain 'B' and resid 1727 through 1752 Processing helix chain 'B' and resid 1754 through 1778 removed outlier: 4.131A pdb=" N LYS B1758 " --> pdb=" O GLU B1754 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS B1774 " --> pdb=" O ASN B1770 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG B1776 " --> pdb=" O ILE B1772 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N ASP B1778 " --> pdb=" O LYS B1774 " (cutoff:3.500A) Processing helix chain 'B' and resid 1781 through 1808 removed outlier: 3.930A pdb=" N TRP B1785 " --> pdb=" O ILE B1781 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ILE B1790 " --> pdb=" O LYS B1786 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N HIS B1796 " --> pdb=" O THR B1792 " (cutoff:3.500A) Processing helix chain 'B' and resid 1814 through 1821 removed outlier: 3.794A pdb=" N GLN B1820 " --> pdb=" O ALA B1816 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N LEU B1821 " --> pdb=" O TRP B1817 " (cutoff:3.500A) Processing helix chain 'B' and resid 1832 through 1837 Processing helix chain 'B' and resid 1841 through 1847 removed outlier: 3.629A pdb=" N LYS B1845 " --> pdb=" O PHE B1841 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LYS B1847 " --> pdb=" O TRP B1843 " (cutoff:3.500A) Processing helix chain 'B' and resid 1877 through 1894 Processing helix chain 'B' and resid 1906 through 1919 Processing helix chain 'B' and resid 1932 through 1947 removed outlier: 3.797A pdb=" N ILE B1939 " --> pdb=" O SER B1935 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLY B1947 " --> pdb=" O LEU B1943 " (cutoff:3.500A) Processing helix chain 'B' and resid 1959 through 1980 removed outlier: 3.783A pdb=" N VAL B1965 " --> pdb=" O GLU B1961 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR B1968 " --> pdb=" O SER B1964 " (cutoff:3.500A) Processing helix chain 'B' and resid 2015 through 2023 removed outlier: 3.641A pdb=" N LEU B2021 " --> pdb=" O ASN B2017 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N ARG B2023 " --> pdb=" O LYS B2019 " (cutoff:3.500A) Processing helix chain 'B' and resid 2031 through 2044 removed outlier: 3.522A pdb=" N GLU B2043 " --> pdb=" O MET B2039 " (cutoff:3.500A) Processing helix chain 'B' and resid 2047 through 2066 removed outlier: 3.618A pdb=" N SER B2057 " --> pdb=" O ARG B2053 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU B2064 " --> pdb=" O MET B2060 " (cutoff:3.500A) Processing helix chain 'B' and resid 2075 through 2094 removed outlier: 3.576A pdb=" N SER B2081 " --> pdb=" O ARG B2077 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLN B2085 " --> pdb=" O SER B2081 " (cutoff:3.500A) Proline residue: B2094 - end of helix Processing helix chain 'B' and resid 2097 through 2115 removed outlier: 3.685A pdb=" N LEU B2101 " --> pdb=" O PRO B2097 " (cutoff:3.500A) Proline residue: B2112 - end of helix removed outlier: 5.111A pdb=" N VAL B2115 " --> pdb=" O MET B2111 " (cutoff:3.500A) Processing helix chain 'B' and resid 2116 through 2131 removed outlier: 3.805A pdb=" N VAL B2120 " --> pdb=" O THR B2116 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ILE B2121 " --> pdb=" O ASP B2117 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP B2128 " --> pdb=" O ARG B2124 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LEU B2129 " --> pdb=" O LEU B2125 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE B2130 " --> pdb=" O ILE B2126 " (cutoff:3.500A) Proline residue: B2131 - end of helix Processing helix chain 'B' and resid 2140 through 2154 Processing helix chain 'B' and resid 2160 through 2177 Processing helix chain 'B' and resid 2189 through 2205 removed outlier: 3.513A pdb=" N TRP B2194 " --> pdb=" O LYS B2190 " (cutoff:3.500A) Processing helix chain 'B' and resid 2214 through 2219 removed outlier: 3.736A pdb=" N VAL B2218 " --> pdb=" O ASN B2214 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N THR B2219 " --> pdb=" O PRO B2215 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2214 through 2219' Processing helix chain 'B' and resid 2220 through 2225 Processing helix chain 'B' and resid 2236 through 2247 removed outlier: 3.503A pdb=" N ILE B2241 " --> pdb=" O VAL B2237 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL B2246 " --> pdb=" O MET B2242 " (cutoff:3.500A) Processing helix chain 'B' and resid 2268 through 2276 removed outlier: 3.952A pdb=" N SER B2274 " --> pdb=" O GLU B2270 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU B2275 " --> pdb=" O TRP B2271 " (cutoff:3.500A) Processing helix chain 'B' and resid 2312 through 2320 removed outlier: 3.984A pdb=" N ALA B2319 " --> pdb=" O THR B2315 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N GLY B2320 " --> pdb=" O VAL B2316 " (cutoff:3.500A) Processing helix chain 'B' and resid 2325 through 2341 removed outlier: 6.191A pdb=" N TRP B2331 " --> pdb=" O THR B2327 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N MET B2332 " --> pdb=" O ASP B2328 " (cutoff:3.500A) Proline residue: B2333 - end of helix Processing helix chain 'B' and resid 2342 through 2351 removed outlier: 3.538A pdb=" N LYS B2351 " --> pdb=" O LEU B2347 " (cutoff:3.500A) Processing helix chain 'B' and resid 2363 through 2379 Processing helix chain 'B' and resid 2381 through 2386 removed outlier: 4.541A pdb=" N HIS B2385 " --> pdb=" O ASN B2381 " (cutoff:3.500A) Processing helix chain 'B' and resid 2397 through 2417 removed outlier: 3.685A pdb=" N ALA B2411 " --> pdb=" O THR B2407 " (cutoff:3.500A) Processing helix chain 'B' and resid 2418 through 2424 removed outlier: 3.529A pdb=" N GLN B2422 " --> pdb=" O PRO B2418 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N LYS B2424 " --> pdb=" O LEU B2420 " (cutoff:3.500A) Processing helix chain 'B' and resid 2425 through 2449 Proline residue: B2447 - end of helix Processing helix chain 'B' and resid 2453 through 2466 removed outlier: 3.793A pdb=" N ASP B2457 " --> pdb=" O ASP B2453 " (cutoff:3.500A) Processing helix chain 'B' and resid 2478 through 2483 removed outlier: 3.546A pdb=" N TYR B2482 " --> pdb=" O LEU B2478 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N TYR B2483 " --> pdb=" O CYS B2479 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2478 through 2483' Processing helix chain 'B' and resid 2506 through 2511 removed outlier: 3.811A pdb=" N ILE B2510 " --> pdb=" O LEU B2506 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N TYR B2511 " --> pdb=" O PHE B2507 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2506 through 2511' Processing helix chain 'B' and resid 2514 through 2531 removed outlier: 3.543A pdb=" N ARG B2519 " --> pdb=" O ILE B2515 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG B2530 " --> pdb=" O ILE B2526 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ARG B2531 " --> pdb=" O HIS B2527 " (cutoff:3.500A) Processing helix chain 'B' and resid 2543 through 2556 removed outlier: 4.384A pdb=" N VAL B2547 " --> pdb=" O GLY B2543 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TYR B2551 " --> pdb=" O VAL B2547 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN B2553 " --> pdb=" O ARG B2549 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N ARG B2556 " --> pdb=" O LEU B2552 " (cutoff:3.500A) Processing helix chain 'B' and resid 2572 through 2585 removed outlier: 4.895A pdb=" N GLU B2585 " --> pdb=" O GLU B2581 " (cutoff:3.500A) Processing helix chain 'B' and resid 2618 through 2630 removed outlier: 3.805A pdb=" N LEU B2624 " --> pdb=" O PRO B2620 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG B2625 " --> pdb=" O ILE B2621 " (cutoff:3.500A) Processing helix chain 'B' and resid 2664 through 2672 removed outlier: 3.921A pdb=" N ASN B2670 " --> pdb=" O ARG B2666 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N SER B2672 " --> pdb=" O GLN B2668 " (cutoff:3.500A) Processing helix chain 'B' and resid 2680 through 2700 removed outlier: 3.769A pdb=" N SER B2690 " --> pdb=" O THR B2686 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N THR B2698 " --> pdb=" O ALA B2694 " (cutoff:3.500A) Processing helix chain 'B' and resid 2703 through 2725 removed outlier: 3.522A pdb=" N ALA B2707 " --> pdb=" O ALA B2703 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N PHE B2708 " --> pdb=" O GLN B2704 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LYS B2709 " --> pdb=" O LYS B2705 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N THR B2725 " --> pdb=" O ILE B2721 " (cutoff:3.500A) Processing helix chain 'B' and resid 2740 through 2760 removed outlier: 4.781A pdb=" N LEU B2744 " --> pdb=" O ASN B2740 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N THR B2754 " --> pdb=" O GLY B2750 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N THR B2755 " --> pdb=" O ILE B2751 " (cutoff:3.500A) Proline residue: B2756 - end of helix removed outlier: 3.825A pdb=" N TYR B2759 " --> pdb=" O THR B2755 " (cutoff:3.500A) Processing helix chain 'B' and resid 2764 through 2784 removed outlier: 5.020A pdb=" N VAL B2768 " --> pdb=" O GLN B2764 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG B2769 " --> pdb=" O GLY B2765 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ASP B2781 " --> pdb=" O ARG B2777 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ARG B2782 " --> pdb=" O THR B2778 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N ILE B2784 " --> pdb=" O GLU B2780 " (cutoff:3.500A) Processing helix chain 'B' and resid 2785 through 2805 removed outlier: 3.503A pdb=" N VAL B2789 " --> pdb=" O ALA B2785 " (cutoff:3.500A) Processing helix chain 'B' and resid 2821 through 2829 removed outlier: 4.758A pdb=" N ALA B2825 " --> pdb=" O THR B2821 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ALA B2826 " --> pdb=" O GLY B2822 " (cutoff:3.500A) Processing helix chain 'B' and resid 2838 through 2857 removed outlier: 3.563A pdb=" N ARG B2844 " --> pdb=" O PRO B2840 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL B2856 " --> pdb=" O GLU B2852 " (cutoff:3.500A) Processing helix chain 'B' and resid 2865 through 2882 removed outlier: 3.671A pdb=" N ILE B2878 " --> pdb=" O ARG B2874 " (cutoff:3.500A) Proline residue: B2882 - end of helix Processing helix chain 'B' and resid 2895 through 2908 removed outlier: 4.462A pdb=" N GLY B2908 " --> pdb=" O THR B2904 " (cutoff:3.500A) Processing helix chain 'B' and resid 2921 through 2938 removed outlier: 3.684A pdb=" N LYS B2935 " --> pdb=" O GLU B2931 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS B2938 " --> pdb=" O LYS B2934 " (cutoff:3.500A) Processing helix chain 'B' and resid 2949 through 2954 removed outlier: 4.601A pdb=" N LYS B2954 " --> pdb=" O ASP B2950 " (cutoff:3.500A) Processing helix chain 'B' and resid 2955 through 2967 removed outlier: 4.528A pdb=" N LEU B2959 " --> pdb=" O GLU B2955 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ILE B2960 " --> pdb=" O GLU B2956 " (cutoff:3.500A) Proline residue: B2961 - end of helix removed outlier: 3.520A pdb=" N ASP B2964 " --> pdb=" O ILE B2960 " (cutoff:3.500A) Processing helix chain 'B' and resid 2976 through 2992 removed outlier: 3.545A pdb=" N SER B2982 " --> pdb=" O GLU B2978 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY B2986 " --> pdb=" O SER B2982 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASN B2989 " --> pdb=" O SER B2985 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLU B2990 " --> pdb=" O GLY B2986 " (cutoff:3.500A) Processing helix chain 'B' and resid 3000 through 3016 removed outlier: 6.373A pdb=" N LEU B3004 " --> pdb=" O ASN B3000 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N THR B3005 " --> pdb=" O LEU B3001 " (cutoff:3.500A) Processing helix chain 'B' and resid 3026 through 3036 removed outlier: 4.623A pdb=" N ARG B3030 " --> pdb=" O GLY B3026 " (cutoff:3.500A) Processing helix chain 'B' and resid 3037 through 3042 removed outlier: 3.814A pdb=" N ASN B3041 " --> pdb=" O PRO B3037 " (cutoff:3.500A) Processing helix chain 'B' and resid 3052 through 3066 removed outlier: 3.755A pdb=" N ASP B3058 " --> pdb=" O GLU B3054 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU B3065 " --> pdb=" O PHE B3061 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N GLU B3066 " --> pdb=" O ARG B3062 " (cutoff:3.500A) Processing helix chain 'B' and resid 3072 through 3100 removed outlier: 3.851A pdb=" N GLN B3076 " --> pdb=" O GLU B3072 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU B3080 " --> pdb=" O GLN B3076 " (cutoff:3.500A) Processing helix chain 'B' and resid 3107 through 3222 Proline residue: B3222 - end of helix Processing helix chain 'B' and resid 3235 through 3245 removed outlier: 3.517A pdb=" N THR B3240 " --> pdb=" O LYS B3236 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU B3241 " --> pdb=" O PRO B3237 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N MET B3242 " --> pdb=" O HIS B3238 " (cutoff:3.500A) Processing helix chain 'B' and resid 3249 through 3264 removed outlier: 4.213A pdb=" N VAL B3254 " --> pdb=" O ALA B3250 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR B3255 " --> pdb=" O GLY B3251 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA B3256 " --> pdb=" O VAL B3252 " (cutoff:3.500A) Processing helix chain 'B' and resid 3272 through 3285 removed outlier: 3.606A pdb=" N LYS B3279 " --> pdb=" O LYS B3275 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N PHE B3283 " --> pdb=" O LYS B3279 " (cutoff:3.500A) Processing helix chain 'B' and resid 3286 through 3298 removed outlier: 3.537A pdb=" N LYS B3295 " --> pdb=" O ILE B3291 " (cutoff:3.500A) Processing helix chain 'B' and resid 3303 through 3316 removed outlier: 3.605A pdb=" N GLU B3308 " --> pdb=" O PRO B3304 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN B3309 " --> pdb=" O ASN B3305 " (cutoff:3.500A) Processing helix chain 'B' and resid 3322 through 3330 removed outlier: 6.706A pdb=" N MET B3326 " --> pdb=" O ASN B3322 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ALA B3327 " --> pdb=" O GLU B3323 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY B3328 " --> pdb=" O LYS B3324 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN B3329 " --> pdb=" O ASP B3325 " (cutoff:3.500A) Processing helix chain 'B' and resid 3331 through 3338 removed outlier: 3.546A pdb=" N LYS B3335 " --> pdb=" O TYR B3331 " (cutoff:3.500A) Processing helix chain 'B' and resid 3340 through 3455 Proline residue: B3355 - end of helix Processing helix chain 'B' and resid 3465 through 3485 removed outlier: 3.621A pdb=" N GLU B3471 " --> pdb=" O LYS B3467 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N TRP B3473 " --> pdb=" O ARG B3469 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N THR B3476 " --> pdb=" O LEU B3472 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N LEU B3478 " --> pdb=" O LYS B3474 " (cutoff:3.500A) Proline residue: B3479 - end of helix removed outlier: 3.828A pdb=" N ILE B3482 " --> pdb=" O LEU B3478 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS B3484 " --> pdb=" O ASP B3480 " (cutoff:3.500A) Processing helix chain 'B' and resid 3493 through 3499 removed outlier: 3.776A pdb=" N ILE B3497 " --> pdb=" O GLU B3493 " (cutoff:3.500A) Processing helix chain 'B' and resid 3500 through 3511 removed outlier: 3.765A pdb=" N LYS B3504 " --> pdb=" O THR B3500 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASN B3509 " --> pdb=" O SER B3505 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLY B3511 " --> pdb=" O TRP B3507 " (cutoff:3.500A) Processing helix chain 'B' and resid 3515 through 3528 removed outlier: 3.668A pdb=" N THR B3526 " --> pdb=" O ALA B3522 " (cutoff:3.500A) Processing helix chain 'B' and resid 3539 through 3550 removed outlier: 3.584A pdb=" N TRP B3544 " --> pdb=" O GLN B3540 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLY B3550 " --> pdb=" O ARG B3546 " (cutoff:3.500A) Processing helix chain 'B' and resid 3562 through 3574 removed outlier: 3.712A pdb=" N SER B3573 " --> pdb=" O SER B3569 " (cutoff:3.500A) Processing helix chain 'B' and resid 3587 through 3595 removed outlier: 3.705A pdb=" N ASP B3591 " --> pdb=" O ASP B3587 " (cutoff:3.500A) Proline residue: B3592 - end of helix Processing helix chain 'B' and resid 3634 through 3642 removed outlier: 4.529A pdb=" N THR B3642 " --> pdb=" O ALA B3638 " (cutoff:3.500A) Processing helix chain 'B' and resid 3650 through 3666 removed outlier: 3.773A pdb=" N GLU B3654 " --> pdb=" O GLU B3650 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLN B3656 " --> pdb=" O GLY B3652 " (cutoff:3.500A) Processing helix chain 'B' and resid 3667 through 3701 Processing helix chain 'B' and resid 3702 through 3748 removed outlier: 3.932A pdb=" N LEU B3707 " --> pdb=" O PRO B3703 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASP B3708 " --> pdb=" O ALA B3704 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N THR B3710 " --> pdb=" O ILE B3706 " (cutoff:3.500A) removed outlier: 8.552A pdb=" N GLU B3711 " --> pdb=" O LEU B3707 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N LEU B3712 " --> pdb=" O ASP B3708 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE B3713 " --> pdb=" O ASN B3709 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU B3745 " --> pdb=" O ASN B3741 " (cutoff:3.500A) Processing helix chain 'B' and resid 3749 through 3769 removed outlier: 3.546A pdb=" N LEU B3760 " --> pdb=" O MET B3756 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL B3766 " --> pdb=" O ILE B3762 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N MET B3767 " --> pdb=" O SER B3763 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ASP B3768 " --> pdb=" O LEU B3764 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N HIS B3769 " --> pdb=" O SER B3765 " (cutoff:3.500A) Processing helix chain 'B' and resid 3774 through 3789 removed outlier: 3.561A pdb=" N PHE B3778 " --> pdb=" O SER B3774 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR B3789 " --> pdb=" O ALA B3785 " (cutoff:3.500A) Processing helix chain 'B' and resid 3795 through 3817 removed outlier: 3.563A pdb=" N ILE B3801 " --> pdb=" O ILE B3797 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N PHE B3817 " --> pdb=" O SER B3813 " (cutoff:3.500A) Processing helix chain 'B' and resid 3818 through 3836 removed outlier: 3.998A pdb=" N LEU B3822 " --> pdb=" O GLU B3818 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ILE B3823 " --> pdb=" O LYS B3819 " (cutoff:3.500A) Processing helix chain 'B' and resid 3843 through 3853 Processing helix chain 'B' and resid 3867 through 3880 removed outlier: 3.672A pdb=" N GLY B3876 " --> pdb=" O ASP B3872 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ASN B3879 " --> pdb=" O GLN B3875 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LEU B3880 " --> pdb=" O GLY B3876 " (cutoff:3.500A) Processing helix chain 'B' and resid 3885 through 3894 removed outlier: 3.515A pdb=" N GLU B3891 " --> pdb=" O ALA B3887 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N GLU B3893 " --> pdb=" O GLN B3889 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA B3894 " --> pdb=" O LEU B3890 " (cutoff:3.500A) Processing helix chain 'B' and resid 3896 through 3905 removed outlier: 4.570A pdb=" N ASP B3900 " --> pdb=" O ASN B3896 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N LEU B3905 " --> pdb=" O TRP B3901 " (cutoff:3.500A) Processing helix chain 'B' and resid 3906 through 3911 removed outlier: 3.658A pdb=" N GLN B3910 " --> pdb=" O GLN B3906 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N LYS B3911 " --> pdb=" O PRO B3907 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 3906 through 3911' Processing helix chain 'B' and resid 3916 through 3923 removed outlier: 3.828A pdb=" N MET B3922 " --> pdb=" O ARG B3918 " (cutoff:3.500A) Proline residue: B3923 - end of helix Processing helix chain 'B' and resid 3924 through 3934 Processing helix chain 'B' and resid 3935 through 3950 removed outlier: 4.614A pdb=" N THR B3939 " --> pdb=" O PRO B3935 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N ILE B3940 " --> pdb=" O ASP B3936 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASN B3943 " --> pdb=" O THR B3939 " (cutoff:3.500A) Processing helix chain 'B' and resid 3952 through 3959 removed outlier: 3.754A pdb=" N PHE B3956 " --> pdb=" O GLN B3952 " (cutoff:3.500A) Processing helix chain 'B' and resid 3964 through 3976 removed outlier: 5.516A pdb=" N ILE B3968 " --> pdb=" O ALA B3964 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE B3973 " --> pdb=" O LEU B3969 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASN B3974 " --> pdb=" O GLU B3970 " (cutoff:3.500A) Processing helix chain 'B' and resid 3992 through 4005 removed outlier: 4.372A pdb=" N GLU B3996 " --> pdb=" O ASP B3992 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS B3999 " --> pdb=" O LYS B3995 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS B4003 " --> pdb=" O LYS B3999 " (cutoff:3.500A) Processing helix chain 'B' and resid 4008 through 4013 removed outlier: 7.308A pdb=" N PHE B4012 " --> pdb=" O PRO B4008 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N PHE B4013 " --> pdb=" O GLY B4009 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 4008 through 4013' Processing helix chain 'B' and resid 4021 through 4036 removed outlier: 3.974A pdb=" N LYS B4034 " --> pdb=" O GLU B4030 " (cutoff:3.500A) Processing helix chain 'B' and resid 4043 through 4048 removed outlier: 4.660A pdb=" N MET B4047 " --> pdb=" O ASN B4043 " (cutoff:3.500A) Proline residue: B4048 - end of helix No H-bonds generated for 'chain 'B' and resid 4043 through 4048' Processing helix chain 'B' and resid 4049 through 4065 removed outlier: 3.568A pdb=" N LYS B4056 " --> pdb=" O ILE B4052 " (cutoff:3.500A) Processing helix chain 'B' and resid 4085 through 4092 removed outlier: 3.506A pdb=" N LEU B4089 " --> pdb=" O PRO B4085 " (cutoff:3.500A) Processing helix chain 'B' and resid 4102 through 4115 removed outlier: 3.664A pdb=" N PHE B4114 " --> pdb=" O ALA B4110 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N SER B4115 " --> pdb=" O TRP B4111 " (cutoff:3.500A) Processing helix chain 'B' and resid 4116 through 4123 removed outlier: 3.870A pdb=" N ASP B4121 " --> pdb=" O GLU B4117 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N ASP B4123 " --> pdb=" O ILE B4119 " (cutoff:3.500A) Processing helix chain 'B' and resid 4124 through 4147 removed outlier: 3.632A pdb=" N ILE B4141 " --> pdb=" O HIS B4137 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG B4145 " --> pdb=" O ILE B4141 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N PHE B4146 " --> pdb=" O GLU B4142 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N GLY B4147 " --> pdb=" O ARG B4143 " (cutoff:3.500A) Processing helix chain 'B' and resid 4158 through 4177 removed outlier: 3.744A pdb=" N LEU B4162 " --> pdb=" O ASN B4158 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER B4165 " --> pdb=" O ASP B4161 " (cutoff:3.500A) Processing helix chain 'B' and resid 4182 through 4192 removed outlier: 3.528A pdb=" N LEU B4186 " --> pdb=" O PRO B4182 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TYR B4188 " --> pdb=" O ASN B4184 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE B4189 " --> pdb=" O ASP B4185 " (cutoff:3.500A) Processing helix chain 'B' and resid 4195 through 4200 removed outlier: 4.212A pdb=" N ILE B4199 " --> pdb=" O TYR B4195 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N VAL B4200 " --> pdb=" O GLY B4196 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 4195 through 4200' Processing helix chain 'B' and resid 4201 through 4217 removed outlier: 6.555A pdb=" N ARG B4205 " --> pdb=" O ASP B4201 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG B4206 " --> pdb=" O ASP B4202 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU B4207 " --> pdb=" O TRP B4203 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU B4212 " --> pdb=" O CYS B4208 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N HIS B4217 " --> pdb=" O PHE B4213 " (cutoff:3.500A) Processing helix chain 'B' and resid 4244 through 4256 removed outlier: 3.653A pdb=" N ILE B4249 " --> pdb=" O TYR B4245 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU B4250 " --> pdb=" O GLU B4246 " (cutoff:3.500A) Processing helix chain 'B' and resid 4260 through 4265 removed outlier: 4.423A pdb=" N TYR B4264 " --> pdb=" O THR B4260 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY B4265 " --> pdb=" O PRO B4261 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 4260 through 4265' Processing helix chain 'B' and resid 4267 through 4290 removed outlier: 3.848A pdb=" N GLU B4271 " --> pdb=" O HIS B4267 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE B4272 " --> pdb=" O PRO B4268 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE B4274 " --> pdb=" O ALA B4270 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU B4288 " --> pdb=" O ASN B4284 " (cutoff:3.500A) Processing helix chain 'B' and resid 4306 through 4322 removed outlier: 4.821A pdb=" N GLU B4322 " --> pdb=" O LEU B4318 " (cutoff:3.500A) Processing helix chain 'B' and resid 4323 through 4328 removed outlier: 5.939A pdb=" N PHE B4328 " --> pdb=" O LYS B4324 " (cutoff:3.500A) Processing helix chain 'B' and resid 4329 through 4338 removed outlier: 3.596A pdb=" N ILE B4333 " --> pdb=" O ASN B4329 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N ASP B4338 " --> pdb=" O LYS B4334 " (cutoff:3.500A) Processing helix chain 'B' and resid 4343 through 4376 removed outlier: 3.544A pdb=" N SER B4375 " --> pdb=" O GLY B4371 " (cutoff:3.500A) Processing helix chain 'B' and resid 4381 through 4394 Processing helix chain 'B' and resid 4397 through 4405 removed outlier: 3.505A pdb=" N LEU B4403 " --> pdb=" O SER B4399 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N ALA B4404 " --> pdb=" O TRP B4400 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N TYR B4405 " --> pdb=" O GLN B4401 " (cutoff:3.500A) Processing helix chain 'B' and resid 4410 through 4432 removed outlier: 3.580A pdb=" N PHE B4428 " --> pdb=" O GLN B4424 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASP B4430 " --> pdb=" O ASN B4426 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N ASP B4431 " --> pdb=" O ILE B4427 " (cutoff:3.500A) Proline residue: B4432 - end of helix Processing helix chain 'B' and resid 4446 through 4463 removed outlier: 3.957A pdb=" N PHE B4450 " --> pdb=" O ASN B4446 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ALA B4463 " --> pdb=" O SER B4459 " (cutoff:3.500A) Processing helix chain 'B' and resid 4465 through 4470 removed outlier: 3.757A pdb=" N LEU B4469 " --> pdb=" O GLU B4465 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N TYR B4470 " --> pdb=" O LEU B4466 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 4465 through 4470' Processing helix chain 'B' and resid 4568 through 4576 removed outlier: 4.092A pdb=" N TRP B4572 " --> pdb=" O PRO B4568 " (cutoff:3.500A) Processing helix chain 'B' and resid 4291 through 4296 removed outlier: 3.673A pdb=" N GLN B4294 " --> pdb=" O PRO B4291 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ARG B4296 " --> pdb=" O GLU B4293 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 303 removed outlier: 4.456A pdb=" N GLN B 303 " --> pdb=" O LEU B 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 298 through 303' Processing helix chain 'C' and resid 629 through 665 Processing helix chain 'C' and resid 670 through 706 Processing helix chain 'C' and resid 732 through 750 Proline residue: C 741 - end of helix removed outlier: 3.616A pdb=" N LYS C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 779 through 809 removed outlier: 3.725A pdb=" N LYS C 785 " --> pdb=" O SER C 781 " (cutoff:3.500A) Processing helix chain 'C' and resid 818 through 854 removed outlier: 3.775A pdb=" N LYS C 822 " --> pdb=" O ILE C 818 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU C 823 " --> pdb=" O GLY C 819 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N MET C 824 " --> pdb=" O SER C 820 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU C 842 " --> pdb=" O TRP C 838 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS C 853 " --> pdb=" O ASP C 849 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N MET C 854 " --> pdb=" O GLU C 850 " (cutoff:3.500A) Processing helix chain 'C' and resid 860 through 879 removed outlier: 5.428A pdb=" N MET C 864 " --> pdb=" O ASN C 860 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLU C 867 " --> pdb=" O ASP C 863 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU C 878 " --> pdb=" O ALA C 874 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N ARG C 879 " --> pdb=" O LEU C 875 " (cutoff:3.500A) Processing helix chain 'C' and resid 885 through 910 removed outlier: 5.434A pdb=" N ILE C 889 " --> pdb=" O SER C 885 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE C 891 " --> pdb=" O ALA C 887 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU C 902 " --> pdb=" O TRP C 898 " (cutoff:3.500A) Proline residue: C 903 - end of helix Processing helix chain 'C' and resid 911 through 916 removed outlier: 4.520A pdb=" N GLU C 916 " --> pdb=" O SER C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 929 removed outlier: 4.012A pdb=" N LEU C 924 " --> pdb=" O HIS C 920 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS C 925 " --> pdb=" O TRP C 921 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU C 927 " --> pdb=" O LYS C 923 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL C 928 " --> pdb=" O LEU C 924 " (cutoff:3.500A) Processing helix chain 'C' and resid 939 through 952 removed outlier: 4.481A pdb=" N ILE C 943 " --> pdb=" O MET C 939 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LYS C 947 " --> pdb=" O ILE C 943 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N LEU C 948 " --> pdb=" O TRP C 944 " (cutoff:3.500A) removed outlier: 8.638A pdb=" N PHE C 949 " --> pdb=" O ASP C 945 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ASP C 950 " --> pdb=" O LEU C 946 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N TYR C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N LYS C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 953 through 982 removed outlier: 4.224A pdb=" N ASP C 977 " --> pdb=" O LYS C 973 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N PHE C 978 " --> pdb=" O LYS C 974 " (cutoff:3.500A) Processing helix chain 'C' and resid 1000 through 1020 removed outlier: 3.507A pdb=" N ASP C1009 " --> pdb=" O GLU C1005 " (cutoff:3.500A) Processing helix chain 'C' and resid 1024 through 1061 removed outlier: 5.755A pdb=" N LYS C1028 " --> pdb=" O ALA C1024 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N GLU C1029 " --> pdb=" O TYR C1025 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS C1032 " --> pdb=" O LYS C1028 " (cutoff:3.500A) Processing helix chain 'C' and resid 1066 through 1072 removed outlier: 5.114A pdb=" N GLU C1070 " --> pdb=" O GLU C1066 " (cutoff:3.500A) Proline residue: C1072 - end of helix Processing helix chain 'C' and resid 1073 through 1096 removed outlier: 4.630A pdb=" N GLN C1077 " --> pdb=" O ASN C1073 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N LYS C1083 " --> pdb=" O VAL C1079 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ASP C1084 " --> pdb=" O GLY C1080 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS C1086 " --> pdb=" O ASP C1082 " (cutoff:3.500A) Processing helix chain 'C' and resid 1097 through 1106 removed outlier: 3.664A pdb=" N CYS C1102 " --> pdb=" O CYS C1098 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ILE C1104 " --> pdb=" O LYS C1100 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N GLU C1105 " --> pdb=" O PHE C1101 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N GLY C1106 " --> pdb=" O CYS C1102 " (cutoff:3.500A) Processing helix chain 'C' and resid 1107 through 1137 removed outlier: 3.545A pdb=" N ASN C1113 " --> pdb=" O LYS C1109 " (cutoff:3.500A) Proline residue: C1137 - end of helix Processing helix chain 'C' and resid 1138 through 1143 removed outlier: 3.748A pdb=" N VAL C1142 " --> pdb=" O ARG C1138 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N SER C1143 " --> pdb=" O PHE C1139 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1138 through 1143' Processing helix chain 'C' and resid 1144 through 1154 removed outlier: 3.569A pdb=" N ASP C1149 " --> pdb=" O ASN C1145 " (cutoff:3.500A) Processing helix chain 'C' and resid 1156 through 1169 removed outlier: 3.973A pdb=" N ILE C1160 " --> pdb=" O SER C1156 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ARG C1162 " --> pdb=" O ALA C1158 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N HIS C1163 " --> pdb=" O LYS C1159 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N SER C1165 " --> pdb=" O ASN C1161 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N LYS C1166 " --> pdb=" O ARG C1162 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE C1167 " --> pdb=" O HIS C1163 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN C1169 " --> pdb=" O SER C1165 " (cutoff:3.500A) Processing helix chain 'C' and resid 1210 through 1237 removed outlier: 3.600A pdb=" N LYS C1216 " --> pdb=" O GLU C1212 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE C1234 " --> pdb=" O ALA C1230 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYS C1235 " --> pdb=" O ASN C1231 " (cutoff:3.500A) Processing helix chain 'C' and resid 1241 through 1250 removed outlier: 3.514A pdb=" N LEU C1246 " --> pdb=" O ARG C1242 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LYS C1247 " --> pdb=" O LYS C1243 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N SER C1248 " --> pdb=" O GLU C1244 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASP C1249 " --> pdb=" O TRP C1245 " (cutoff:3.500A) Proline residue: C1250 - end of helix Processing helix chain 'C' and resid 1251 through 1276 removed outlier: 3.805A pdb=" N LEU C1255 " --> pdb=" O SER C1251 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU C1271 " --> pdb=" O GLU C1267 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY C1276 " --> pdb=" O LYS C1272 " (cutoff:3.500A) Processing helix chain 'C' and resid 1279 through 1300 removed outlier: 3.619A pdb=" N PHE C1284 " --> pdb=" O ALA C1280 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL C1299 " --> pdb=" O LEU C1295 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N GLN C1300 " --> pdb=" O ILE C1296 " (cutoff:3.500A) Processing helix chain 'C' and resid 1305 through 1332 removed outlier: 3.651A pdb=" N LYS C1310 " --> pdb=" O PRO C1306 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N HIS C1320 " --> pdb=" O THR C1316 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN C1330 " --> pdb=" O HIS C1326 " (cutoff:3.500A) Processing helix chain 'C' and resid 1338 through 1345 removed outlier: 3.893A pdb=" N GLN C1344 " --> pdb=" O GLN C1340 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N LEU C1345 " --> pdb=" O TRP C1341 " (cutoff:3.500A) Processing helix chain 'C' and resid 1379 through 1396 removed outlier: 3.514A pdb=" N TYR C1386 " --> pdb=" O THR C1382 " (cutoff:3.500A) Processing helix chain 'C' and resid 1408 through 1421 removed outlier: 3.688A pdb=" N THR C1413 " --> pdb=" O LYS C1409 " (cutoff:3.500A) Processing helix chain 'C' and resid 1434 through 1449 Processing helix chain 'C' and resid 1461 through 1482 removed outlier: 3.513A pdb=" N LEU C1465 " --> pdb=" O LEU C1461 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N SER C1466 " --> pdb=" O PRO C1462 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N VAL C1467 " --> pdb=" O GLU C1463 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL C1470 " --> pdb=" O SER C1466 " (cutoff:3.500A) Processing helix chain 'C' and resid 1516 through 1524 removed outlier: 3.612A pdb=" N LEU C1522 " --> pdb=" O GLY C1518 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N ARG C1524 " --> pdb=" O LYS C1520 " (cutoff:3.500A) Processing helix chain 'C' and resid 1532 through 1545 removed outlier: 3.577A pdb=" N ASN C1539 " --> pdb=" O LEU C1535 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU C1544 " --> pdb=" O MET C1540 " (cutoff:3.500A) Processing helix chain 'C' and resid 1548 through 1567 removed outlier: 4.045A pdb=" N LEU C1552 " --> pdb=" O GLU C1548 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS C1554 " --> pdb=" O LYS C1550 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR C1560 " --> pdb=" O PHE C1556 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ASP C1565 " --> pdb=" O MET C1561 " (cutoff:3.500A) Processing helix chain 'C' and resid 1576 through 1594 Processing helix chain 'C' and resid 1598 through 1615 removed outlier: 3.608A pdb=" N ASN C1611 " --> pdb=" O LEU C1607 " (cutoff:3.500A) Proline residue: C1613 - end of helix Processing helix chain 'C' and resid 1619 through 1632 removed outlier: 3.519A pdb=" N PHE C1631 " --> pdb=" O LEU C1627 " (cutoff:3.500A) Proline residue: C1632 - end of helix Processing helix chain 'C' and resid 1641 through 1656 removed outlier: 3.531A pdb=" N GLU C1654 " --> pdb=" O ASP C1650 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN C1655 " --> pdb=" O VAL C1651 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N LYS C1656 " --> pdb=" O CYS C1652 " (cutoff:3.500A) Processing helix chain 'C' and resid 1660 through 1677 removed outlier: 3.743A pdb=" N LEU C1665 " --> pdb=" O PRO C1661 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS C1666 " --> pdb=" O GLU C1662 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA C1675 " --> pdb=" O SER C1671 " (cutoff:3.500A) Processing helix chain 'C' and resid 1689 through 1705 removed outlier: 3.768A pdb=" N TRP C1694 " --> pdb=" O LYS C1690 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LYS C1703 " --> pdb=" O LYS C1699 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N THR C1704 " --> pdb=" O ALA C1700 " (cutoff:3.500A) Processing helix chain 'C' and resid 1714 through 1719 removed outlier: 3.838A pdb=" N VAL C1718 " --> pdb=" O ASP C1714 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N SER C1719 " --> pdb=" O PRO C1715 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1714 through 1719' Processing helix chain 'C' and resid 1720 through 1725 removed outlier: 3.671A pdb=" N TYR C1724 " --> pdb=" O THR C1720 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N GLY C1725 " --> pdb=" O LYS C1721 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1720 through 1725' Processing helix chain 'C' and resid 1736 through 1749 removed outlier: 3.643A pdb=" N MET C1741 " --> pdb=" O LEU C1737 " (cutoff:3.500A) Proline residue: C1749 - end of helix Processing helix chain 'C' and resid 1763 through 1775 removed outlier: 3.715A pdb=" N ILE C1767 " --> pdb=" O ASP C1763 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N GLU C1768 " --> pdb=" O ALA C1764 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N SER C1769 " --> pdb=" O ASN C1765 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N MET C1770 " --> pdb=" O TRP C1766 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N SER C1772 " --> pdb=" O GLU C1768 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N VAL C1773 " --> pdb=" O SER C1769 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ASP C1775 " --> pdb=" O ASN C1771 " (cutoff:3.500A) Processing helix chain 'C' and resid 1807 through 1815 removed outlier: 5.156A pdb=" N GLY C1815 " --> pdb=" O VAL C1811 " (cutoff:3.500A) Processing helix chain 'C' and resid 1824 through 1839 removed outlier: 4.010A pdb=" N ARG C1828 " --> pdb=" O GLY C1824 " (cutoff:3.500A) Processing helix chain 'C' and resid 1842 through 1867 removed outlier: 3.833A pdb=" N SER C1846 " --> pdb=" O ASP C1842 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU C1852 " --> pdb=" O ASN C1848 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS C1855 " --> pdb=" O THR C1851 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL C1857 " --> pdb=" O PHE C1853 " (cutoff:3.500A) Proline residue: C1858 - end of helix removed outlier: 3.532A pdb=" N LYS C1865 " --> pdb=" O LEU C1861 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N HIS C1867 " --> pdb=" O HIS C1863 " (cutoff:3.500A) Processing helix chain 'C' and resid 1875 through 1895 removed outlier: 3.569A pdb=" N GLN C1879 " --> pdb=" O SER C1875 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR C1889 " --> pdb=" O LYS C1885 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU C1890 " --> pdb=" O SER C1886 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ASP C1894 " --> pdb=" O LEU C1890 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL C1895 " --> pdb=" O LEU C1891 " (cutoff:3.500A) Processing helix chain 'C' and resid 1899 through 1912 removed outlier: 4.905A pdb=" N VAL C1903 " --> pdb=" O GLU C1899 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR C1904 " --> pdb=" O TYR C1900 " (cutoff:3.500A) Processing helix chain 'C' and resid 1921 through 1934 removed outlier: 3.995A pdb=" N ASP C1925 " --> pdb=" O ASP C1921 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY C1932 " --> pdb=" O THR C1928 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N ALA C1933 " --> pdb=" O TRP C1929 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N TRP C1934 " --> pdb=" O TRP C1930 " (cutoff:3.500A) Processing helix chain 'C' and resid 1978 through 1983 removed outlier: 3.801A pdb=" N ILE C1982 " --> pdb=" O THR C1978 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N THR C1983 " --> pdb=" O MET C1979 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1978 through 1983' Processing helix chain 'C' and resid 1986 through 2003 removed outlier: 3.576A pdb=" N ALA C1991 " --> pdb=" O ILE C1987 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL C2002 " --> pdb=" O SER C1998 " (cutoff:3.500A) Processing helix chain 'C' and resid 2016 through 2032 removed outlier: 3.904A pdb=" N ALA C2020 " --> pdb=" O LYS C2016 " (cutoff:3.500A) Proline residue: C2032 - end of helix Processing helix chain 'C' and resid 2047 through 2059 removed outlier: 3.845A pdb=" N THR C2058 " --> pdb=" O GLN C2054 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU C2059 " --> pdb=" O ILE C2055 " (cutoff:3.500A) Processing helix chain 'C' and resid 2093 through 2105 removed outlier: 3.543A pdb=" N ALA C2097 " --> pdb=" O GLN C2093 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU C2098 " --> pdb=" O THR C2094 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU C2099 " --> pdb=" O ALA C2095 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TYR C2105 " --> pdb=" O GLN C2101 " (cutoff:3.500A) Processing helix chain 'C' and resid 2138 through 2146 removed outlier: 4.349A pdb=" N HIS C2144 " --> pdb=" O ARG C2140 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N PHE C2145 " --> pdb=" O TYR C2141 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N TRP C2146 " --> pdb=" O GLN C2142 " (cutoff:3.500A) Processing helix chain 'C' and resid 2154 through 2174 removed outlier: 3.583A pdb=" N THR C2164 " --> pdb=" O LEU C2160 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N PHE C2165 " --> pdb=" O ILE C2161 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N ARG C2172 " --> pdb=" O GLY C2168 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N PHE C2173 " --> pdb=" O HIS C2169 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N LYS C2174 " --> pdb=" O LEU C2170 " (cutoff:3.500A) Processing helix chain 'C' and resid 2175 through 2200 removed outlier: 3.678A pdb=" N TYR C2180 " --> pdb=" O THR C2176 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N ASN C2182 " --> pdb=" O GLN C2178 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N ILE C2183 " --> pdb=" O GLU C2179 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL C2185 " --> pdb=" O SER C2181 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG C2186 " --> pdb=" O ASN C2182 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLN C2197 " --> pdb=" O GLN C2193 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ARG C2200 " --> pdb=" O THR C2196 " (cutoff:3.500A) Processing helix chain 'C' and resid 2211 through 2226 removed outlier: 3.990A pdb=" N MET C2215 " --> pdb=" O ASN C2211 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL C2218 " --> pdb=" O HIS C2214 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE C2219 " --> pdb=" O MET C2215 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY C2221 " --> pdb=" O ASN C2217 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU C2222 " --> pdb=" O VAL C2218 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER C2225 " --> pdb=" O GLY C2221 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N ASP C2226 " --> pdb=" O LEU C2222 " (cutoff:3.500A) Processing helix chain 'C' and resid 2232 through 2248 removed outlier: 3.811A pdb=" N LEU C2236 " --> pdb=" O GLU C2232 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ILE C2237 " --> pdb=" O PRO C2233 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS C2238 " --> pdb=" O ASP C2234 " (cutoff:3.500A) Processing helix chain 'C' and resid 2254 through 2273 removed outlier: 3.863A pdb=" N LEU C2258 " --> pdb=" O SER C2254 " (cutoff:3.500A) Processing helix chain 'C' and resid 2278 through 2283 removed outlier: 4.160A pdb=" N PHE C2282 " --> pdb=" O PHE C2278 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N GLY C2283 " --> pdb=" O SER C2279 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2278 through 2283' Processing helix chain 'C' and resid 2309 through 2327 removed outlier: 4.170A pdb=" N GLU C2313 " --> pdb=" O ASN C2309 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LYS C2314 " --> pdb=" O ASN C2310 " (cutoff:3.500A) Processing helix chain 'C' and resid 2335 through 2351 removed outlier: 3.506A pdb=" N LYS C2340 " --> pdb=" O GLU C2336 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU C2350 " --> pdb=" O CYS C2346 " (cutoff:3.500A) Proline residue: C2351 - end of helix Processing helix chain 'C' and resid 2365 through 2378 removed outlier: 4.937A pdb=" N LEU C2369 " --> pdb=" O GLY C2365 " (cutoff:3.500A) Processing helix chain 'C' and resid 2391 through 2407 Processing helix chain 'C' and resid 2418 through 2423 removed outlier: 3.809A pdb=" N ILE C2422 " --> pdb=" O THR C2418 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N THR C2423 " --> pdb=" O GLU C2419 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2418 through 2423' Processing helix chain 'C' and resid 2424 through 2437 removed outlier: 4.204A pdb=" N LEU C2428 " --> pdb=" O ASN C2424 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL C2429 " --> pdb=" O GLU C2425 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N TYR C2430 " --> pdb=" O ARG C2426 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE C2431 " --> pdb=" O PHE C2427 " (cutoff:3.500A) Processing helix chain 'C' and resid 2445 through 2464 removed outlier: 3.573A pdb=" N GLN C2455 " --> pdb=" O ALA C2451 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA C2458 " --> pdb=" O ASN C2454 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LYS C2459 " --> pdb=" O GLN C2455 " (cutoff:3.500A) Processing helix chain 'C' and resid 2469 through 2485 removed outlier: 4.345A pdb=" N TRP C2473 " --> pdb=" O ARG C2469 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASP C2478 " --> pdb=" O ASN C2474 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N HIS C2485 " --> pdb=" O LYS C2481 " (cutoff:3.500A) Processing helix chain 'C' and resid 2495 through 2504 removed outlier: 5.055A pdb=" N ARG C2499 " --> pdb=" O ASP C2495 " (cutoff:3.500A) Proline residue: C2504 - end of helix Processing helix chain 'C' and resid 2519 through 2532 Processing helix chain 'C' and resid 2538 through 2567 removed outlier: 3.511A pdb=" N LYS C2547 " --> pdb=" O GLU C2543 " (cutoff:3.500A) Proline residue: C2550 - end of helix Processing helix chain 'C' and resid 2574 through 2699 removed outlier: 3.518A pdb=" N PHE C2578 " --> pdb=" O THR C2574 " (cutoff:3.500A) Proline residue: C2689 - end of helix Processing helix chain 'C' and resid 2701 through 2711 removed outlier: 3.519A pdb=" N GLN C2707 " --> pdb=" O LYS C2703 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS C2710 " --> pdb=" O PHE C2706 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER C2711 " --> pdb=" O GLN C2707 " (cutoff:3.500A) Processing helix chain 'C' and resid 2717 through 2730 removed outlier: 3.679A pdb=" N GLU C2721 " --> pdb=" O ALA C2717 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA C2725 " --> pdb=" O GLU C2721 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TYR C2728 " --> pdb=" O ALA C2724 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LEU C2730 " --> pdb=" O THR C2726 " (cutoff:3.500A) Processing helix chain 'C' and resid 2750 through 2759 removed outlier: 3.530A pdb=" N LEU C2755 " --> pdb=" O TRP C2751 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LYS C2756 " --> pdb=" O LYS C2752 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS C2759 " --> pdb=" O LEU C2755 " (cutoff:3.500A) Processing helix chain 'C' and resid 2760 through 2777 removed outlier: 5.266A pdb=" N ALA C2777 " --> pdb=" O ASP C2773 " (cutoff:3.500A) Processing helix chain 'C' and resid 2783 through 2797 Proline residue: C2796 - end of helix Processing helix chain 'C' and resid 2799 through 2807 removed outlier: 3.923A pdb=" N SER C2805 " --> pdb=" O GLU C2801 " (cutoff:3.500A) Processing helix chain 'C' and resid 2808 through 2846 removed outlier: 3.623A pdb=" N GLY C2812 " --> pdb=" O ALA C2808 " (cutoff:3.500A) Proline residue: C2832 - end of helix Processing helix chain 'C' and resid 2859 through 2928 Processing helix chain 'C' and resid 2942 through 2962 removed outlier: 3.695A pdb=" N ASN C2947 " --> pdb=" O LYS C2943 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILE C2950 " --> pdb=" O ARG C2946 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ASN C2953 " --> pdb=" O MET C2949 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE C2954 " --> pdb=" O ILE C2950 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N MET C2955 " --> pdb=" O ASN C2951 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N LYS C2956 " --> pdb=" O GLN C2952 " (cutoff:3.500A) Processing helix chain 'C' and resid 2970 through 2976 removed outlier: 4.660A pdb=" N ILE C2974 " --> pdb=" O ASN C2970 " (cutoff:3.500A) Processing helix chain 'C' and resid 2977 through 2988 removed outlier: 3.565A pdb=" N ILE C2981 " --> pdb=" O ASP C2977 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS C2986 " --> pdb=" O ALA C2982 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLN C2987 " --> pdb=" O LEU C2983 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N LYS C2988 " --> pdb=" O TRP C2984 " (cutoff:3.500A) Processing helix chain 'C' and resid 2992 through 3005 Processing helix chain 'C' and resid 3016 through 3027 removed outlier: 3.696A pdb=" N THR C3020 " --> pdb=" O LEU C3016 " (cutoff:3.500A) Processing helix chain 'C' and resid 3038 through 3052 removed outlier: 5.115A pdb=" N ASN C3042 " --> pdb=" O SER C3038 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ARG C3043 " --> pdb=" O LYS C3039 " (cutoff:3.500A) Processing helix chain 'C' and resid 3065 through 3073 removed outlier: 3.703A pdb=" N MET C3069 " --> pdb=" O ASP C3065 " (cutoff:3.500A) Proline residue: C3070 - end of helix Processing helix chain 'C' and resid 3112 through 3120 removed outlier: 3.511A pdb=" N GLN C3116 " --> pdb=" O PRO C3112 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ALA C3120 " --> pdb=" O GLN C3116 " (cutoff:3.500A) Processing helix chain 'C' and resid 3127 through 3145 removed outlier: 3.528A pdb=" N LEU C3138 " --> pdb=" O GLN C3134 " (cutoff:3.500A) Proline residue: C3145 - end of helix Processing helix chain 'C' and resid 3146 through 3176 removed outlier: 3.833A pdb=" N ILE C3152 " --> pdb=" O ALA C3148 " (cutoff:3.500A) Processing helix chain 'C' and resid 3182 through 3225 removed outlier: 5.519A pdb=" N ILE C3187 " --> pdb=" O ILE C3183 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N GLU C3188 " --> pdb=" O LEU C3184 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N LEU C3189 " --> pdb=" O ASP C3185 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ILE C3190 " --> pdb=" O ASP C3186 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS C3198 " --> pdb=" O GLU C3194 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE C3212 " --> pdb=" O ALA C3208 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLU C3222 " --> pdb=" O ASN C3218 " (cutoff:3.500A) Processing helix chain 'C' and resid 3226 through 3245 removed outlier: 3.684A pdb=" N SER C3242 " --> pdb=" O LEU C3238 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N LYS C3243 " --> pdb=" O SER C3239 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL C3244 " --> pdb=" O ASP C3240 " (cutoff:3.500A) Processing helix chain 'C' and resid 3251 through 3267 removed outlier: 3.770A pdb=" N ALA C3265 " --> pdb=" O ARG C3261 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ILE C3266 " --> pdb=" O ALA C3262 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N SER C3267 " --> pdb=" O ILE C3263 " (cutoff:3.500A) Processing helix chain 'C' and resid 3380 through 3408 removed outlier: 3.853A pdb=" N GLY C3407 " --> pdb=" O THR C3403 " (cutoff:3.500A) Processing helix chain 'C' and resid 3412 through 3429 removed outlier: 3.685A pdb=" N ALA C3417 " --> pdb=" O LYS C3413 " (cutoff:3.500A) Processing helix chain 'C' and resid 3432 through 3442 removed outlier: 3.696A pdb=" N VAL C3436 " --> pdb=" O ASN C3432 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASP C3437 " --> pdb=" O SER C3433 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE C3441 " --> pdb=" O ASP C3437 " (cutoff:3.500A) Processing helix chain 'C' and resid 3453 through 3461 removed outlier: 3.662A pdb=" N LEU C3459 " --> pdb=" O LEU C3455 " (cutoff:3.500A) Processing helix chain 'C' and resid 3463 through 3469 Processing helix chain 'C' and resid 3479 through 3487 removed outlier: 3.557A pdb=" N LEU C3483 " --> pdb=" O PHE C3479 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLU C3484 " --> pdb=" O CYS C3480 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR C3485 " --> pdb=" O GLN C3481 " (cutoff:3.500A) Processing helix chain 'C' and resid 3488 through 3497 removed outlier: 4.268A pdb=" N LYS C3492 " --> pdb=" O LEU C3488 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TRP C3493 " --> pdb=" O GLN C3489 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU C3496 " --> pdb=" O LYS C3492 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N GLU C3497 " --> pdb=" O TRP C3493 " (cutoff:3.500A) Processing helix chain 'C' and resid 3512 through 3523 removed outlier: 3.510A pdb=" N ARG C3516 " --> pdb=" O SER C3512 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU C3517 " --> pdb=" O LYS C3513 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU C3518 " --> pdb=" O PHE C3514 " (cutoff:3.500A) Processing helix chain 'C' and resid 3524 through 3540 removed outlier: 4.239A pdb=" N LEU C3528 " --> pdb=" O ARG C3524 " (cutoff:3.500A) Proline residue: C3529 - end of helix removed outlier: 3.570A pdb=" N GLN C3534 " --> pdb=" O SER C3530 " (cutoff:3.500A) Processing helix chain 'C' and resid 3542 through 3547 removed outlier: 6.641A pdb=" N GLU C3546 " --> pdb=" O GLU C3542 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N GLN C3547 " --> pdb=" O ARG C3543 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 3542 through 3547' Processing helix chain 'C' and resid 3551 through 3560 removed outlier: 3.634A pdb=" N GLU C3558 " --> pdb=" O GLU C3554 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N SER C3560 " --> pdb=" O PHE C3556 " (cutoff:3.500A) Processing helix chain 'C' and resid 3575 through 3587 removed outlier: 3.644A pdb=" N VAL C3579 " --> pdb=" O PRO C3575 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR C3585 " --> pdb=" O ARG C3581 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE C3586 " --> pdb=" O VAL C3582 " (cutoff:3.500A) Processing helix chain 'C' and resid 3604 through 3617 removed outlier: 3.659A pdb=" N ALA C3608 " --> pdb=" O GLN C3604 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N GLN C3617 " --> pdb=" O PHE C3613 " (cutoff:3.500A) Processing helix chain 'C' and resid 3626 through 3631 removed outlier: 4.780A pdb=" N MET C3630 " --> pdb=" O ASN C3626 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N GLN C3631 " --> pdb=" O VAL C3627 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 3626 through 3631' Processing helix chain 'C' and resid 3639 through 3650 Processing helix chain 'C' and resid 3677 through 3684 removed outlier: 3.614A pdb=" N SER C3684 " --> pdb=" O ILE C3680 " (cutoff:3.500A) Processing helix chain 'C' and resid 3694 through 3707 removed outlier: 3.590A pdb=" N LYS C3705 " --> pdb=" O ARG C3701 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N PHE C3706 " --> pdb=" O ALA C3702 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N ASP C3707 " --> pdb=" O TYR C3703 " (cutoff:3.500A) Processing helix chain 'C' and resid 3708 through 3714 removed outlier: 4.349A pdb=" N CYS C3714 " --> pdb=" O PHE C3710 " (cutoff:3.500A) Processing helix chain 'C' and resid 3717 through 3742 removed outlier: 3.526A pdb=" N LYS C3739 " --> pdb=" O MET C3735 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N LYS C3740 " --> pdb=" O LEU C3736 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N PHE C3741 " --> pdb=" O GLY C3737 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLY C3742 " --> pdb=" O ARG C3738 " (cutoff:3.500A) Processing helix chain 'C' and resid 3753 through 3771 removed outlier: 3.753A pdb=" N LEU C3757 " --> pdb=" O ASN C3753 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N CYS C3760 " --> pdb=" O ASP C3756 " (cutoff:3.500A) Processing helix chain 'C' and resid 3775 through 3785 removed outlier: 3.617A pdb=" N LEU C3779 " --> pdb=" O PRO C3775 " (cutoff:3.500A) Processing helix chain 'C' and resid 3787 through 3793 removed outlier: 4.790A pdb=" N HIS C3791 " --> pdb=" O MET C3787 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE C3792 " --> pdb=" O TYR C3788 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N THR C3793 " --> pdb=" O GLY C3789 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 3787 through 3793' Processing helix chain 'C' and resid 3794 through 3809 Processing helix chain 'C' and resid 3833 through 3844 removed outlier: 3.654A pdb=" N GLU C3842 " --> pdb=" O ARG C3838 " (cutoff:3.500A) Processing helix chain 'C' and resid 3849 through 3854 removed outlier: 4.382A pdb=" N PHE C3853 " --> pdb=" O SER C3849 " (cutoff:3.500A) Processing helix chain 'C' and resid 3856 through 3880 removed outlier: 4.004A pdb=" N GLU C3860 " --> pdb=" O HIS C3856 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ILE C3861 " --> pdb=" O PRO C3857 " (cutoff:3.500A) Processing helix chain 'C' and resid 3886 through 3905 removed outlier: 4.076A pdb=" N LYS C3890 " --> pdb=" O GLY C3886 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLY C3893 " --> pdb=" O LYS C3889 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL C3894 " --> pdb=" O LYS C3890 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL C3896 " --> pdb=" O ASP C3892 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR C3897 " --> pdb=" O GLY C3893 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR C3899 " --> pdb=" O MET C3895 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASP C3900 " --> pdb=" O VAL C3896 " (cutoff:3.500A) Processing helix chain 'C' and resid 3912 through 3919 removed outlier: 3.564A pdb=" N LYS C3917 " --> pdb=" O LEU C3913 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N VAL C3918 " --> pdb=" O ILE C3914 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYS C3919 " --> pdb=" O GLU C3915 " (cutoff:3.500A) Processing helix chain 'C' and resid 3922 through 3954 removed outlier: 3.640A pdb=" N VAL C3927 " --> pdb=" O PRO C3923 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS C3940 " --> pdb=" O ASN C3936 " (cutoff:3.500A) Processing helix chain 'C' and resid 3960 through 3973 Processing helix chain 'C' and resid 3976 through 3983 removed outlier: 3.678A pdb=" N LYS C3982 " --> pdb=" O THR C3978 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N ALA C3983 " --> pdb=" O TRP C3979 " (cutoff:3.500A) Processing helix chain 'C' and resid 3989 through 4009 Processing helix chain 'C' and resid 4018 through 4023 removed outlier: 3.716A pdb=" N LEU C4022 " --> pdb=" O CYS C4018 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N PHE C4023 " --> pdb=" O ILE C4019 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 4018 through 4023' Processing helix chain 'C' and resid 4024 through 4041 removed outlier: 3.793A pdb=" N TYR C4028 " --> pdb=" O ASN C4024 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA C4039 " --> pdb=" O PHE C4035 " (cutoff:3.500A) Processing helix chain 'C' and resid 4043 through 4048 removed outlier: 3.558A pdb=" N ILE C4047 " --> pdb=" O PRO C4043 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N THR C4048 " --> pdb=" O LEU C4044 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 4043 through 4048' Processing helix chain 'C' and resid 4058 through 4063 removed outlier: 3.986A pdb=" N VAL C4062 " --> pdb=" O GLY C4058 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N VAL C4063 " --> pdb=" O PRO C4059 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 4058 through 4063' Processing helix chain 'C' and resid 4152 through 4160 removed outlier: 4.824A pdb=" N TRP C4156 " --> pdb=" O ASP C4152 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE C4157 " --> pdb=" O PRO C4153 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 149 Proline residue: D 149 - end of helix Processing helix chain 'D' and resid 154 through 164 removed outlier: 5.305A pdb=" N ASN D 164 " --> pdb=" O GLN D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 217 removed outlier: 3.671A pdb=" N GLN D 217 " --> pdb=" O MET D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 258 Processing helix chain 'D' and resid 259 through 266 Processing helix chain 'D' and resid 632 through 655 removed outlier: 3.992A pdb=" N MET D 636 " --> pdb=" O ASP D 632 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N GLU D 637 " --> pdb=" O LYS D 633 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N LYS D 640 " --> pdb=" O MET D 636 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ASN D 641 " --> pdb=" O GLU D 637 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 101 removed outlier: 3.521A pdb=" N THR E 92 " --> pdb=" O GLU E 88 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LYS E 101 " --> pdb=" O LYS E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 127 removed outlier: 3.620A pdb=" N ALA E 108 " --> pdb=" O SER E 104 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS E 110 " --> pdb=" O PRO E 106 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ILE E 126 " --> pdb=" O GLN E 122 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ASP E 127 " --> pdb=" O ASN E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 491 through 496 Processing helix chain 'E' and resid 500 through 536 Processing helix chain 'E' and resid 540 through 568 Proline residue: E 567 - end of helix Processing helix chain 'F' and resid 6 through 18 removed outlier: 3.727A pdb=" N GLN F 10 " --> pdb=" O ASN F 6 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU F 11 " --> pdb=" O ALA F 7 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N GLU F 18 " --> pdb=" O LEU F 14 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 66 removed outlier: 3.575A pdb=" N LEU F 51 " --> pdb=" O HIS F 47 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN F 64 " --> pdb=" O LYS F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 133 Processing helix chain 'G' and resid 2 through 20 removed outlier: 4.140A pdb=" N SER G 6 " --> pdb=" O ILE G 2 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 40 Processing helix chain 'G' and resid 57 through 70 removed outlier: 4.026A pdb=" N GLU G 61 " --> pdb=" O MET G 57 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 119 Proline residue: G 104 - end of helix removed outlier: 3.753A pdb=" N LEU G 117 " --> pdb=" O VAL G 113 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP G 118 " --> pdb=" O VAL G 114 " (cutoff:3.500A) Proline residue: G 119 - end of helix Processing helix chain 'H' and resid 2 through 8 removed outlier: 3.827A pdb=" N GLN H 8 " --> pdb=" O LEU H 4 " (cutoff:3.500A) Processing helix chain 'H' and resid 17 through 35 Processing helix chain 'H' and resid 37 through 53 Processing helix chain 'I' and resid 6 through 11 removed outlier: 5.021A pdb=" N ASP I 11 " --> pdb=" O VAL I 7 " (cutoff:3.500A) Processing helix chain 'I' and resid 12 through 20 removed outlier: 4.296A pdb=" N ILE I 20 " --> pdb=" O ARG I 16 " (cutoff:3.500A) Processing helix chain 'I' and resid 31 through 50 removed outlier: 3.558A pdb=" N GLU I 37 " --> pdb=" O ASP I 33 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 71 Processing helix chain 'J' and resid 33 through 51 Processing helix chain 'J' and resid 56 through 72 removed outlier: 3.887A pdb=" N ILE J 60 " --> pdb=" O GLU J 56 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA J 61 " --> pdb=" O GLY J 57 " (cutoff:3.500A) Processing helix chain 'K' and resid 18 through 36 removed outlier: 4.388A pdb=" N LYS K 22 " --> pdb=" O MET K 18 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN K 23 " --> pdb=" O LYS K 19 " (cutoff:3.500A) Processing helix chain 'K' and resid 38 through 54 removed outlier: 3.518A pdb=" N SER K 43 " --> pdb=" O GLU K 39 " (cutoff:3.500A) Processing helix chain 'L' and resid 9 through 15 removed outlier: 4.532A pdb=" N GLU L 14 " --> pdb=" O ARG L 10 " (cutoff:3.500A) Proline residue: L 15 - end of helix Processing helix chain 'L' and resid 27 through 46 Proline residue: L 46 - end of helix Processing helix chain 'L' and resid 49 through 65 Proline residue: L 65 - end of helix Processing helix chain 'M' and resid 13 through 31 removed outlier: 3.590A pdb=" N LYS M 18 " --> pdb=" O GLU M 14 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS M 29 " --> pdb=" O ILE M 25 " (cutoff:3.500A) Processing helix chain 'M' and resid 33 through 49 removed outlier: 3.615A pdb=" N LYS M 47 " --> pdb=" O TYR M 43 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE M 48 " --> pdb=" O GLU M 44 " (cutoff:3.500A) Processing helix chain 'N' and resid 9 through 25 Processing helix chain 'N' and resid 40 through 62 removed outlier: 3.591A pdb=" N ASN N 44 " --> pdb=" O LYS N 40 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU N 45 " --> pdb=" O ASP N 41 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU N 61 " --> pdb=" O GLY N 57 " (cutoff:3.500A) Processing helix chain 'O' and resid 13 through 23 Processing helix chain 'O' and resid 31 through 47 removed outlier: 4.360A pdb=" N GLN O 35 " --> pdb=" O PRO O 31 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASP O 44 " --> pdb=" O GLU O 40 " (cutoff:3.500A) Processing helix chain 'O' and resid 54 through 75 removed outlier: 4.157A pdb=" N GLN O 58 " --> pdb=" O ASN O 54 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU O 59 " --> pdb=" O ASN O 55 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU O 61 " --> pdb=" O ASN O 57 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG O 62 " --> pdb=" O GLN O 58 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU O 69 " --> pdb=" O LEU O 65 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N LYS O 75 " --> pdb=" O ILE O 71 " (cutoff:3.500A) Processing helix chain 'P' and resid 15 through 27 removed outlier: 3.952A pdb=" N ASN P 27 " --> pdb=" O TYR P 23 " (cutoff:3.500A) Processing helix chain 'P' and resid 43 through 57 Proline residue: P 48 - end of helix Processing helix chain 'P' and resid 73 through 83 Processing helix chain 'P' and resid 107 through 118 Processing helix chain 'Q' and resid 6 through 19 Proline residue: Q 19 - end of helix Processing helix chain 'Q' and resid 42 through 49 removed outlier: 4.151A pdb=" N THR Q 48 " --> pdb=" O PRO Q 44 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N LEU Q 49 " --> pdb=" O VAL Q 45 " (cutoff:3.500A) Processing helix chain 'Q' and resid 90 through 95 removed outlier: 4.747A pdb=" N GLY Q 95 " --> pdb=" O GLU Q 91 " (cutoff:3.500A) Processing helix chain 'Q' and resid 112 through 117 removed outlier: 4.775A pdb=" N CYS Q 116 " --> pdb=" O GLY Q 112 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N SER Q 117 " --> pdb=" O LEU Q 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 112 through 117' Processing helix chain 'Q' and resid 132 through 140 removed outlier: 3.685A pdb=" N ASP Q 136 " --> pdb=" O TRP Q 132 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS Q 137 " --> pdb=" O GLU Q 133 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ASP Q 140 " --> pdb=" O ASP Q 136 " (cutoff:3.500A) Processing helix chain 'Q' and resid 152 through 159 removed outlier: 4.023A pdb=" N LYS Q 159 " --> pdb=" O TYR Q 155 " (cutoff:3.500A) Processing helix chain 'Q' and resid 161 through 171 Proline residue: Q 171 - end of helix Processing helix chain 'Q' and resid 182 through 193 Processing helix chain 'R' and resid 8 through 24 removed outlier: 4.018A pdb=" N ASP R 12 " --> pdb=" O LEU R 8 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N CYS R 16 " --> pdb=" O ASP R 12 " (cutoff:3.500A) Processing helix chain 'R' and resid 31 through 43 removed outlier: 3.663A pdb=" N ASP R 35 " --> pdb=" O ILE R 31 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LEU R 36 " --> pdb=" O LYS R 32 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU R 38 " --> pdb=" O SER R 34 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ALA R 39 " --> pdb=" O ASP R 35 " (cutoff:3.500A) Processing helix chain 'R' and resid 47 through 59 removed outlier: 4.262A pdb=" N ASP R 51 " --> pdb=" O LEU R 47 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL R 59 " --> pdb=" O MET R 55 " (cutoff:3.500A) Processing helix chain 'R' and resid 67 through 79 removed outlier: 4.823A pdb=" N ASP R 71 " --> pdb=" O ILE R 67 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N PHE R 72 " --> pdb=" O LYS R 68 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N TYR R 77 " --> pdb=" O LEU R 73 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN R 79 " --> pdb=" O ILE R 75 " (cutoff:3.500A) Processing helix chain 'R' and resid 87 through 98 removed outlier: 5.470A pdb=" N LEU R 91 " --> pdb=" O ASP R 87 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL R 92 " --> pdb=" O ASP R 88 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N MET R 98 " --> pdb=" O ALA R 94 " (cutoff:3.500A) Processing helix chain 'R' and resid 105 through 116 removed outlier: 4.786A pdb=" N ASP R 109 " --> pdb=" O THR R 105 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N GLN R 115 " --> pdb=" O ASN R 111 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ILE R 116 " --> pdb=" O ARG R 112 " (cutoff:3.500A) Processing helix chain 'R' and resid 121 through 134 removed outlier: 4.788A pdb=" N ILE R 125 " --> pdb=" O PHE R 121 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ILE R 134 " --> pdb=" O LEU R 130 " (cutoff:3.500A) Processing helix chain 'R' and resid 141 through 150 Processing sheet with id= 1, first strand: chain 'A' and resid 95 through 100 Processing sheet with id= 2, first strand: chain 'A' and resid 931 through 934 Processing sheet with id= 3, first strand: chain 'A' and resid 1447 through 1450 No H-bonds generated for sheet with id= 3 Processing sheet with id= 4, first strand: chain 'A' and resid 1635 through 1638 removed outlier: 3.529A pdb=" N GLN A1658 " --> pdb=" O GLU A1665 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'A' and resid 1813 through 1816 Processing sheet with id= 6, first strand: chain 'A' and resid 1893 through 1897 removed outlier: 4.389A pdb=" N SER A1971 " --> pdb=" O LEU A1919 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE A1973 " --> pdb=" O GLY A1921 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY A1868 " --> pdb=" O TYR A1972 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N MET A1976 " --> pdb=" O PRO A1870 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N GLY A1872 " --> pdb=" O MET A1976 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL A1997 " --> pdb=" O ALA A1869 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'A' and resid 1953 through 1956 removed outlier: 5.671A pdb=" N LYS A1953 " --> pdb=" O LEU A1966 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'A' and resid 2180 through 2186 removed outlier: 4.221A pdb=" N THR A2227 " --> pdb=" O PRO A2180 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYS A2182 " --> pdb=" O THR A2227 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N ASN A2267 " --> pdb=" O HIS A2226 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N THR A2228 " --> pdb=" O ASN A2267 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLU A2273 " --> pdb=" O CYS A2232 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N HIS A2151 " --> pdb=" O CYS A2268 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE A2153 " --> pdb=" O VAL A2270 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N PHE A2272 " --> pdb=" O PHE A2153 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'A' and resid 2252 through 2255 removed outlier: 7.129A pdb=" N LYS A2252 " --> pdb=" O MET A2264 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'A' and resid 2515 through 2521 removed outlier: 4.779A pdb=" N LEU A2516 " --> pdb=" O MET A2554 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS A2518 " --> pdb=" O THR A2556 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASP A2560 " --> pdb=" O THR A2520 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N MET A2555 " --> pdb=" O ASN A2604 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ASN A2487 " --> pdb=" O LEU A2605 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N PHE A2632 " --> pdb=" O LEU A2490 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'A' and resid 2586 through 2589 removed outlier: 6.460A pdb=" N GLY A2586 " --> pdb=" O MET A2602 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'A' and resid 2886 through 2890 Processing sheet with id= 13, first strand: chain 'A' and resid 3528 through 3531 removed outlier: 3.505A pdb=" N MET A3625 " --> pdb=" O PRO A3528 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N LYS A3622 " --> pdb=" O LEU A3576 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N CYS A3554 " --> pdb=" O THR A3577 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR A3556 " --> pdb=" O ILE A3579 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'A' and resid 3606 through 3609 removed outlier: 4.585A pdb=" N GLN A3606 " --> pdb=" O LEU A3617 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU A3617 " --> pdb=" O GLN A3606 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'A' and resid 4014 through 4018 removed outlier: 3.584A pdb=" N GLU A4015 " --> pdb=" O TRP A4040 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'A' and resid 4072 through 4077 Processing sheet with id= 17, first strand: chain 'A' and resid 4503 through 4508 removed outlier: 7.119A pdb=" N ILE A4555 " --> pdb=" O LYS A4508 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL A4558 " --> pdb=" O VAL A4524 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'A' and resid 4593 through 4598 removed outlier: 3.670A pdb=" N PHE A4593 " --> pdb=" O VAL A4580 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'B' and resid 53 through 59 removed outlier: 7.007A pdb=" N LYS B 83 " --> pdb=" O ASP B 107 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N ASP B 107 " --> pdb=" O LYS B 83 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N LYS B 85 " --> pdb=" O ALA B 105 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ALA B 105 " --> pdb=" O LYS B 85 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N LYS B 87 " --> pdb=" O ASN B 103 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'B' and resid 901 through 904 No H-bonds generated for sheet with id= 20 Processing sheet with id= 21, first strand: chain 'B' and resid 1643 through 1646 removed outlier: 4.148A pdb=" N GLY B1661 " --> pdb=" O THR B1645 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ILE B1660 " --> pdb=" O PHE B1672 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'B' and resid 1822 through 1825 removed outlier: 6.003A pdb=" N CYS B1852 " --> pdb=" O TYR B1863 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'B' and resid 1921 through 1926 removed outlier: 4.155A pdb=" N GLY B1999 " --> pdb=" O ALA B1948 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE B2002 " --> pdb=" O GLY B1897 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N MET B2004 " --> pdb=" O PRO B1899 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY B1901 " --> pdb=" O MET B2004 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'B' and resid 2208 through 2213 removed outlier: 4.586A pdb=" N GLU B2209 " --> pdb=" O HIS B2258 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TRP B2260 " --> pdb=" O GLU B2209 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ASP B2211 " --> pdb=" O TRP B2260 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASP B2264 " --> pdb=" O LEU B2213 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N HIS B2178 " --> pdb=" O MET B2299 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE B2305 " --> pdb=" O VAL B2182 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'B' and resid 2560 through 2566 removed outlier: 3.657A pdb=" N ILE B2534 " --> pdb=" O PHE B2650 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'B' and resid 2590 through 2593 removed outlier: 9.167A pdb=" N ARG B2590 " --> pdb=" O ARG B2642 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE B2644 " --> pdb=" O ARG B2590 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N LYS B2643 " --> pdb=" O ILE B2633 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N GLY B2631 " --> pdb=" O LEU B2645 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'B' and resid 2909 through 2913 removed outlier: 3.572A pdb=" N GLU B2910 " --> pdb=" O ALA B2943 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N MET B2947 " --> pdb=" O ASP B2912 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'B' and resid 3552 through 3557 removed outlier: 3.922A pdb=" N THR B3554 " --> pdb=" O ALA B3576 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'B' and resid 3598 through 3601 removed outlier: 4.238A pdb=" N LEU B3605 " --> pdb=" O TYR B3616 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'B' and resid 4037 through 4042 removed outlier: 5.169A pdb=" N ARG B4073 " --> pdb=" O HIS B4037 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU B3987 " --> pdb=" O ALA B4078 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'B' and resid 4471 through 4476 removed outlier: 4.180A pdb=" N VAL B4524 " --> pdb=" O THR B4476 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'B' and resid 4560 through 4564 Processing sheet with id= 33, first strand: chain 'C' and resid 7 through 10 removed outlier: 3.506A pdb=" N THR C 8 " --> pdb=" O ALA C 351 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N LEU C 349 " --> pdb=" O LEU C 10 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N SER C 325 " --> pdb=" O PHE C 338 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLY C 340 " --> pdb=" O SER C 323 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N SER C 323 " --> pdb=" O GLY C 340 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'C' and resid 58 through 63 No H-bonds generated for sheet with id= 34 Processing sheet with id= 35, first strand: chain 'C' and resid 85 through 90 removed outlier: 3.764A pdb=" N ALA C 86 " --> pdb=" O PHE C 98 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N CYS C 88 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY C 100 " --> pdb=" O PHE C 108 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'C' and resid 119 through 123 Processing sheet with id= 37, first strand: chain 'C' and resid 149 through 154 removed outlier: 5.723A pdb=" N SER C 150 " --> pdb=" O PHE C 161 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'C' and resid 212 through 217 removed outlier: 4.080A pdb=" N ILE C 234 " --> pdb=" O PRO C 212 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER C 224 " --> pdb=" O SER C 221 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'C' and resid 252 through 261 removed outlier: 6.766A pdb=" N ASN C 252 " --> pdb=" O GLY C 271 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY C 271 " --> pdb=" O ASN C 252 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N SER C 254 " --> pdb=" O PHE C 269 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N SER C 260 " --> pdb=" O SER C 263 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N GLY C 271 " --> pdb=" O VAL C 288 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL C 288 " --> pdb=" O GLY C 271 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG C 286 " --> pdb=" O VAL C 273 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'C' and resid 365 through 368 removed outlier: 4.863A pdb=" N THR C 378 " --> pdb=" O THR C 420 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N LYS C 414 " --> pdb=" O GLY C 384 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'C' and resid 394 through 397 removed outlier: 4.211A pdb=" N SER C 394 " --> pdb=" O CYS C 434 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N CYS C 434 " --> pdb=" O SER C 394 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N THR C 432 " --> pdb=" O LYS C 396 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'C' and resid 459 through 462 removed outlier: 4.858A pdb=" N ILE C 459 " --> pdb=" O GLN C 480 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA C 481 " --> pdb=" O ASP C 516 " (cutoff:3.500A) removed outlier: 9.237A pdb=" N ASP C 516 " --> pdb=" O ALA C 481 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LYS C 517 " --> pdb=" O LYS C 513 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'C' and resid 496 through 500 Processing sheet with id= 44, first strand: chain 'C' and resid 985 through 989 removed outlier: 3.580A pdb=" N VAL C 987 " --> pdb=" O THR C 996 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N HIS C 989 " --> pdb=" O ILE C 994 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N ILE C 994 " --> pdb=" O HIS C 989 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'C' and resid 1172 through 1175 removed outlier: 4.638A pdb=" N MET C1190 " --> pdb=" O GLN C1175 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'C' and resid 1346 through 1349 removed outlier: 5.671A pdb=" N ALA C1354 " --> pdb=" O TYR C1365 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'C' and resid 1423 through 1428 removed outlier: 3.580A pdb=" N CYS C1453 " --> pdb=" O TYR C1425 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N GLY C1500 " --> pdb=" O CYS C1450 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N CYS C1399 " --> pdb=" O VAL C1501 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N MET C1505 " --> pdb=" O PRO C1401 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'C' and resid 1484 through 1488 removed outlier: 6.021A pdb=" N GLU C1484 " --> pdb=" O LEU C1495 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'C' and resid 1708 through 1713 removed outlier: 4.172A pdb=" N THR C1709 " --> pdb=" O PRO C1753 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE C1711 " --> pdb=" O TRP C1755 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ASP C1759 " --> pdb=" O ILE C1713 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N HIS C1678 " --> pdb=" O MET C1794 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N GLY C1684 " --> pdb=" O ILE C1800 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'C' and resid 1778 through 1782 removed outlier: 5.978A pdb=" N LYS C1778 " --> pdb=" O LEU C1790 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LEU C1790 " --> pdb=" O LYS C1778 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N GLU C1786 " --> pdb=" O LEU C1782 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'C' and resid 1949 through 1953 Processing sheet with id= 52, first strand: chain 'C' and resid 2034 through 2041 removed outlier: 3.659A pdb=" N ALA C2036 " --> pdb=" O GLN C2074 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE C2040 " --> pdb=" O PHE C2078 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ASN C2121 " --> pdb=" O VAL C2073 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU C2075 " --> pdb=" O ASN C2121 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLN C2123 " --> pdb=" O LEU C2075 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N SER C2006 " --> pdb=" O VAL C2124 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N ASN C2011 " --> pdb=" O ILE C2150 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'C' and resid 2106 through 2110 removed outlier: 5.840A pdb=" N GLY C2106 " --> pdb=" O ILE C2119 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ALA C2115 " --> pdb=" O ASP C2110 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'C' and resid 2486 through 2491 removed outlier: 3.668A pdb=" N VAL C2359 " --> pdb=" O ASP C2513 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N VAL C2361 " --> pdb=" O PHE C2515 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'C' and resid 3031 through 3034 removed outlier: 3.710A pdb=" N ILE C3056 " --> pdb=" O LYS C3099 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU C3058 " --> pdb=" O PHE C3101 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N LYS C3105 " --> pdb=" O MET C3060 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'C' and resid 3083 through 3086 removed outlier: 5.826A pdb=" N LYS C3083 " --> pdb=" O LEU C3094 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU C3094 " --> pdb=" O LYS C3083 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'C' and resid 3594 through 3599 removed outlier: 3.577A pdb=" N GLN C3625 " --> pdb=" O ILE C3598 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N ARG C3658 " --> pdb=" O HIS C3620 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE C3622 " --> pdb=" O ARG C3658 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU C3685 " --> pdb=" O PRO C3564 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'C' and resid 4049 through 4054 removed outlier: 3.608A pdb=" N ASN C4052 " --> pdb=" O ASN C4109 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N VAL C4107 " --> pdb=" O THR C4054 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'C' and resid 4080 through 4084 removed outlier: 3.812A pdb=" N TYR C4092 " --> pdb=" O GLU C4083 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'C' and resid 4142 through 4146 removed outlier: 3.530A pdb=" N MET C4163 " --> pdb=" O PRO C4127 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'C' and resid 93 through 98 removed outlier: 8.464A pdb=" N ASP C 93 " --> pdb=" O THR C 116 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR C 116 " --> pdb=" O ASP C 93 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'C' and resid 264 through 269 removed outlier: 7.296A pdb=" N TRP C 264 " --> pdb=" O ILE C 296 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'D' and resid 85 through 89 removed outlier: 3.629A pdb=" N ILE D 86 " --> pdb=" O ASP D 99 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LYS D 97 " --> pdb=" O VAL D 88 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'D' and resid 302 through 305 removed outlier: 6.033A pdb=" N LEU D 311 " --> pdb=" O ASN D 305 " (cutoff:3.500A) removed outlier: 8.514A pdb=" N ASP D 310 " --> pdb=" O LEU D 334 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE D 312 " --> pdb=" O TYR D 332 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LEU D 328 " --> pdb=" O LEU D 316 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY D 327 " --> pdb=" O CYS D 346 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'D' and resid 351 through 356 removed outlier: 6.065A pdb=" N LEU D 362 " --> pdb=" O HIS D 356 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N ALA D 361 " --> pdb=" O ILE D 377 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR D 371 " --> pdb=" O LEU D 367 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N VAL D 372 " --> pdb=" O SER D 388 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'D' and resid 401 through 405 removed outlier: 3.558A pdb=" N GLN D 401 " --> pdb=" O ILE D 417 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N ASN D 413 " --> pdb=" O ASN D 405 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N TYR D 412 " --> pdb=" O LEU D 428 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N VAL D 423 " --> pdb=" O VAL D 438 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU D 434 " --> pdb=" O ILE D 427 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'D' and resid 461 through 464 removed outlier: 3.949A pdb=" N CYS D 461 " --> pdb=" O GLY D 475 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N HIS D 470 " --> pdb=" O ARG D 486 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N THR D 476 " --> pdb=" O LYS D 480 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N LYS D 480 " --> pdb=" O THR D 476 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU D 494 " --> pdb=" O LYS D 483 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'D' and resid 505 through 509 removed outlier: 6.121A pdb=" N THR D 515 " --> pdb=" O ASN D 509 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N ARG D 514 " --> pdb=" O SER D 530 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N TRP D 523 " --> pdb=" O LEU D 541 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'D' and resid 548 through 551 removed outlier: 5.707A pdb=" N VAL D 557 " --> pdb=" O ALA D 551 " (cutoff:3.500A) removed outlier: 9.093A pdb=" N THR D 556 " --> pdb=" O LEU D 571 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'D' and resid 592 through 596 removed outlier: 4.940A pdb=" N ILE D 601 " --> pdb=" O ASN D 596 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N GLY D 610 " --> pdb=" O ASP D 606 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'E' and resid 150 through 154 removed outlier: 3.954A pdb=" N MET E 151 " --> pdb=" O ILE E 487 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N LYS E 474 " --> pdb=" O LEU E 490 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'E' and resid 166 through 170 removed outlier: 3.512A pdb=" N GLU E 166 " --> pdb=" O SER E 180 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LYS E 176 " --> pdb=" O HIS E 170 " (cutoff:3.500A) removed outlier: 8.733A pdb=" N THR E 175 " --> pdb=" O LEU E 202 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR E 198 " --> pdb=" O VAL E 179 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE E 210 " --> pdb=" O VAL E 199 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'E' and resid 230 through 235 removed outlier: 4.280A pdb=" N LEU E 239 " --> pdb=" O CYS E 235 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'E' and resid 267 through 271 removed outlier: 3.684A pdb=" N GLU E 278 " --> pdb=" O LEU E 271 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU E 302 " --> pdb=" O TRP E 290 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'E' and resid 321 through 324 removed outlier: 5.900A pdb=" N SER E 331 " --> pdb=" O LYS E 347 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N SER E 341 " --> pdb=" O THR E 337 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LYS E 348 " --> pdb=" O PRO E 352 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'E' and resid 372 through 375 removed outlier: 3.523A pdb=" N SER E 372 " --> pdb=" O VAL E 386 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'E' and resid 413 through 417 removed outlier: 3.700A pdb=" N ASP E 414 " --> pdb=" O VAL E 428 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N GLY E 423 " --> pdb=" O TYR E 439 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N TRP E 433 " --> pdb=" O ARG E 429 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE E 448 " --> pdb=" O VAL E 436 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'F' and resid 21 through 26 removed outlier: 4.962A pdb=" N TYR F 85 " --> pdb=" O THR F 81 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU F 79 " --> pdb=" O TYR F 87 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'G' and resid 86 through 90 removed outlier: 3.760A pdb=" N ARG G 87 " --> pdb=" O ILE G 78 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ALA G 89 " --> pdb=" O TYR G 76 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N TYR G 76 " --> pdb=" O ALA G 89 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLY G 75 " --> pdb=" O ILE G 148 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE G 143 " --> pdb=" O ASP G 140 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 'H' and resid 13 through 16 removed outlier: 3.507A pdb=" N ASN H 13 " --> pdb=" O TYR H 78 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TYR H 76 " --> pdb=" O ASP H 15 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N TYR H 75 " --> pdb=" O LYS H 90 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LYS H 90 " --> pdb=" O TYR H 75 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE H 77 " --> pdb=" O LEU H 88 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU H 88 " --> pdb=" O ILE H 77 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU H 87 " --> pdb=" O ILE H 60 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N HIS H 58 " --> pdb=" O PHE H 89 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N THR H 56 " --> pdb=" O THR H 91 " (cutoff:3.500A) Processing sheet with id= 81, first strand: chain 'I' and resid 74 through 80 removed outlier: 6.016A pdb=" N THR I 74 " --> pdb=" O SER I 110 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N THR I 93 " --> pdb=" O LYS I 109 " (cutoff:3.500A) Processing sheet with id= 82, first strand: chain 'J' and resid 75 through 80 removed outlier: 6.538A pdb=" N TYR J 75 " --> pdb=" O THR J 110 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N ARG J 94 " --> pdb=" O GLN J 109 " (cutoff:3.500A) Processing sheet with id= 83, first strand: chain 'K' and resid 8 through 12 removed outlier: 3.732A pdb=" N PHE K 77 " --> pdb=" O ASP K 11 " (cutoff:3.500A) Processing sheet with id= 84, first strand: chain 'K' and resid 57 through 62 removed outlier: 5.434A pdb=" N ASN K 57 " --> pdb=" O LYS K 92 " (cutoff:3.500A) Processing sheet with id= 85, first strand: chain 'L' and resid 18 through 22 removed outlier: 3.622A pdb=" N ARG L 22 " --> pdb=" O PHE L 95 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N PHE L 95 " --> pdb=" O ARG L 22 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N VAL L 92 " --> pdb=" O LYS L 109 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS L 109 " --> pdb=" O VAL L 92 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU L 98 " --> pdb=" O LYS L 103 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LYS L 103 " --> pdb=" O LEU L 98 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER L 104 " --> pdb=" O GLY L 79 " (cutoff:3.500A) Processing sheet with id= 86, first strand: chain 'M' and resid 52 through 58 removed outlier: 9.073A pdb=" N GLY M 52 " --> pdb=" O ALA M 87 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ALA M 87 " --> pdb=" O GLY M 52 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS M 86 " --> pdb=" O LYS M 71 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LYS M 71 " --> pdb=" O LYS M 86 " (cutoff:3.500A) Processing sheet with id= 87, first strand: chain 'N' and resid 64 through 74 removed outlier: 6.707A pdb=" N HIS N 64 " --> pdb=" O VAL N 117 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL N 117 " --> pdb=" O HIS N 64 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR N 107 " --> pdb=" O GLN N 74 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU N 97 " --> pdb=" O VAL N 112 " (cutoff:3.500A) Processing sheet with id= 88, first strand: chain 'O' and resid 79 through 87 removed outlier: 3.513A pdb=" N GLY O 128 " --> pdb=" O ASN O 109 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ASN O 109 " --> pdb=" O GLY O 128 " (cutoff:3.500A) Processing sheet with id= 89, first strand: chain 'P' and resid 10 through 14 removed outlier: 4.869A pdb=" N THR P 11 " --> pdb=" O ASP P 65 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N VAL P 13 " --> pdb=" O LEU P 67 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU P 69 " --> pdb=" O VAL P 13 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP P 100 " --> pdb=" O PHE P 92 " (cutoff:3.500A) 6868 hydrogen bonds defined for protein. 20517 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: 79.64 Time building geometry restraints manager: 41.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.44 - 0.94: 9 0.94 - 1.43: 50746 1.43 - 1.93: 70973 1.93 - 2.43: 7 2.43 - 2.93: 6 Warning: very small bond lengths. Bond restraints: 121741 Sorted by residual: bond pdb=" C HIS D 216 " pdb=" N GLN D 217 " ideal model delta sigma weight residual 1.332 2.932 -1.600 1.40e-02 5.10e+03 1.31e+04 bond pdb=" C LEU B 260 " pdb=" N LYS B 264 " ideal model delta sigma weight residual 1.333 2.884 -1.551 1.51e-02 4.39e+03 1.05e+04 bond pdb=" C LEU A 40 " pdb=" N LEU A 41 " ideal model delta sigma weight residual 1.332 2.755 -1.422 1.40e-02 5.10e+03 1.03e+04 bond pdb=" C ASP A 115 " pdb=" N ASN A 116 " ideal model delta sigma weight residual 1.331 2.808 -1.478 1.48e-02 4.57e+03 9.97e+03 bond pdb=" C LYS A 5 " pdb=" N TYR A 6 " ideal model delta sigma weight residual 1.329 2.674 -1.345 1.44e-02 4.82e+03 8.73e+03 ... (remaining 121736 not shown) Histogram of bond angle deviations from ideal: 4.53 - 36.37: 3 36.37 - 68.21: 4 68.21 - 100.05: 97 100.05 - 131.89: 164643 131.89 - 163.73: 264 Bond angle restraints: 165011 Sorted by residual: angle pdb=" CA ILE A1171 " pdb=" C ILE A1171 " pdb=" N THR A1172 " ideal model delta sigma weight residual 116.60 8.71 107.89 1.45e+00 4.76e-01 5.54e+03 angle pdb=" CA LYS B 70 " pdb=" C LYS B 70 " pdb=" N CYS B 71 " ideal model delta sigma weight residual 115.63 25.00 90.63 1.36e+00 5.41e-01 4.44e+03 angle pdb=" C ILE A1171 " pdb=" N THR A1172 " pdb=" CA THR A1172 " ideal model delta sigma weight residual 121.54 4.53 117.01 1.91e+00 2.74e-01 3.75e+03 angle pdb=" O GLN B 50 " pdb=" C GLN B 50 " pdb=" N GLY B 51 " ideal model delta sigma weight residual 122.59 42.52 80.07 1.33e+00 5.65e-01 3.62e+03 angle pdb=" O SER D 238 " pdb=" C SER D 238 " pdb=" N THR D 239 " ideal model delta sigma weight residual 123.11 79.70 43.41 7.50e-01 1.78e+00 3.35e+03 ... (remaining 165006 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.30: 72005 29.30 - 58.61: 1894 58.61 - 87.91: 115 87.91 - 117.22: 2 117.22 - 146.52: 10 Dihedral angle restraints: 74026 sinusoidal: 28359 harmonic: 45667 Sorted by residual: dihedral pdb=" CA ASP P 70 " pdb=" C ASP P 70 " pdb=" N GLN P 71 " pdb=" CA GLN P 71 " ideal model delta harmonic sigma weight residual -180.00 -57.88 -122.12 0 5.00e+00 4.00e-02 5.97e+02 dihedral pdb=" CA SER D 238 " pdb=" C SER D 238 " pdb=" N THR D 239 " pdb=" CA THR D 239 " ideal model delta harmonic sigma weight residual -180.00 -92.64 -87.36 0 5.00e+00 4.00e-02 3.05e+02 dihedral pdb=" CA ILE A1171 " pdb=" C ILE A1171 " pdb=" N THR A1172 " pdb=" CA THR A1172 " ideal model delta harmonic sigma weight residual -180.00 -102.27 -77.73 0 5.00e+00 4.00e-02 2.42e+02 ... (remaining 74023 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.301: 18563 0.301 - 0.603: 45 0.603 - 0.904: 4 0.904 - 1.205: 1 1.205 - 1.507: 2 Chirality restraints: 18615 Sorted by residual: chirality pdb=" CA LEU B 137 " pdb=" N LEU B 137 " pdb=" C LEU B 137 " pdb=" CB LEU B 137 " both_signs ideal model delta sigma weight residual False 2.51 1.00 1.51 2.00e-01 2.50e+01 5.67e+01 chirality pdb=" CA THR C 467 " pdb=" N THR C 467 " pdb=" C THR C 467 " pdb=" CB THR C 467 " both_signs ideal model delta sigma weight residual False 2.53 1.23 1.30 2.00e-01 2.50e+01 4.21e+01 chirality pdb=" CA ASN B 138 " pdb=" N ASN B 138 " pdb=" C ASN B 138 " pdb=" CB ASN B 138 " both_signs ideal model delta sigma weight residual False 2.51 1.46 1.05 2.00e-01 2.50e+01 2.77e+01 ... (remaining 18612 not shown) Planarity restraints: 21359 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 260 " -0.147 2.00e-02 2.50e+03 2.68e-01 7.17e+02 pdb=" C LEU B 260 " 0.445 2.00e-02 2.50e+03 pdb=" O LEU B 260 " -0.254 2.00e-02 2.50e+03 pdb=" N LYS B 264 " -0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 70 " -0.221 2.00e-02 2.50e+03 1.91e-01 3.66e+02 pdb=" C LYS B 70 " -0.156 2.00e-02 2.50e+03 pdb=" O LYS B 70 " 0.156 2.00e-02 2.50e+03 pdb=" N CYS B 71 " 0.221 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS D 216 " -0.051 2.00e-02 2.50e+03 1.89e-01 3.58e+02 pdb=" C HIS D 216 " 0.313 2.00e-02 2.50e+03 pdb=" O HIS D 216 " -0.197 2.00e-02 2.50e+03 pdb=" N GLN D 217 " -0.064 2.00e-02 2.50e+03 ... (remaining 21356 not shown) Histogram of nonbonded interaction distances: 0.38 - 1.23: 52 1.23 - 2.07: 536 2.07 - 2.91: 47288 2.91 - 3.76: 246873 3.76 - 4.60: 429456 Warning: very small nonbonded interaction distances. Nonbonded interactions: 724205 Sorted by model distance: nonbonded pdb=" CD1 ILE B 902 " pdb=" CD1 LEU B1076 " model vdw 0.384 3.400 nonbonded pdb=" O ALA C 544 " pdb=" CB LYS C 705 " model vdw 0.449 3.100 nonbonded pdb=" O SER B 58 " pdb=" O SER B 68 " model vdw 0.582 2.800 nonbonded pdb=" ND2 ASN B 526 " pdb=" CE LYS E 515 " model vdw 0.611 3.250 nonbonded pdb=" C LYS B 70 " pdb=" CB CYS B 71 " model vdw 0.613 2.720 ... (remaining 724200 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 3.040 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: 2.150 Extract box with map and model: 14.580 Check model and map are aligned: 1.250 Set scattering table: 0.760 Process input model: 342.910 Find NCS groups from input model: 8.520 Set up NCS constraints: 0.330 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: 0.020 Load rotamer database and sin/cos tables:2.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 375.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5798 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 : 0.018 1.600 121585 Z= 1.194 Angle : 1.934 117.008 164623 Z= 1.459 Chirality : 0.102 1.507 18615 Planarity : 0.008 0.268 21279 Dihedral : 12.819 146.519 44259 Min Nonbonded Distance : 0.384 Molprobity Statistics. All-atom Clashscore : 37.45 Ramachandran Plot: Outliers : 0.78 % Allowed : 4.58 % Favored : 94.63 % Rotamer: Outliers : 2.43 % Allowed : 8.62 % Favored : 88.96 % Cbeta Deviations : 0.34 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.07), residues: 15444 helix: 1.20 (0.06), residues: 8282 sheet: -0.16 (0.14), residues: 1350 loop : -1.84 (0.07), residues: 5812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP B 856 HIS 0.008 0.002 HIS A3809 PHE 0.040 0.002 PHE A4131 TYR 0.034 0.002 TYR A4168 ARG 0.008 0.001 ARG A4445 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 30888 Ramachandran restraints generated. 15444 Oldfield, 0 Emsley, 15444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 30888 Ramachandran restraints generated. 15444 Oldfield, 0 Emsley, 15444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue SER 3 is missing expected H atoms. Skipping. Residue VAL 5 is missing expected H atoms. Skipping. Residue MET 6 is missing expected H atoms. Skipping. Residue LEU 8 is missing expected H atoms. Skipping. Residue SER 9 is missing expected H atoms. Skipping. Residue ILE 13 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue ALA 19 is missing expected H atoms. Skipping. Residue SER 21 is missing expected H atoms. Skipping. Residue TYR 23 is missing expected H atoms. Skipping. Residue LEU 28 is missing expected H atoms. Skipping. Residue ALA 30 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue VAL 33 is missing expected H atoms. Skipping. Residue SER 34 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue LEU 38 is missing expected H atoms. Skipping. Residue ALA 39 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue SER 48 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Residue MET 55 is missing expected H atoms. Skipping. Residue ILE 56 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Residue VAL 59 is missing expected H atoms. Skipping. Residue LYS 62 is missing expected H atoms. Skipping. Residue THR 64 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue ILE 67 is missing expected H atoms. Skipping. Residue LYS 68 is missing expected H atoms. Skipping. Residue SER 70 is missing expected H atoms. Skipping. Residue LEU 73 is missing expected H atoms. Skipping. Residue ILE 75 is missing expected H atoms. Skipping. Residue TYR 76 is missing expected H atoms. Skipping. Residue TYR 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue ALA 82 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Evaluate side-chains 3208 residues out of total 14031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 291 poor density : 2917 time to evaluate : 9.031 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: 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revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 702 LEU cc_start: 0.2754 (mt) cc_final: 0.2526 (mt) REVERT: A 1149 ILE cc_start: 0.4769 (tt) cc_final: 0.3240 (tp) REVERT: A 1581 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7498 (mp) REVERT: A 1605 VAL cc_start: 0.8629 (OUTLIER) cc_final: 0.8200 (p) REVERT: A 1641 SER cc_start: 0.7323 (t) cc_final: 0.5700 (t) REVERT: A 1656 ILE cc_start: 0.6827 (mt) cc_final: 0.6430 (pt) REVERT: A 1722 ILE cc_start: 0.9567 (mt) cc_final: 0.9357 (tt) REVERT: A 1750 MET cc_start: 0.9387 (tpt) cc_final: 0.9088 (tpt) REVERT: A 1761 MET cc_start: 0.9135 (tpt) cc_final: 0.8472 (tpp) REVERT: A 1814 ILE cc_start: 0.9472 (mp) cc_final: 0.9252 (mt) REVERT: A 1884 ASP cc_start: 0.9006 (m-30) cc_final: 0.8723 (t0) REVERT: A 1898 CYS cc_start: 0.9255 (m) cc_final: 0.8720 (m) REVERT: A 1984 GLN cc_start: 0.8449 (tp-100) cc_final: 0.8225 (tm-30) REVERT: A 2026 LYS cc_start: 0.8859 (OUTLIER) cc_final: 0.8570 (mmtp) REVERT: A 2034 CYS cc_start: 0.8975 (OUTLIER) cc_final: 0.8685 (t) REVERT: A 2035 GLU cc_start: 0.9148 (tt0) cc_final: 0.8846 (tm-30) REVERT: A 2072 MET cc_start: 0.8993 (tmm) cc_final: 0.8727 (tmm) REVERT: A 2075 MET cc_start: 0.8742 (tmt) cc_final: 0.8263 (tmt) REVERT: A 2089 ASP cc_start: 0.8885 (OUTLIER) cc_final: 0.8471 (t0) REVERT: A 2111 LYS cc_start: 0.8867 (mmmt) cc_final: 0.8308 (mptt) REVERT: A 2113 TYR cc_start: 0.8852 (m-80) cc_final: 0.8378 (m-80) REVERT: A 2122 GLU cc_start: 0.9382 (OUTLIER) cc_final: 0.8934 (tm-30) REVERT: A 2123 GLU cc_start: 0.9666 (tm-30) cc_final: 0.9411 (tm-30) REVERT: A 2179 SER cc_start: 0.9514 (p) cc_final: 0.9257 (t) REVERT: A 2200 LYS cc_start: 0.8840 (tttp) cc_final: 0.8618 (tppt) REVERT: A 2225 LYS cc_start: 0.8860 (pttt) cc_final: 0.8507 (pttt) REVERT: A 2264 MET cc_start: 0.8802 (ttp) cc_final: 0.8029 (ttt) REVERT: A 2321 ASP cc_start: 0.9261 (m-30) cc_final: 0.8995 (m-30) REVERT: A 2333 ASN cc_start: 0.9144 (m-40) cc_final: 0.8638 (m110) REVERT: A 2338 GLU cc_start: 0.8949 (mt-10) cc_final: 0.8726 (mp0) REVERT: A 2340 GLN cc_start: 0.8824 (OUTLIER) cc_final: 0.8500 (pp30) REVERT: A 2349 MET cc_start: 0.9327 (ttm) cc_final: 0.8912 (tpp) REVERT: A 2359 ASN cc_start: 0.9296 (m-40) cc_final: 0.9078 (m-40) REVERT: A 2360 ILE cc_start: 0.9234 (mt) cc_final: 0.8977 (mm) REVERT: A 2384 GLU cc_start: 0.9080 (tt0) cc_final: 0.8864 (tp30) REVERT: A 2398 ILE cc_start: 0.9008 (pt) cc_final: 0.8764 (mt) REVERT: A 2459 LEU cc_start: 0.8959 (tp) cc_final: 0.8680 (tt) REVERT: A 2487 ASN cc_start: 0.8965 (OUTLIER) cc_final: 0.8726 (m-40) REVERT: A 2521 ASN cc_start: 0.8906 (m-40) cc_final: 0.8682 (t0) REVERT: A 2554 MET cc_start: 0.8749 (ttm) cc_final: 0.8380 (tmm) REVERT: A 2555 MET cc_start: 0.8706 (ttp) cc_final: 0.8326 (ttp) REVERT: A 2593 LYS cc_start: 0.9304 (tmtt) cc_final: 0.8992 (tptt) REVERT: A 2611 MET cc_start: 0.8767 (ptm) cc_final: 0.8565 (ptm) REVERT: A 2634 MET cc_start: 0.9042 (mmm) cc_final: 0.8778 (mmm) REVERT: A 2650 HIS cc_start: 0.8244 (t-90) cc_final: 0.7600 (t-90) REVERT: A 2657 PHE cc_start: 0.9127 (m-80) cc_final: 0.8616 (m-80) REVERT: A 2716 ASP cc_start: 0.8707 (m-30) cc_final: 0.8416 (t0) REVERT: A 2743 ASP cc_start: 0.8011 (m-30) cc_final: 0.7807 (m-30) REVERT: A 2752 ASP cc_start: 0.9302 (m-30) cc_final: 0.8987 (m-30) REVERT: A 2837 MET cc_start: 0.8627 (ttm) cc_final: 0.8009 (tmm) REVERT: A 2858 GLN cc_start: 0.8614 (mm110) cc_final: 0.8145 (mt0) REVERT: A 2905 ASP cc_start: 0.9025 (m-30) cc_final: 0.8618 (t0) REVERT: A 2982 GLU cc_start: 0.9158 (mt-10) cc_final: 0.8695 (mm-30) REVERT: A 2997 ILE cc_start: 0.9156 (mt) cc_final: 0.8936 (mm) REVERT: A 2998 MET cc_start: 0.9057 (mmm) cc_final: 0.8808 (mmm) REVERT: A 3019 PHE cc_start: 0.8845 (m-80) cc_final: 0.8600 (m-10) REVERT: A 3022 CYS cc_start: 0.9125 (p) cc_final: 0.8433 (p) REVERT: A 3072 GLU cc_start: 0.9352 (tt0) cc_final: 0.9124 (tm-30) REVERT: A 3080 LYS cc_start: 0.8632 (mptt) cc_final: 0.8088 (mmtm) REVERT: A 3203 PRO cc_start: 0.4198 (OUTLIER) cc_final: 0.3732 (Cg_endo) REVERT: A 3220 ILE cc_start: 0.5659 (mt) cc_final: 0.4200 (mt) REVERT: A 3276 SER cc_start: 0.3762 (t) cc_final: 0.2466 (t) REVERT: A 3489 GLU cc_start: 0.9292 (tp30) cc_final: 0.8949 (tm-30) REVERT: A 3490 LEU cc_start: 0.9470 (tp) cc_final: 0.9171 (tp) REVERT: A 3495 ILE cc_start: 0.9187 (OUTLIER) cc_final: 0.8895 (tp) REVERT: A 3510 LYS cc_start: 0.9097 (tptm) cc_final: 0.8835 (tptp) REVERT: A 3558 LEU cc_start: 0.8882 (tt) cc_final: 0.8241 (pt) REVERT: A 3572 MET cc_start: 0.9235 (mtt) cc_final: 0.8914 (mtp) REVERT: A 3581 GLU cc_start: 0.9125 (tt0) cc_final: 0.8621 (pt0) REVERT: A 3590 MET cc_start: 0.9475 (ppp) cc_final: 0.9177 (ppp) REVERT: A 3608 VAL cc_start: 0.8802 (t) cc_final: 0.8210 (p) REVERT: A 3609 ASN cc_start: 0.9319 (p0) cc_final: 0.9025 (t0) REVERT: A 3615 MET cc_start: 0.9056 (mtt) cc_final: 0.8564 (mpp) REVERT: A 3625 MET cc_start: 0.9302 (mtp) cc_final: 0.9084 (mpp) REVERT: A 3633 SER cc_start: 0.9431 (m) cc_final: 0.9181 (p) REVERT: A 3687 ASP cc_start: 0.9247 (t0) cc_final: 0.8923 (t0) REVERT: A 3695 LEU cc_start: 0.9668 (tp) cc_final: 0.9433 (mt) REVERT: A 3725 GLU cc_start: 0.9212 (tt0) cc_final: 0.8923 (tm-30) REVERT: A 3730 LEU cc_start: 0.9398 (mt) cc_final: 0.8672 (mm) REVERT: A 3739 GLU cc_start: 0.9411 (mt-10) cc_final: 0.9202 (mt-10) REVERT: A 3768 ASN cc_start: 0.9105 (t0) cc_final: 0.8632 (t0) REVERT: A 3770 MET cc_start: 0.9551 (mmm) cc_final: 0.9041 (mmm) REVERT: A 3794 LEU cc_start: 0.8329 (mt) cc_final: 0.8042 (tp) REVERT: A 3841 ILE cc_start: 0.9140 (mt) cc_final: 0.8859 (mm) REVERT: A 3856 LEU cc_start: 0.8821 (mt) cc_final: 0.8501 (mt) REVERT: A 3861 GLU cc_start: 0.8614 (mm-30) cc_final: 0.8066 (mm-30) REVERT: A 3905 ASN cc_start: 0.9120 (m-40) cc_final: 0.8743 (t0) REVERT: A 3956 GLN cc_start: 0.8887 (mt0) cc_final: 0.8670 (tp40) REVERT: A 4015 GLU cc_start: 0.8855 (mm-30) cc_final: 0.8472 (mt-10) REVERT: A 4019 MET cc_start: 0.8759 (mmm) cc_final: 0.8156 (tpp) REVERT: A 4060 VAL cc_start: 0.9230 (p) cc_final: 0.8974 (p) REVERT: A 4066 ILE cc_start: 0.8970 (mt) cc_final: 0.8732 (mm) REVERT: A 4069 ASP cc_start: 0.9226 (m-30) cc_final: 0.8517 (p0) REVERT: A 4177 MET cc_start: 0.8826 (mmm) cc_final: 0.8459 (tpp) REVERT: A 4187 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7760 (mp) REVERT: A 4209 ASP cc_start: 0.8961 (OUTLIER) cc_final: 0.8700 (t0) REVERT: A 4212 ASP cc_start: 0.8293 (m-30) cc_final: 0.7873 (m-30) REVERT: A 4232 ASP cc_start: 0.9054 (m-30) cc_final: 0.8328 (p0) REVERT: A 4295 GLU cc_start: 0.9211 (tt0) cc_final: 0.8700 (tp30) REVERT: A 4308 SER cc_start: 0.8679 (m) cc_final: 0.8438 (t) REVERT: A 4321 GLN cc_start: 0.9173 (tt0) cc_final: 0.8953 (tp-100) REVERT: A 4342 GLU cc_start: 0.9330 (OUTLIER) cc_final: 0.9036 (tp30) REVERT: A 4371 GLU cc_start: 0.9099 (pt0) cc_final: 0.8385 (mm-30) REVERT: A 4405 GLU cc_start: 0.9623 (tt0) cc_final: 0.9127 (tm-30) REVERT: A 4434 ASN cc_start: 0.8922 (m-40) cc_final: 0.8484 (m-40) REVERT: A 4444 ASP cc_start: 0.9101 (m-30) cc_final: 0.8572 (t0) REVERT: A 4497 SER cc_start: 0.8223 (OUTLIER) cc_final: 0.7636 (m) REVERT: A 4532 GLU cc_start: 0.8493 (tt0) cc_final: 0.8030 (tt0) REVERT: A 4572 MET cc_start: 0.8769 (ttt) cc_final: 0.8268 (tpp) REVERT: B 547 LEU cc_start: 0.7842 (mt) cc_final: 0.7341 (mt) REVERT: B 569 VAL cc_start: 0.7985 (t) cc_final: 0.7578 (t) REVERT: B 696 THR cc_start: 0.5707 (m) cc_final: 0.5457 (m) REVERT: B 1208 LYS cc_start: 0.7413 (OUTLIER) cc_final: 0.7019 (mmmt) REVERT: B 1213 PRO cc_start: 0.8088 (OUTLIER) cc_final: 0.7387 (Cg_endo) REVERT: B 1662 MET cc_start: 0.9169 (ptp) cc_final: 0.8482 (ptt) REVERT: B 1693 MET cc_start: 0.8965 (ttp) cc_final: 0.8551 (ttp) REVERT: B 1765 GLU cc_start: 0.9450 (tt0) cc_final: 0.8650 (tp30) REVERT: B 1895 MET cc_start: 0.8756 (ptp) cc_final: 0.8501 (ptp) REVERT: B 2004 MET cc_start: 0.8687 (ttm) cc_final: 0.7512 (tmm) REVERT: B 2032 LEU cc_start: 0.9011 (tp) cc_final: 0.8547 (tp) REVERT: B 2035 ILE cc_start: 0.9466 (mt) cc_final: 0.9115 (pt) REVERT: B 2039 MET cc_start: 0.9087 (mtt) cc_final: 0.8849 (mmp) REVERT: B 2047 MET cc_start: 0.8916 (mmt) cc_final: 0.8688 (mtp) REVERT: B 2060 MET cc_start: 0.9396 (mtp) cc_final: 0.9000 (mmp) REVERT: B 2103 MET cc_start: 0.9308 (tpp) cc_final: 0.8970 (ttp) REVERT: B 2260 TRP cc_start: 0.8957 (p90) cc_final: 0.7530 (p90) REVERT: B 2273 GLU cc_start: 0.9636 (tp30) cc_final: 0.9337 (mm-30) REVERT: B 2318 ARG cc_start: 0.9516 (mtt-85) cc_final: 0.8805 (mtt-85) REVERT: B 2332 MET cc_start: 0.8681 (mmt) cc_final: 0.8133 (mmm) REVERT: B 2353 MET cc_start: 0.8258 (mmm) cc_final: 0.7824 (mmm) REVERT: B 2356 MET cc_start: 0.9083 (mmm) cc_final: 0.8413 (tpp) REVERT: B 2410 ASP cc_start: 0.9203 (m-30) cc_final: 0.8877 (t0) REVERT: B 2429 LYS cc_start: 0.8959 (mttm) cc_final: 0.8618 (tptm) REVERT: B 2520 LEU cc_start: 0.9336 (mt) cc_final: 0.8992 (mp) REVERT: B 2523 MET cc_start: 0.9286 (mmp) cc_final: 0.9009 (mmm) REVERT: B 2693 ASN cc_start: 0.8865 (m-40) cc_final: 0.8549 (t0) REVERT: B 2856 VAL cc_start: 0.9385 (m) cc_final: 0.8784 (p) REVERT: B 2860 MET cc_start: 0.8945 (mmm) cc_final: 0.8115 (mtm) REVERT: B 2947 MET cc_start: 0.9129 (tpt) cc_final: 0.8871 (tpt) REVERT: B 3031 ILE cc_start: 0.9308 (OUTLIER) cc_final: 0.9093 (mt) REVERT: B 3082 MET cc_start: 0.9511 (mmt) cc_final: 0.9170 (mmm) REVERT: B 3094 GLU cc_start: 0.9265 (tp30) cc_final: 0.9047 (tm-30) REVERT: B 3103 TYR cc_start: 0.8717 (m-80) cc_final: 0.8268 (m-80) REVERT: B 3113 GLU cc_start: 0.9239 (mt-10) cc_final: 0.8839 (pt0) REVERT: B 3517 MET cc_start: 0.8660 (ttt) cc_final: 0.8244 (tmm) REVERT: B 3533 LEU cc_start: 0.9536 (tt) cc_final: 0.9278 (tt) REVERT: B 3540 GLN cc_start: 0.9157 (OUTLIER) cc_final: 0.8956 (tp40) REVERT: B 3582 ILE cc_start: 0.8074 (tp) cc_final: 0.7621 (tp) REVERT: B 3625 MET cc_start: 0.8708 (ppp) cc_final: 0.8472 (ppp) REVERT: B 3653 LEU cc_start: 0.9157 (tp) cc_final: 0.8867 (tp) REVERT: B 3660 MET cc_start: 0.9496 (mmt) cc_final: 0.9223 (mtt) REVERT: B 3737 GLU cc_start: 0.9489 (mt-10) cc_final: 0.9151 (mm-30) REVERT: B 3833 MET cc_start: 0.9176 (ttm) cc_final: 0.8964 (mtm) REVERT: B 3881 GLU cc_start: 0.8228 (tt0) cc_final: 0.7976 (mp0) REVERT: B 3884 ARG cc_start: 0.9322 (ttm-80) cc_final: 0.9085 (ptp-110) REVERT: B 3906 GLN cc_start: 0.9531 (mt0) cc_final: 0.9237 (mp10) REVERT: B 3914 LEU cc_start: 0.7864 (tp) cc_final: 0.7539 (tt) REVERT: B 3919 LEU cc_start: 0.7859 (mt) cc_final: 0.7612 (tt) REVERT: B 3922 MET cc_start: 0.8740 (mpt) cc_final: 0.8412 (mpt) REVERT: B 3929 VAL cc_start: 0.8429 (t) cc_final: 0.8012 (p) REVERT: B 4005 ARG cc_start: 0.9532 (ttt180) cc_final: 0.9302 (ttt-90) REVERT: B 4107 MET cc_start: 0.9516 (mmm) cc_final: 0.9307 (tpt) REVERT: B 4121 ASP cc_start: 0.8846 (t0) cc_final: 0.8537 (m-30) REVERT: B 4159 MET cc_start: 0.8411 (mmm) cc_final: 0.7985 (mmm) REVERT: B 4247 LYS cc_start: 0.9564 (tptt) cc_final: 0.9179 (tppt) REVERT: B 4328 PHE cc_start: 0.8714 (OUTLIER) cc_final: 0.8446 (m-80) REVERT: B 4356 MET cc_start: 0.9621 (tpp) cc_final: 0.9242 (tpp) REVERT: B 4384 MET cc_start: 0.9386 (mmt) cc_final: 0.9053 (mmm) REVERT: B 4385 GLU cc_start: 0.9611 (mm-30) cc_final: 0.9222 (mt-10) REVERT: B 4440 MET cc_start: 0.8468 (mmm) cc_final: 0.8163 (mpp) REVERT: B 4474 GLU cc_start: 0.8746 (mt-10) cc_final: 0.8507 (mp0) REVERT: B 4482 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7477 (pp20) REVERT: B 4540 LYS cc_start: 0.9149 (mptp) cc_final: 0.8933 (pttm) REVERT: B 4570 ARG cc_start: 0.7971 (OUTLIER) cc_final: 0.7511 (ttp-170) REVERT: B 4581 MET cc_start: 0.8399 (mmt) cc_final: 0.7783 (mmm) REVERT: C 10 LEU cc_start: 0.6164 (OUTLIER) cc_final: 0.5952 (tm) REVERT: C 85 HIS cc_start: 0.4470 (OUTLIER) cc_final: 0.4258 (p-80) REVERT: C 106 LEU cc_start: 0.7454 (OUTLIER) cc_final: 0.7140 (mp) REVERT: C 114 LEU cc_start: 0.6471 (OUTLIER) cc_final: 0.5858 (tm) REVERT: C 913 MET cc_start: 0.8618 (mmp) cc_final: 0.8351 (mmt) REVERT: C 914 ASN cc_start: 0.8709 (t0) cc_final: 0.8290 (m110) REVERT: C 997 LEU cc_start: 0.8955 (mt) cc_final: 0.8666 (mm) REVERT: C 1005 GLU cc_start: 0.9628 (mt-10) cc_final: 0.9348 (mm-30) REVERT: C 1059 ASN cc_start: 0.9247 (m-40) cc_final: 0.8843 (m110) REVERT: C 1085 MET cc_start: 0.9448 (mmm) cc_final: 0.9193 (mmm) REVERT: C 1190 MET cc_start: 0.7937 (mtp) cc_final: 0.7363 (tpp) REVERT: C 1206 LEU cc_start: 0.9630 (mt) cc_final: 0.9092 (tt) REVERT: C 1240 MET cc_start: 0.9331 (mtm) cc_final: 0.9109 (ptm) REVERT: C 1268 ASP cc_start: 0.9206 (m-30) cc_final: 0.8852 (t0) REVERT: C 1281 MET cc_start: 0.9512 (ttt) cc_final: 0.9009 (tpp) REVERT: C 1367 TYR cc_start: 0.8495 (m-80) cc_final: 0.7895 (m-80) REVERT: C 1383 ASP cc_start: 0.9239 (t0) cc_final: 0.8566 (t0) REVERT: C 1386 TYR cc_start: 0.8901 (m-10) cc_final: 0.8699 (m-10) REVERT: C 1428 ASN cc_start: 0.9015 (m110) cc_final: 0.8456 (t0) REVERT: C 1433 MET cc_start: 0.9014 (mtt) cc_final: 0.8268 (mtt) REVERT: C 1438 MET cc_start: 0.9714 (mmm) cc_final: 0.9382 (mmp) REVERT: C 1499 CYS cc_start: 0.9399 (OUTLIER) cc_final: 0.8850 (p) REVERT: C 1707 LYS cc_start: 0.9453 (mmtm) cc_final: 0.9222 (tptt) REVERT: C 1774 MET cc_start: 0.8246 (mtm) cc_final: 0.7832 (mtm) REVERT: C 1981 ASN cc_start: 0.9037 (OUTLIER) cc_final: 0.8715 (m-40) REVERT: C 1982 ILE cc_start: 0.9304 (mm) cc_final: 0.8944 (mm) REVERT: C 2128 MET cc_start: 0.9545 (ptp) cc_final: 0.9075 (ppp) REVERT: C 2241 ILE cc_start: 0.9177 (mt) cc_final: 0.8856 (mt) REVERT: C 2330 MET cc_start: 0.9125 (ttt) cc_final: 0.8817 (tpt) REVERT: C 2339 MET cc_start: 0.9590 (mtt) cc_final: 0.9297 (mpp) REVERT: C 2346 CYS cc_start: 0.9552 (m) cc_final: 0.9305 (m) REVERT: C 2432 ASN cc_start: 0.9229 (OUTLIER) cc_final: 0.8923 (p0) REVERT: C 2486 MET cc_start: 0.9033 (mtp) cc_final: 0.8700 (ttm) REVERT: C 2543 GLU cc_start: 0.9517 (tp30) cc_final: 0.8996 (tp30) REVERT: C 2549 MET cc_start: 0.9323 (mmt) cc_final: 0.8948 (mmp) REVERT: C 2588 MET cc_start: 0.9430 (tpp) cc_final: 0.9177 (tpp) REVERT: C 2593 ARG cc_start: 0.9041 (tpt90) cc_final: 0.8575 (tpp-160) REVERT: C 2594 GLU cc_start: 0.9170 (mt-10) cc_final: 0.8571 (pt0) REVERT: C 2937 TYR cc_start: 0.8478 (m-80) cc_final: 0.8136 (m-80) REVERT: C 2965 MET cc_start: 0.8486 (ptm) cc_final: 0.8206 (ptp) REVERT: C 3050 GLU cc_start: 0.8809 (tt0) cc_final: 0.8600 (pt0) REVERT: C 3053 TYR cc_start: 0.9252 (m-80) cc_final: 0.8606 (m-80) REVERT: C 3056 ILE cc_start: 0.9375 (mt) cc_final: 0.9149 (mp) REVERT: C 3058 GLU cc_start: 0.8816 (OUTLIER) cc_final: 0.8449 (mp0) REVERT: C 3131 LEU cc_start: 0.9394 (OUTLIER) cc_final: 0.9148 (tp) REVERT: C 3150 MET cc_start: 0.9431 (ttm) cc_final: 0.8902 (tmm) REVERT: C 3175 LYS cc_start: 0.9108 (mmmt) cc_final: 0.7946 (mmmt) REVERT: C 3214 GLU cc_start: 0.9495 (tt0) cc_final: 0.9135 (tp30) REVERT: C 3216 LYS cc_start: 0.8956 (mtpt) cc_final: 0.8666 (tppt) REVERT: C 3405 ARG cc_start: 0.8765 (OUTLIER) cc_final: 0.8318 (ttm170) REVERT: C 3540 MET cc_start: 0.8519 (mtp) cc_final: 0.8188 (mtp) REVERT: C 3623 MET cc_start: 0.9186 (tpp) cc_final: 0.8771 (tpp) REVERT: C 3958 ASN cc_start: 0.8998 (m110) cc_final: 0.8530 (p0) REVERT: C 3959 MET cc_start: 0.8331 (mmm) cc_final: 0.8088 (tpt) REVERT: C 4050 GLN cc_start: 0.8294 (OUTLIER) cc_final: 0.7778 (tt0) REVERT: C 4165 MET cc_start: 0.8981 (mtp) cc_final: 0.8684 (mtm) REVERT: D 248 MET cc_start: 0.6761 (mmm) cc_final: 0.6364 (tpp) REVERT: D 460 LEU cc_start: 0.6998 (mt) cc_final: 0.5860 (mm) REVERT: F 62 VAL cc_start: 0.7895 (OUTLIER) cc_final: 0.7183 (t) REVERT: F 73 ASP cc_start: 0.4739 (p0) cc_final: 0.4111 (p0) REVERT: I 26 ASN cc_start: 0.3502 (t0) cc_final: 0.3222 (t0) REVERT: L 30 LEU cc_start: 0.7676 (mt) cc_final: 0.5486 (mt) REVERT: L 53 ILE cc_start: 0.7665 (mt) cc_final: 0.7388 (tp) REVERT: L 74 TRP cc_start: 0.5862 (m100) cc_final: 0.5645 (m100) REVERT: L 98 LEU cc_start: 0.5346 (mt) cc_final: 0.5030 (mt) REVERT: M 56 ILE cc_start: 0.5261 (mt) cc_final: 0.4894 (mt) REVERT: O 86 VAL cc_start: 0.4538 (p) cc_final: 0.3846 (p) outliers start: 291 outliers final: 54 residues processed: 3162 average time/residue: 1.0322 time to fit residues: 5578.9609 Evaluate side-chains 1745 residues out of total 14031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 1658 time to evaluate : 9.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1553 random chunks: chunk 1311 optimal weight: 5.9990 chunk 1177 optimal weight: 5.9990 chunk 653 optimal weight: 5.9990 chunk 402 optimal weight: 0.9980 chunk 794 optimal weight: 6.9990 chunk 628 optimal weight: 0.9980 chunk 1217 optimal weight: 1.9990 chunk 471 optimal weight: 5.9990 chunk 740 optimal weight: 4.9990 chunk 905 optimal weight: 9.9990 chunk 1410 optimal weight: 10.0000 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 678 HIS ** A 687 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 741 ASN A 786 GLN ** A 804 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1047 ASN A1101 HIS A1205 GLN ** A1515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1655 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1718 GLN ** A1791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1901 GLN A1916 GLN A1940 GLN A1950 GLN A1984 GLN A2037 GLN ** A2220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2251 ASN A2279 ASN ** A2340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2458 GLN ** A2474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2487 ASN A2508 ASN A2613 HIS A2654 GLN A2889 GLN A3020 ASN A3113 GLN ** A3158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3299 ASN A3344 GLN A3439 GLN A3504 ASN ** A3536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3606 GLN A3651 GLN A3746 GLN ** A3801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3815 ASN A3888 GLN A4044 GLN A4088 GLN A4185 HIS ** A4448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4607 HIS ** B 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 573 HIS B 581 ASN ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 894 ASN ** B 975 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1079 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1131 HIS B1135 HIS B1188 GLN B1522 GLN ** B1566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1827 ASN B1850 ASN B1930 GLN B1993 GLN ** B2038 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2148 GLN B2203 ASN ** B2214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2325 ASN ** B2345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2489 ASN B2504 GLN B2591 ASN B2646 GLN B2724 ASN ** B2758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2871 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2957 GLN B3042 ASN B3076 GLN ** B3238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3475 ASN B3521 ASN ** B3604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3640 GLN ** B3656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3820 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3873 GLN B3879 ASN ** B3952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4106 ASN ** B4152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4170 ASN B4176 ASN ** B4267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B4401 GLN B4412 GLN B4420 GLN B4448 GLN B4509 GLN C 9 GLN ** C 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 17 GLN ** C 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1051 GLN C1163 HIS C1238 GLN ** C1274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1279 ASN C1300 GLN C1366 ASN C1391 GLN C1428 ASN ** C1458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1570 GLN C1572 HIS ** C1705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1888 GLN C2066 GLN ** C2107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2214 HIS C2483 ASN ** C2516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2707 GLN ** C2708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2743 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2951 ASN ** C3004 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3157 GLN ** C3178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3617 GLN ** C3654 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3693 GLN ** C3858 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C4034 GLN ** D 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 216 HIS ** D 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 324 GLN ** D 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 411 ASN ** D 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 GLN ** E 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 122 GLN E 170 HIS ** E 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 366 HIS ** E 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 GLN ** F 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 54 HIS ** H 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 45 GLN ** J 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 76 ASN ** L 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 104 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6103 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 121585 Z= 0.245 Angle : 0.631 12.971 164623 Z= 0.345 Chirality : 0.040 0.446 18615 Planarity : 0.004 0.104 21279 Dihedral : 6.169 148.246 16700 Min Nonbonded Distance : 1.700 Molprobity Statistics. All-atom Clashscore : 47.52 Ramachandran Plot: Outliers : 0.31 % Allowed : 3.37 % Favored : 96.32 % Rotamer: Outliers : 0.11 % Allowed : 2.81 % Favored : 97.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.78 (0.07), residues: 15467 helix: 1.83 (0.05), residues: 8600 sheet: -0.13 (0.13), residues: 1467 loop : -1.52 (0.08), residues: 5400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP C 220 HIS 0.016 0.002 HIS E 560 PHE 0.034 0.002 PHE A3046 TYR 0.039 0.002 TYR D 208 ARG 0.013 0.001 ARG B3415 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 30934 Ramachandran restraints generated. 15467 Oldfield, 0 Emsley, 15467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 30934 Ramachandran restraints generated. 15467 Oldfield, 0 Emsley, 15467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue SER 3 is missing expected H atoms. Skipping. Residue VAL 5 is missing expected H atoms. Skipping. Residue MET 6 is missing expected H atoms. Skipping. Residue LEU 8 is missing expected H atoms. Skipping. Residue SER 9 is missing expected H atoms. Skipping. Residue ILE 13 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue ALA 19 is missing expected H atoms. Skipping. Residue SER 21 is missing expected H atoms. Skipping. Residue TYR 23 is missing expected H atoms. Skipping. Residue LEU 28 is missing expected H atoms. Skipping. Residue ALA 30 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue VAL 33 is missing expected H atoms. Skipping. Residue SER 34 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue LEU 38 is missing expected H atoms. Skipping. Residue ALA 39 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue SER 48 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Residue MET 55 is missing expected H atoms. Skipping. Residue ILE 56 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Residue VAL 59 is missing expected H atoms. Skipping. Residue LYS 62 is missing expected H atoms. Skipping. Residue THR 64 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue ILE 67 is missing expected H atoms. Skipping. Residue LYS 68 is missing expected H atoms. Skipping. Residue SER 70 is missing expected H atoms. Skipping. Residue LEU 73 is missing expected H atoms. Skipping. Residue ILE 75 is missing expected H atoms. Skipping. Residue TYR 76 is missing expected H atoms. Skipping. Residue TYR 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue ALA 82 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Evaluate side-chains 1893 residues out of total 14031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 1880 time to evaluate : 10.270 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 rever------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1553 random chunks: chunk 783 optimal weight: 3.9990 chunk 437 optimal weight: 7.9990 chunk 1173 optimal weight: 0.9990 chunk 960 optimal weight: 50.0000 chunk 389 optimal weight: 9.9990 chunk 1412 optimal weight: 9.9990 chunk 1526 optimal weight: 9.9990 chunk 1258 optimal weight: 4.9990 chunk 1401 optimal weight: 4.9990 chunk 481 optimal weight: 10.0000 chunk 1133 optimal weight: 8.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 681 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 687 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 741 ASN ** A 837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 952 GLN A1047 ASN A1444 GLN ** A1533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1547 ASN ** A1578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1690 ASN A1708 GLN A1902 HIS ** A2220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2623 ASN A2832 ASN A2939 ASN ** A3079 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3343 HIS ** A3536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3667 GLN A3683 GLN A3694 ASN ** A3722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3918 ASN ** A3984 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4137 HIS ** A4448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 428 HIS ** B 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 HIS ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 611 GLN ** B 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1079 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2017 ASN B2203 ASN ** B2307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2724 ASN ** B2758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2871 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3552 ASN ** B3604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3834 GLN ** B3888 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4045 HIS ** B4106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B4412 GLN C 9 GLN ** C 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 17 GLN ** C 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2074 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2217 ASN C2220 GLN C2264 ASN ** C2315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2355 HIS ** C2743 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3004 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3159 ASN C3178 ASN ** C3245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3412 HIS C3460 ASN C3537 HIS ** C3547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3604 GLN C3631 GLN ** C3654 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3858 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C4123 GLN ** D 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 387 GLN D 411 ASN ** D 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 572 ASN ** E 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 122 GLN ** E 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 ASN F 57 ASN ** G 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 43 GLN ** I 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 71 HIS ** J 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 59 HIS M 33 GLN ** M 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 51 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6272 moved from start: 0.4788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.198 121585 Z= 0.291 Angle : 0.610 11.905 164623 Z= 0.330 Chirality : 0.038 0.272 18615 Planarity : 0.004 0.115 21279 Dihedral : 5.816 125.341 16700 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 56.51 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.45 % Favored : 95.29 % Rotamer: Outliers : 0.14 % Allowed : 3.41 % Favored : 96.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.07), residues: 15467 helix: 1.99 (0.05), residues: 8641 sheet: -0.22 (0.13), residues: 1456 loop : -1.47 (0.08), residues: 5370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B4038 HIS 0.012 0.002 HIS E 560 PHE 0.039 0.002 PHE A 655 TYR 0.034 0.002 TYR H 78 ARG 0.025 0.001 ARG H 73 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 30934 Ramachandran restraints generated. 15467 Oldfield, 0 Emsley, 15467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 30934 Ramachandran restraints generated. 15467 Oldfield, 0 Emsley, 15467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue SER 3 is missing expected H atoms. Skipping. Residue VAL 5 is missing expected H atoms. Skipping. Residue MET 6 is missing expected H atoms. Skipping. Residue LEU 8 is missing expected H atoms. Skipping. Residue SER 9 is missing expected H atoms. Skipping. Residue ILE 13 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue ALA 19 is missing expected H atoms. Skipping. Residue SER 21 is missing expected H atoms. Skipping. Residue TYR 23 is missing expected H atoms. Skipping. Residue LEU 28 is missing expected H atoms. Skipping. Residue ALA 30 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue VAL 33 is missing expected H atoms. Skipping. Residue SER 34 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue LEU 38 is missing expected H atoms. Skipping. Residue ALA 39 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue SER 48 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Residue MET 55 is missing expected H atoms. Skipping. Residue ILE 56 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Residue VAL 59 is missing expected H atoms. Skipping. Residue LYS 62 is missing expected H atoms. Skipping. Residue THR 64 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue ILE 67 is missing expected H atoms. Skipping. Residue LYS 68 is missing expected H atoms. Skipping. Residue SER 70 is missing expected H atoms. Skipping. Residue LEU 73 is missing expected H atoms. Skipping. Residue ILE 75 is missing expected H atoms. Skipping. Residue TYR 76 is missing expected H atoms. Skipping. Residue TYR 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue ALA 82 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Evaluate side-chains 1560 residues out of total 14031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 1543 time to evaluate : 10.048 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1552 MET cc_start: 0.5304 (ttt) cc_final: 0.4857 (ttt) REVERT: A 1665 GLU cc_start: 0.8442 (tm-30) cc_final: 0.8083 (tm-30) REVERT: A 1750 MET cc_start: 0.9444 (tpt) cc_final: 0.9147 (tpt) REVERT: A 1761 MET cc_start: 0.9061 (tpt) cc_final: 0.8517 (tpp) REVERT: A 1770 GLU cc_start: 0.8809 (mm-30) cc_final: 0.8609 (mt-10) REVERT: A 1814 ILE cc_start: 0.9398 (mp) cc_final: 0.8982 (tp) REVERT: A 1952 MET cc_start: 0.9223 (mtt) cc_final: 0.8687 (mmm) REVERT: A 1984 GLN cc_start: 0.8378 (tp40) cc_final: 0.8095 (tm-30) REVERT: A 2035 GLU cc_start: 0.9109 (tt0) cc_final: 0.8873 (tm-30) REVERT: A 2123 GLU cc_start: 0.9542 (tm-30) cc_final: 0.8787 (tp30) REVERT: A 2189 LYS cc_start: 0.9089 (mmpt) cc_final: 0.8761 (mmmt) REVERT: A 2196 MET cc_start: 0.8914 (ttt) cc_final: 0.8607 (ttm) REVERT: A 2239 ILE cc_start: 0.9596 (tp) cc_final: 0.9334 (mm) REVERT: A 2264 MET cc_start: 0.8644 (ttp) cc_final: 0.8045 (ttt) REVERT: A 2333 ASN cc_start: 0.9060 (m-40) cc_final: 0.8530 (m110) REVERT: A 2348 MET cc_start: 0.8851 (mmt) cc_final: 0.8601 (tpp) REVERT: A 2391 MET cc_start: 0.8456 (mtp) cc_final: 0.8035 (mtp) REVERT: A 2572 ASP cc_start: 0.9295 (m-30) cc_final: 0.8844 (m-30) REVERT: A 2573 GLN cc_start: 0.9023 (mp10) cc_final: 0.8773 (mm-40) REVERT: A 2577 GLU cc_start: 0.9250 (mm-30) cc_final: 0.8706 (tp30) REVERT: A 2590 MET cc_start: 0.8869 (mtt) cc_final: 0.8580 (mmm) REVERT: A 2634 MET cc_start: 0.8722 (mmm) cc_final: 0.8461 (mmm) REVERT: A 2650 HIS cc_start: 0.8159 (t-90) cc_final: 0.7896 (t70) REVERT: A 2657 PHE cc_start: 0.8857 (m-80) cc_final: 0.8472 (m-80) REVERT: A 2683 MET cc_start: 0.9031 (mmp) cc_final: 0.8770 (mmm) REVERT: A 2698 GLU cc_start: 0.8755 (mp0) cc_final: 0.8549 (mp0) REVERT: A 2837 MET cc_start: 0.8694 (ttm) cc_final: 0.7611 (tmm) REVERT: A 2858 GLN cc_start: 0.8170 (mm110) cc_final: 0.7677 (mt0) REVERT: A 2877 THR cc_start: 0.9406 (m) cc_final: 0.9073 (p) REVERT: A 2949 ASN cc_start: 0.9245 (m-40) cc_final: 0.8780 (t0) REVERT: A 3238 ASN cc_start: 0.3475 (m110) cc_final: 0.3270 (m-40) REVERT: A 3288 LYS cc_start: 0.5007 (tmtt) cc_final: 0.4726 (tptm) REVERT: A 3453 PHE cc_start: 0.8705 (t80) cc_final: 0.8443 (t80) REVERT: A 3477 MET cc_start: 0.8872 (mmm) cc_final: 0.8447 (mmm) REVERT: A 3489 GLU cc_start: 0.9337 (tp30) cc_final: 0.9020 (tp30) REVERT: A 3502 GLU cc_start: 0.9637 (mm-30) cc_final: 0.9222 (tp30) REVERT: A 3510 LYS cc_start: 0.8899 (tptm) cc_final: 0.8427 (tptp) REVERT: A 3581 GLU cc_start: 0.9055 (tt0) cc_final: 0.8648 (pt0) REVERT: A 3590 MET cc_start: 0.9352 (ppp) cc_final: 0.9030 (ppp) REVERT: A 3633 SER cc_start: 0.9296 (m) cc_final: 0.9015 (p) REVERT: A 3671 GLU cc_start: 0.8886 (tt0) cc_final: 0.8541 (pt0) REVERT: A 3680 ASP cc_start: 0.9506 (m-30) cc_final: 0.9295 (t0) REVERT: A 3695 LEU cc_start: 0.9572 (tp) cc_final: 0.9299 (mt) REVERT: A 3725 GLU cc_start: 0.9355 (tt0) cc_final: 0.9041 (mt-10) REVERT: A 3730 LEU cc_start: 0.9225 (mt) cc_final: 0.8837 (mm) REVERT: A 3746 GLN cc_start: 0.9066 (mt0) cc_final: 0.8787 (mt0) REVERT: A 3794 LEU cc_start: 0.7664 (mt) cc_final: 0.7433 (tp) REVERT: A 3841 ILE cc_start: 0.8934 (tt) cc_final: 0.8507 (pt) REVERT: A 3905 ASN cc_start: 0.9223 (m-40) cc_final: 0.8907 (t0) REVERT: A 4015 GLU cc_start: 0.8685 (mm-30) cc_final: 0.8388 (mp0) REVERT: A 4019 MET cc_start: 0.9042 (mmm) cc_final: 0.8168 (tpp) REVERT: A 4032 MET cc_start: 0.9189 (mmm) cc_final: 0.8757 (mmm) REVERT: A 4069 ASP cc_start: 0.9015 (m-30) cc_final: 0.8387 (p0) REVERT: A 4177 MET cc_start: 0.8895 (mmm) cc_final: 0.8613 (tpp) REVERT: A 4191 MET cc_start: 0.8987 (ttm) cc_final: 0.8707 (ttp) REVERT: A 4221 GLU cc_start: 0.9106 (mt-10) cc_final: 0.8857 (mm-30) REVERT: A 4232 ASP cc_start: 0.9149 (m-30) cc_final: 0.8396 (p0) REVERT: A 4295 GLU cc_start: 0.9312 (tt0) cc_final: 0.8722 (tp30) REVERT: A 4327 MET cc_start: 0.8193 (mmm) cc_final: 0.7990 (mmm) REVERT: A 4371 GLU cc_start: 0.8917 (pt0) cc_final: 0.8408 (mm-30) REVERT: A 4405 GLU cc_start: 0.9631 (tt0) cc_final: 0.9243 (tm-30) REVERT: A 4572 MET cc_start: 0.8576 (ttt) cc_final: 0.8224 (tpp) REVERT: B 547 LEU cc_start: 0.7934 (mt) cc_final: 0.7661 (mt) REVERT: B 1765 GLU cc_start: 0.9443 (tt0) cc_final: 0.9207 (tp30) REVERT: B 1794 ASP cc_start: 0.9029 (t0) cc_final: 0.8316 (t0) REVERT: B 1799 ASP cc_start: 0.9092 (m-30) cc_final: 0.8835 (t0) REVERT: B 1895 MET cc_start: 0.8720 (ptp) cc_final: 0.8437 (ptp) REVERT: B 1931 MET cc_start: 0.9157 (mmm) cc_final: 0.8923 (mmm) REVERT: B 1953 ASP cc_start: 0.9365 (t0) cc_final: 0.8530 (p0) REVERT: B 2004 MET cc_start: 0.8452 (ttm) cc_final: 0.7304 (tmm) REVERT: B 2077 ARG cc_start: 0.9459 (ttm110) cc_final: 0.9258 (ttm110) REVERT: B 2080 LYS cc_start: 0.9417 (ttpt) cc_final: 0.9169 (tptp) REVERT: B 2108 ASP cc_start: 0.9568 (t70) cc_final: 0.9247 (m-30) REVERT: B 2238 ILE cc_start: 0.9674 (tt) cc_final: 0.9446 (tp) REVERT: B 2260 TRP cc_start: 0.8590 (p90) cc_final: 0.7415 (p90) REVERT: B 2279 MET cc_start: 0.8389 (ttt) cc_final: 0.7031 (ttt) REVERT: B 2318 ARG cc_start: 0.9491 (mtt-85) cc_final: 0.8896 (ttp80) REVERT: B 2356 MET cc_start: 0.7696 (mmp) cc_final: 0.7495 (mmm) REVERT: B 2410 ASP cc_start: 0.9312 (m-30) cc_final: 0.8682 (t0) REVERT: B 2422 GLN cc_start: 0.8780 (tm-30) cc_final: 0.8522 (tm-30) REVERT: B 2423 MET cc_start: 0.7707 (ttp) cc_final: 0.7181 (ttp) REVERT: B 2523 MET cc_start: 0.9422 (mmp) cc_final: 0.9062 (mmm) REVERT: B 2606 ASP cc_start: 0.7727 (m-30) cc_final: 0.7512 (m-30) REVERT: B 2860 MET cc_start: 0.8863 (mmm) cc_final: 0.8210 (mtm) REVERT: B 2869 MET cc_start: 0.9240 (mtp) cc_final: 0.8885 (mtm) REVERT: B 2947 MET cc_start: 0.8943 (tpt) cc_final: 0.8590 (tpt) REVERT: B 3068 GLU cc_start: 0.8102 (pm20) cc_final: 0.7864 (pm20) REVERT: B 3259 VAL cc_start: 0.7245 (t) cc_final: 0.6930 (t) REVERT: B 3484 LYS cc_start: 0.8898 (mptt) cc_final: 0.8513 (mmtp) REVERT: B 3508 LYS cc_start: 0.9334 (tptm) cc_final: 0.9065 (mttt) REVERT: B 3653 LEU cc_start: 0.9234 (tp) cc_final: 0.8947 (tp) REVERT: B 3737 GLU cc_start: 0.9477 (mt-10) cc_final: 0.9272 (mm-30) REVERT: B 3767 MET cc_start: 0.8626 (tmm) cc_final: 0.8329 (tmm) REVERT: B 3884 ARG cc_start: 0.9375 (ttm-80) cc_final: 0.9124 (mtm110) REVERT: B 3978 GLU cc_start: 0.8688 (tt0) cc_final: 0.8123 (tm-30) REVERT: B 4043 ASN cc_start: 0.9383 (m-40) cc_final: 0.9148 (m-40) REVERT: B 4073 ARG cc_start: 0.8852 (mtm-85) cc_final: 0.8628 (mpt-90) REVERT: B 4121 ASP cc_start: 0.8603 (t0) cc_final: 0.8219 (m-30) REVERT: B 4159 MET cc_start: 0.8758 (mmm) cc_final: 0.7600 (mmm) REVERT: B 4340 GLU cc_start: 0.8497 (mp0) cc_final: 0.8206 (mp0) REVERT: B 4352 GLU cc_start: 0.9093 (tm-30) cc_final: 0.8776 (tm-30) REVERT: B 4356 MET cc_start: 0.9651 (tpp) cc_final: 0.8942 (tpp) REVERT: B 4367 LEU cc_start: 0.9365 (tp) cc_final: 0.9068 (pp) REVERT: B 4385 GLU cc_start: 0.9637 (mm-30) cc_final: 0.9318 (mp0) REVERT: B 4431 ASP cc_start: 0.8939 (t0) cc_final: 0.8703 (t0) REVERT: B 4440 MET cc_start: 0.8388 (mmm) cc_final: 0.8083 (mpp) REVERT: B 4581 MET cc_start: 0.8240 (mmt) cc_final: 0.7858 (mmm) REVERT: C 78 VAL cc_start: 0.6900 (t) cc_final: 0.6638 (p) REVERT: C 850 GLU cc_start: 0.9227 (mt-10) cc_final: 0.9015 (pt0) REVERT: C 1085 MET cc_start: 0.9261 (mmp) cc_final: 0.8910 (mmp) REVERT: C 1164 MET cc_start: 0.9515 (tpt) cc_final: 0.9228 (tpp) REVERT: C 1240 MET cc_start: 0.9419 (mtm) cc_final: 0.9023 (ptm) REVERT: C 1268 ASP cc_start: 0.9289 (m-30) cc_final: 0.8801 (t0) REVERT: C 1281 MET cc_start: 0.9164 (ttm) cc_final: 0.8856 (tpp) REVERT: C 1433 MET cc_start: 0.9089 (mtt) cc_final: 0.8416 (mtt) REVERT: C 1438 MET cc_start: 0.9705 (mmm) cc_final: 0.9277 (mmp) REVERT: C 1561 MET cc_start: 0.9278 (tmm) cc_final: 0.9057 (tmm) REVERT: C 2001 MET cc_start: 0.9320 (mmp) cc_final: 0.9058 (mmm) REVERT: C 2128 MET cc_start: 0.9393 (ptp) cc_final: 0.8929 (ppp) REVERT: C 2191 LEU cc_start: 0.9494 (tp) cc_final: 0.9283 (tp) REVERT: C 2330 MET cc_start: 0.8832 (mmm) cc_final: 0.8468 (mmm) REVERT: C 2452 MET cc_start: 0.8981 (mtp) cc_final: 0.8758 (mtp) REVERT: C 2512 ILE cc_start: 0.8952 (pt) cc_final: 0.8735 (mp) REVERT: C 2521 GLU cc_start: 0.9558 (pm20) cc_final: 0.9339 (pm20) REVERT: C 2937 TYR cc_start: 0.9096 (m-80) cc_final: 0.8392 (m-80) REVERT: C 3050 GLU cc_start: 0.8973 (tt0) cc_final: 0.8703 (pt0) REVERT: C 3060 MET cc_start: 0.8065 (mtm) cc_final: 0.7619 (mpp) REVERT: C 3069 MET cc_start: 0.9729 (mmp) cc_final: 0.9379 (mmm) REVERT: C 3150 MET cc_start: 0.9459 (ttm) cc_final: 0.9120 (tmm) REVERT: C 3162 LYS cc_start: 0.9667 (ttpt) cc_final: 0.9420 (ptmm) REVERT: C 3195 TYR cc_start: 0.9375 (t80) cc_final: 0.9051 (t80) REVERT: C 3623 MET cc_start: 0.8902 (tpp) cc_final: 0.8652 (tpp) REVERT: C 3787 MET cc_start: 0.8715 (mmp) cc_final: 0.8464 (mmp) REVERT: C 3958 ASN cc_start: 0.9168 (m110) cc_final: 0.8725 (p0) REVERT: C 4105 MET cc_start: 0.9037 (mmm) cc_final: 0.8717 (mmp) REVERT: C 4165 MET cc_start: 0.9029 (mpp) cc_final: 0.8352 (mpp) REVERT: D 248 MET cc_start: 0.6169 (tpp) cc_final: 0.5397 (tpp) REVERT: E 116 VAL cc_start: 0.8392 (t) cc_final: 0.7912 (p) REVERT: L 57 LEU cc_start: 0.7418 (tp) cc_final: 0.7158 (tp) REVERT: N 22 LYS cc_start: 0.7507 (mmmt) cc_final: 0.7288 (mmmt) REVERT: O 125 ILE cc_start: 0.6757 (pt) cc_final: 0.6234 (pt) outliers start: 17 outliers final: 4 residues processed: 1558 average time/residue: 1.0254 time to fit residues: 2774.7621 Evaluate side-chains 1138 residues out of total 14031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1134 time to evaluate : 10.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1553 random chunks: chunk 1395 optimal weight: 20.0000 chunk 1062 optimal weight: 0.1980 chunk 733 optimal weight: 0.5980 chunk 156 optimal weight: 2.9990 chunk 674 optimal weight: 7.9990 chunk 948 optimal weight: 0.0770 chunk 1417 optimal weight: 10.0000 chunk 1501 optimal weight: 0.6980 chunk 740 optimal weight: 3.9990 chunk 1343 optimal weight: 9.9990 chunk 404 optimal weight: 0.7980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 647 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 681 ASN ** A 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 741 ASN ** A 804 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 952 GLN ** A1486 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2181 HIS ** A2220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3020 ASN A3079 GLN A3154 GLN A3536 GLN ** A3801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3956 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3984 ASN ** A4448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4485 HIS ** B 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1079 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1728 GLN B2203 ASN ** B2214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2871 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2930 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3000 ASN ** B3053 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3347 ASN ** B3435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3560 GLN ** B3604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3640 GLN ** B3714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3746 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3810 GLN ** B3820 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3888 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4417 ASN ** C 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 HIS ** C 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 HIS C1045 GLN C1258 ASN ** C1274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1309 GLN C1391 GLN ** C1705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2074 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2743 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2819 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2987 GLN ** C3004 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3178 ASN ** C3245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3631 GLN ** C3654 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3858 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 149 GLN I 43 GLN ** I 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 71 HIS K 59 HIS ** L 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 56 ASN ** M 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6180 moved from start: 0.5010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 121585 Z= 0.128 Angle : 0.462 14.720 164623 Z= 0.248 Chirality : 0.037 0.169 18615 Planarity : 0.003 0.072 21279 Dihedral : 5.344 117.377 16700 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 50.73 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.37 % Favored : 96.39 % Rotamer: Outliers : 0.03 % Allowed : 1.40 % Favored : 98.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.03 % Twisted Proline : 0.00 % 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: 1.64 (0.07), residues: 15467 helix: 2.61 (0.05), residues: 8636 sheet: -0.08 (0.13), residues: 1452 loop : -1.19 (0.08), residues: 5379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP B4414 HIS 0.011 0.001 HIS M 39 PHE 0.052 0.001 PHE A 655 TYR 0.025 0.001 TYR A 651 ARG 0.015 0.000 ARG L 22 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 30934 Ramachandran restraints generated. 15467 Oldfield, 0 Emsley, 15467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 30934 Ramachandran restraints generated. 15467 Oldfield, 0 Emsley, 15467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue SER 3 is missing expected H atoms. Skipping. Residue VAL 5 is missing expected H atoms. Skipping. Residue MET 6 is missing expected H atoms. Skipping. Residue LEU 8 is missing expected H atoms. Skipping. Residue SER 9 is missing expected H atoms. Skipping. Residue ILE 13 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue ALA 19 is missing expected H atoms. Skipping. Residue SER 21 is missing expected H atoms. Skipping. Residue TYR 23 is missing expected H atoms. Skipping. Residue LEU 28 is missing expected H atoms. Skipping. Residue ALA 30 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue VAL 33 is missing expected H atoms. Skipping. Residue SER 34 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue LEU 38 is missing expected H atoms. Skipping. Residue ALA 39 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue SER 48 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Residue MET 55 is missing expected H atoms. Skipping. Residue ILE 56 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Residue VAL 59 is missing expected H atoms. Skipping. Residue LYS 62 is missing expected H atoms. Skipping. Residue THR 64 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue ILE 67 is missing expected H atoms. Skipping. Residue LYS 68 is missing expected H atoms. Skipping. Residue SER 70 is missing expected H atoms. Skipping. Residue LEU 73 is missing expected H atoms. Skipping. Residue ILE 75 is missing expected H atoms. Skipping. Residue TYR 76 is missing expected H atoms. Skipping. Residue TYR 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue ALA 82 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Evaluate side-chains 1519 residues out of total 14031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1516 time to evaluate : 10.104 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1550 LYS cc_start: 0.6424 (ptpt) cc_final: 0.6168 (ptmt) REVERT: A 1665 GLU cc_start: 0.8306 (tm-30) cc_final: 0.8019 (tm-30) REVERT: A 1750 MET cc_start: 0.9364 (tpt) cc_final: 0.8994 (tpt) REVERT: A 1761 MET cc_start: 0.9067 (tpt) cc_final: 0.8506 (tpp) REVERT: A 1770 GLU cc_start: 0.8824 (mm-30) cc_final: 0.8610 (mt-10) REVERT: A 1814 ILE cc_start: 0.9409 (mp) cc_final: 0.9000 (tp) REVERT: A 2035 GLU cc_start: 0.9077 (tt0) cc_final: 0.8801 (tm-30) REVERT: A 2036 GLU cc_start: 0.9410 (mt-10) cc_final: 0.9139 (mt-10) REVERT: A 2072 MET cc_start: 0.9097 (tmm) cc_final: 0.8647 (tmm) REVERT: A 2123 GLU cc_start: 0.9456 (tm-30) cc_final: 0.8702 (tp30) REVERT: A 2239 ILE cc_start: 0.9571 (tp) cc_final: 0.9247 (mm) REVERT: A 2264 MET cc_start: 0.8622 (ttp) cc_final: 0.7555 (ttt) REVERT: A 2268 CYS cc_start: 0.8659 (t) cc_final: 0.8451 (t) REVERT: A 2301 GLU cc_start: 0.8713 (pm20) cc_final: 0.8391 (pp20) REVERT: A 2348 MET cc_start: 0.8821 (mmt) cc_final: 0.8561 (tpp) REVERT: A 2554 MET cc_start: 0.7716 (tpp) cc_final: 0.7152 (tpp) REVERT: A 2555 MET cc_start: 0.7907 (ttm) cc_final: 0.7490 (tpp) REVERT: A 2572 ASP cc_start: 0.9286 (m-30) cc_final: 0.9063 (m-30) REVERT: A 2590 MET cc_start: 0.8869 (mtt) cc_final: 0.8624 (mmm) REVERT: A 2634 MET cc_start: 0.8769 (mmm) cc_final: 0.8542 (mmt) REVERT: A 2650 HIS cc_start: 0.8192 (t-90) cc_final: 0.7388 (t70) REVERT: A 2657 PHE cc_start: 0.8863 (m-80) cc_final: 0.8536 (m-80) REVERT: A 2683 MET cc_start: 0.8853 (mmp) cc_final: 0.8632 (mmm) REVERT: A 2831 ARG cc_start: 0.9327 (mmm160) cc_final: 0.8561 (tpp80) REVERT: A 2837 MET cc_start: 0.8605 (ttm) cc_final: 0.7767 (tmm) REVERT: A 2858 GLN cc_start: 0.8211 (mm110) cc_final: 0.7732 (mt0) REVERT: A 2877 THR cc_start: 0.9354 (m) cc_final: 0.9009 (p) REVERT: A 2949 ASN cc_start: 0.9236 (m-40) cc_final: 0.8676 (t0) REVERT: A 3020 ASN cc_start: 0.9210 (m110) cc_final: 0.8981 (m-40) REVERT: A 3063 MET cc_start: 0.9574 (mmt) cc_final: 0.8670 (mmt) REVERT: A 3453 PHE cc_start: 0.8654 (t80) cc_final: 0.8203 (t80) REVERT: A 3477 MET cc_start: 0.8812 (mmm) cc_final: 0.8480 (mmm) REVERT: A 3490 LEU cc_start: 0.9509 (tt) cc_final: 0.9259 (tt) REVERT: A 3502 GLU cc_start: 0.9608 (mm-30) cc_final: 0.9197 (tp30) REVERT: A 3510 LYS cc_start: 0.8772 (tptm) cc_final: 0.8357 (tptp) REVERT: A 3581 GLU cc_start: 0.8973 (tt0) cc_final: 0.8641 (pt0) REVERT: A 3590 MET cc_start: 0.9418 (ppp) cc_final: 0.9142 (ppp) REVERT: A 3609 ASN cc_start: 0.9520 (p0) cc_final: 0.9291 (t0) REVERT: A 3633 SER cc_start: 0.9286 (m) cc_final: 0.8989 (p) REVERT: A 3642 THR cc_start: 0.8675 (t) cc_final: 0.8466 (t) REVERT: A 3671 GLU cc_start: 0.8867 (tt0) cc_final: 0.8516 (pt0) REVERT: A 3672 ASP cc_start: 0.9446 (t0) cc_final: 0.9227 (t0) REVERT: A 3680 ASP cc_start: 0.9484 (m-30) cc_final: 0.9176 (t0) REVERT: A 3725 GLU cc_start: 0.9373 (tt0) cc_final: 0.9053 (mt-10) REVERT: A 3730 LEU cc_start: 0.9318 (mt) cc_final: 0.8937 (mm) REVERT: A 3746 GLN cc_start: 0.9078 (mt0) cc_final: 0.8685 (mt0) REVERT: A 3770 MET cc_start: 0.9341 (mmm) cc_final: 0.9059 (mmm) REVERT: A 3794 LEU cc_start: 0.7692 (mt) cc_final: 0.7481 (tp) REVERT: A 3841 ILE cc_start: 0.8853 (tt) cc_final: 0.8494 (pt) REVERT: A 3905 ASN cc_start: 0.9171 (m-40) cc_final: 0.8863 (t0) REVERT: A 4015 GLU cc_start: 0.8646 (mm-30) cc_final: 0.8301 (mp0) REVERT: A 4019 MET cc_start: 0.9034 (mmm) cc_final: 0.7994 (tpp) REVERT: A 4069 ASP cc_start: 0.9055 (m-30) cc_final: 0.8388 (p0) REVERT: A 4177 MET cc_start: 0.8966 (mmm) cc_final: 0.8669 (tpp) REVERT: A 4221 GLU cc_start: 0.9011 (mt-10) cc_final: 0.8639 (mm-30) REVERT: A 4232 ASP cc_start: 0.9135 (m-30) cc_final: 0.8301 (p0) REVERT: A 4292 GLU cc_start: 0.9228 (tt0) cc_final: 0.8976 (tt0) REVERT: A 4295 GLU cc_start: 0.9286 (tt0) cc_final: 0.8794 (tm-30) REVERT: A 4296 MET cc_start: 0.8886 (tmm) cc_final: 0.8642 (tmm) REVERT: A 4371 GLU cc_start: 0.8890 (pt0) cc_final: 0.8335 (mm-30) REVERT: A 4388 ASP cc_start: 0.9212 (m-30) cc_final: 0.8916 (t0) REVERT: A 4405 GLU cc_start: 0.9625 (tt0) cc_final: 0.9195 (tm-30) REVERT: A 4527 LYS cc_start: 0.8633 (pttt) cc_final: 0.8333 (tmmt) REVERT: A 4572 MET cc_start: 0.8644 (ttt) cc_final: 0.8239 (tpp) REVERT: A 4576 TYR cc_start: 0.8087 (t80) cc_final: 0.7754 (t80) REVERT: B 547 LEU cc_start: 0.7804 (mt) cc_final: 0.7528 (mt) REVERT: B 1765 GLU cc_start: 0.9432 (tt0) cc_final: 0.9178 (tp30) REVERT: B 1794 ASP cc_start: 0.8955 (t0) cc_final: 0.8180 (t0) REVERT: B 1799 ASP cc_start: 0.9054 (m-30) cc_final: 0.8667 (t0) REVERT: B 1895 MET cc_start: 0.8628 (ptp) cc_final: 0.8328 (ptp) REVERT: B 1941 MET cc_start: 0.8840 (mmp) cc_final: 0.8610 (mmp) REVERT: B 1953 ASP cc_start: 0.9344 (t0) cc_final: 0.8605 (p0) REVERT: B 2004 MET cc_start: 0.8266 (ttm) cc_final: 0.7099 (tmm) REVERT: B 2080 LYS cc_start: 0.9409 (ttpt) cc_final: 0.9134 (tptp) REVERT: B 2108 ASP cc_start: 0.9556 (t70) cc_final: 0.9253 (m-30) REVERT: B 2111 MET cc_start: 0.8971 (mmm) cc_final: 0.8755 (mmp) REVERT: B 2238 ILE cc_start: 0.9626 (tt) cc_final: 0.9398 (tp) REVERT: B 2260 TRP cc_start: 0.8489 (p90) cc_final: 0.6548 (p90) REVERT: B 2279 MET cc_start: 0.8595 (ttt) cc_final: 0.8379 (ttt) REVERT: B 2318 ARG cc_start: 0.9516 (mtt-85) cc_final: 0.9140 (ttm110) REVERT: B 2356 MET cc_start: 0.7672 (mmp) cc_final: 0.7444 (mmm) REVERT: B 2364 ASP cc_start: 0.9230 (t0) cc_final: 0.9014 (p0) REVERT: B 2410 ASP cc_start: 0.9242 (m-30) cc_final: 0.8574 (t0) REVERT: B 2422 GLN cc_start: 0.8800 (tm-30) cc_final: 0.8519 (tm-30) REVERT: B 2523 MET cc_start: 0.9450 (mmp) cc_final: 0.9148 (mmm) REVERT: B 2860 MET cc_start: 0.8785 (mmm) cc_final: 0.8064 (mtm) REVERT: B 2869 MET cc_start: 0.9221 (mtp) cc_final: 0.8903 (mtm) REVERT: B 2912 ASP cc_start: 0.8820 (t0) cc_final: 0.8239 (p0) REVERT: B 2947 MET cc_start: 0.8946 (tpt) cc_final: 0.8657 (tpt) REVERT: B 3068 GLU cc_start: 0.7841 (pm20) cc_final: 0.7453 (pm20) REVERT: B 3259 VAL cc_start: 0.7115 (t) cc_final: 0.6845 (t) REVERT: B 3484 LYS cc_start: 0.8903 (mptt) cc_final: 0.8401 (mptt) REVERT: B 3508 LYS cc_start: 0.9318 (tptm) cc_final: 0.9059 (mttt) REVERT: B 3585 GLU cc_start: 0.9028 (mp0) cc_final: 0.8756 (mp0) REVERT: B 3737 GLU cc_start: 0.9476 (mt-10) cc_final: 0.9239 (mm-30) REVERT: B 3767 MET cc_start: 0.8674 (tmm) cc_final: 0.8356 (tmm) REVERT: B 3978 GLU cc_start: 0.8655 (tt0) cc_final: 0.8096 (tm-30) REVERT: B 4040 MET cc_start: 0.8271 (ttt) cc_final: 0.7942 (tpt) REVERT: B 4043 ASN cc_start: 0.9341 (m-40) cc_final: 0.9114 (m-40) REVERT: B 4121 ASP cc_start: 0.8614 (t0) cc_final: 0.8236 (m-30) REVERT: B 4159 MET cc_start: 0.8640 (mmm) cc_final: 0.7440 (mmm) REVERT: B 4352 GLU cc_start: 0.9054 (tm-30) cc_final: 0.8744 (tm-30) REVERT: B 4356 MET cc_start: 0.9686 (tpp) cc_final: 0.8931 (tpp) REVERT: B 4385 GLU cc_start: 0.9653 (mm-30) cc_final: 0.9426 (mp0) REVERT: B 4431 ASP cc_start: 0.8903 (t0) cc_final: 0.8643 (t0) REVERT: B 4456 GLN cc_start: 0.9285 (mt0) cc_final: 0.9001 (tt0) REVERT: C 850 GLU cc_start: 0.9160 (mt-10) cc_final: 0.8951 (pt0) REVERT: C 1085 MET cc_start: 0.9251 (mmp) cc_final: 0.8939 (mmm) REVERT: C 1107 MET cc_start: 0.7114 (mmm) cc_final: 0.6913 (mmm) REVERT: C 1162 ARG cc_start: 0.9378 (tmt170) cc_final: 0.9100 (tpt90) REVERT: C 1164 MET cc_start: 0.9529 (tpt) cc_final: 0.9303 (tpp) REVERT: C 1240 MET cc_start: 0.9426 (mtm) cc_final: 0.8936 (ptm) REVERT: C 1268 ASP cc_start: 0.9153 (m-30) cc_final: 0.8629 (t0) REVERT: C 1326 HIS cc_start: 0.8613 (t-90) cc_final: 0.8107 (t-90) REVERT: C 1367 TYR cc_start: 0.8354 (m-80) cc_final: 0.7942 (m-80) REVERT: C 1433 MET cc_start: 0.8980 (mtt) cc_final: 0.8387 (mtp) REVERT: C 1438 MET cc_start: 0.9671 (mmm) cc_final: 0.9301 (mmm) REVERT: C 1510 LEU cc_start: 0.9237 (tt) cc_final: 0.9036 (tt) REVERT: C 1561 MET cc_start: 0.9313 (tmm) cc_final: 0.9056 (tmm) REVERT: C 2001 MET cc_start: 0.9284 (mmp) cc_final: 0.9009 (mmm) REVERT: C 2128 MET cc_start: 0.9284 (ptp) cc_final: 0.8952 (ppp) REVERT: C 2190 MET cc_start: 0.9329 (mtm) cc_final: 0.8957 (ptm) REVERT: C 2512 ILE cc_start: 0.8912 (pt) cc_final: 0.8663 (mp) REVERT: C 2521 GLU cc_start: 0.9542 (pm20) cc_final: 0.9280 (pm20) REVERT: C 2937 TYR cc_start: 0.9036 (m-80) cc_final: 0.8552 (m-80) REVERT: C 3050 GLU cc_start: 0.8940 (tt0) cc_final: 0.8731 (pt0) REVERT: C 3069 MET cc_start: 0.9725 (mmp) cc_final: 0.9368 (mmm) REVERT: C 3150 MET cc_start: 0.9416 (ttm) cc_final: 0.9118 (tmm) REVERT: C 3162 LYS cc_start: 0.9734 (ttpt) cc_final: 0.9458 (ptmm) REVERT: C 3623 MET cc_start: 0.8871 (tpp) cc_final: 0.8615 (tpp) REVERT: C 3958 ASN cc_start: 0.9135 (m110) cc_final: 0.8735 (p0) REVERT: C 4165 MET cc_start: 0.8895 (mpp) cc_final: 0.7986 (mpp) REVERT: E 116 VAL cc_start: 0.8245 (t) cc_final: 0.7913 (p) REVERT: F 33 LEU cc_start: 0.7151 (mp) cc_final: 0.6879 (mp) REVERT: G 116 ASP cc_start: 0.7341 (m-30) cc_final: 0.7040 (m-30) REVERT: I 107 ILE cc_start: 0.6325 (pt) cc_final: 0.6038 (pt) REVERT: L 29 HIS cc_start: 0.5193 (p-80) cc_final: 0.4981 (p-80) REVERT: L 42 ILE cc_start: 0.8268 (pt) cc_final: 0.8064 (pt) REVERT: L 76 CYS cc_start: 0.5127 (t) cc_final: 0.4871 (t) REVERT: L 107 LEU cc_start: 0.5981 (pp) cc_final: 0.5536 (pp) REVERT: N 22 LYS cc_start: 0.7635 (mmmt) cc_final: 0.7296 (mmmt) outliers start: 3 outliers final: 1 residues processed: 1519 average time/residue: 1.0100 time to fit residues: 2681.4100 Evaluate side-chains 1127 residues out of total 14031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1126 time to evaluate : 11.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1553 random chunks: chunk 1250 optimal weight: 9.9990 chunk 852 optimal weight: 9.9990 chunk 21 optimal weight: 5.9990 chunk 1117 optimal weight: 0.9980 chunk 619 optimal weight: 10.0000 chunk 1280 optimal weight: 3.9990 chunk 1037 optimal weight: 0.0770 chunk 1 optimal weight: 8.9990 chunk 766 optimal weight: 0.0070 chunk 1347 optimal weight: 0.9980 chunk 378 optimal weight: 4.9990 overall best weight: 1.2158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 647 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1205 GLN ** A1486 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2037 GLN ** A2220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2735 HIS ** A2939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2972 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3956 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 832 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1062 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1079 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1480 HIS B1524 ASN B2203 ASN ** B2214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2930 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3053 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3746 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3810 GLN ** B3820 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3888 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1570 GLN ** C1705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2074 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2743 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2920 GLN ** C3004 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3157 GLN C3178 ASN ** C3547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3604 GLN ** C3654 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 196 GLN ** E 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6203 moved from start: 0.5243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 121585 Z= 0.133 Angle : 0.441 14.862 164623 Z= 0.237 Chirality : 0.036 0.261 18615 Planarity : 0.003 0.065 21279 Dihedral : 5.074 108.069 16700 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 53.30 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.03 % Favored : 95.72 % Rotamer: Outliers : 0.03 % Allowed : 1.07 % Favored : 98.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.03 % Twisted Proline : 0.00 % 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: 1.90 (0.07), residues: 15467 helix: 2.81 (0.05), residues: 8638 sheet: -0.00 (0.13), residues: 1449 loop : -1.07 (0.08), residues: 5380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP A 654 HIS 0.009 0.001 HIS E 560 PHE 0.038 0.001 PHE O 42 TYR 0.024 0.001 TYR N 53 ARG 0.007 0.000 ARG C1592 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 30934 Ramachandran restraints generated. 15467 Oldfield, 0 Emsley, 15467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 30934 Ramachandran restraints generated. 15467 Oldfield, 0 Emsley, 15467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue SER 3 is missing expected H atoms. Skipping. Residue VAL 5 is missing expected H atoms. Skipping. Residue MET 6 is missing expected H atoms. Skipping. Residue LEU 8 is missing expected H atoms. Skipping. Residue SER 9 is missing expected H atoms. Skipping. Residue ILE 13 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue ALA 19 is missing expected H atoms. Skipping. Residue SER 21 is missing expected H atoms. Skipping. Residue TYR 23 is missing expected H atoms. Skipping. Residue LEU 28 is missing expected H atoms. Skipping. Residue ALA 30 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue VAL 33 is missing expected H atoms. Skipping. Residue SER 34 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue LEU 38 is missing expected H atoms. Skipping. Residue ALA 39 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue SER 48 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Residue MET 55 is missing expected H atoms. Skipping. Residue ILE 56 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Residue VAL 59 is missing expected H atoms. Skipping. Residue LYS 62 is missing expected H atoms. Skipping. Residue THR 64 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue ILE 67 is missing expected H atoms. Skipping. Residue LYS 68 is missing expected H atoms. Skipping. Residue SER 70 is missing expected H atoms. Skipping. Residue LEU 73 is missing expected H atoms. Skipping. Residue ILE 75 is missing expected H atoms. Skipping. Residue TYR 76 is missing expected H atoms. Skipping. Residue TYR 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue ALA 82 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Evaluate side-chains 1419 residues out of total 14031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1416 time to evaluate : 10.098 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1550 LYS cc_start: 0.6581 (ptpt) cc_final: 0.6115 (ptmt) REVERT: A 1665 GLU cc_start: 0.8326 (tm-30) cc_final: 0.8036 (tm-30) REVERT: A 1750 MET cc_start: 0.9371 (tpt) cc_final: 0.9007 (tpt) REVERT: A 1761 MET cc_start: 0.9102 (tpt) cc_final: 0.8507 (tpp) REVERT: A 1770 GLU cc_start: 0.8818 (mm-30) cc_final: 0.8593 (mt-10) REVERT: A 1814 ILE cc_start: 0.9384 (mp) cc_final: 0.8971 (tp) REVERT: A 1984 GLN cc_start: 0.8026 (tm-30) cc_final: 0.7665 (tm-30) REVERT: A 2035 GLU cc_start: 0.9067 (tt0) cc_final: 0.8814 (tm-30) REVERT: A 2036 GLU cc_start: 0.9392 (mt-10) cc_final: 0.9126 (mt-10) REVERT: A 2072 MET cc_start: 0.9102 (tmm) cc_final: 0.8535 (tmm) REVERT: A 2123 GLU cc_start: 0.9426 (tm-30) cc_final: 0.8726 (tp30) REVERT: A 2239 ILE cc_start: 0.9560 (tp) cc_final: 0.9236 (mm) REVERT: A 2264 MET cc_start: 0.8586 (ttp) cc_final: 0.7518 (ttt) REVERT: A 2268 CYS cc_start: 0.8716 (t) cc_final: 0.8483 (t) REVERT: A 2333 ASN cc_start: 0.8850 (m-40) cc_final: 0.8301 (m110) REVERT: A 2348 MET cc_start: 0.8805 (mmt) cc_final: 0.7841 (tpp) REVERT: A 2488 SER cc_start: 0.8486 (p) cc_final: 0.8207 (p) REVERT: A 2554 MET cc_start: 0.7979 (tpp) cc_final: 0.7513 (tpp) REVERT: A 2555 MET cc_start: 0.8038 (ttm) cc_final: 0.7603 (tpp) REVERT: A 2572 ASP cc_start: 0.9266 (m-30) cc_final: 0.9063 (m-30) REVERT: A 2590 MET cc_start: 0.9047 (mtt) cc_final: 0.8826 (mmm) REVERT: A 2634 MET cc_start: 0.8759 (mmm) cc_final: 0.8544 (mmt) REVERT: A 2650 HIS cc_start: 0.7811 (t-90) cc_final: 0.7401 (t70) REVERT: A 2657 PHE cc_start: 0.8585 (m-80) cc_final: 0.8377 (m-80) REVERT: A 2683 MET cc_start: 0.8761 (mmp) cc_final: 0.8554 (mmm) REVERT: A 2831 ARG cc_start: 0.9344 (mmm160) cc_final: 0.8444 (tpp80) REVERT: A 2837 MET cc_start: 0.8677 (ttm) cc_final: 0.7653 (tmm) REVERT: A 2858 GLN cc_start: 0.8106 (mm110) cc_final: 0.7602 (mt0) REVERT: A 2877 THR cc_start: 0.9360 (m) cc_final: 0.8991 (p) REVERT: A 2949 ASN cc_start: 0.9282 (m-40) cc_final: 0.8717 (t0) REVERT: A 3020 ASN cc_start: 0.9325 (m110) cc_final: 0.9120 (m-40) REVERT: A 3063 MET cc_start: 0.9556 (mmt) cc_final: 0.8661 (mmt) REVERT: A 3453 PHE cc_start: 0.8601 (t80) cc_final: 0.8108 (t80) REVERT: A 3477 MET cc_start: 0.8772 (mmm) cc_final: 0.8443 (mmm) REVERT: A 3502 GLU cc_start: 0.9600 (mm-30) cc_final: 0.9199 (tp30) REVERT: A 3510 LYS cc_start: 0.8776 (tptm) cc_final: 0.8446 (tptp) REVERT: A 3581 GLU cc_start: 0.9089 (tt0) cc_final: 0.8751 (pt0) REVERT: A 3590 MET cc_start: 0.9430 (ppp) cc_final: 0.9175 (ppp) REVERT: A 3609 ASN cc_start: 0.9553 (p0) cc_final: 0.9283 (t0) REVERT: A 3633 SER cc_start: 0.9249 (m) cc_final: 0.8956 (p) REVERT: A 3671 GLU cc_start: 0.8879 (tt0) cc_final: 0.8573 (pt0) REVERT: A 3672 ASP cc_start: 0.9461 (t0) cc_final: 0.9248 (t0) REVERT: A 3680 ASP cc_start: 0.9460 (m-30) cc_final: 0.9178 (t0) REVERT: A 3725 GLU cc_start: 0.9352 (tt0) cc_final: 0.9031 (tm-30) REVERT: A 3746 GLN cc_start: 0.9021 (mt0) cc_final: 0.8694 (mt0) REVERT: A 3794 LEU cc_start: 0.7709 (mt) cc_final: 0.7477 (tp) REVERT: A 3841 ILE cc_start: 0.8815 (tt) cc_final: 0.8494 (pt) REVERT: A 3905 ASN cc_start: 0.9169 (m-40) cc_final: 0.8862 (t0) REVERT: A 4015 GLU cc_start: 0.8634 (mm-30) cc_final: 0.8303 (mp0) REVERT: A 4019 MET cc_start: 0.9045 (mmm) cc_final: 0.7978 (tpp) REVERT: A 4069 ASP cc_start: 0.9051 (m-30) cc_final: 0.8382 (p0) REVERT: A 4177 MET cc_start: 0.8990 (mmm) cc_final: 0.8711 (tpp) REVERT: A 4221 GLU cc_start: 0.8983 (mt-10) cc_final: 0.8620 (mm-30) REVERT: A 4232 ASP cc_start: 0.9122 (m-30) cc_final: 0.8312 (p0) REVERT: A 4295 GLU cc_start: 0.9294 (tt0) cc_final: 0.8796 (tm-30) REVERT: A 4296 MET cc_start: 0.8933 (tmm) cc_final: 0.8670 (tmm) REVERT: A 4388 ASP cc_start: 0.9225 (m-30) cc_final: 0.8924 (t0) REVERT: A 4405 GLU cc_start: 0.9623 (tt0) cc_final: 0.9203 (tm-30) REVERT: A 4527 LYS cc_start: 0.8610 (pttt) cc_final: 0.8325 (tmmt) REVERT: A 4572 MET cc_start: 0.8583 (ttt) cc_final: 0.8212 (tpp) REVERT: B 547 LEU cc_start: 0.7813 (mt) cc_final: 0.7534 (mt) REVERT: B 629 ILE cc_start: 0.6302 (pt) cc_final: 0.5680 (pt) REVERT: B 1087 LEU cc_start: 0.8114 (pp) cc_final: 0.7731 (pp) REVERT: B 1765 GLU cc_start: 0.9427 (tt0) cc_final: 0.9189 (tp30) REVERT: B 1794 ASP cc_start: 0.8989 (t0) cc_final: 0.8232 (t0) REVERT: B 1895 MET cc_start: 0.8555 (ptp) cc_final: 0.8298 (ptp) REVERT: B 1953 ASP cc_start: 0.9358 (t0) cc_final: 0.8623 (p0) REVERT: B 2004 MET cc_start: 0.8006 (ttm) cc_final: 0.6802 (tmm) REVERT: B 2080 LYS cc_start: 0.9417 (ttpt) cc_final: 0.9128 (tptp) REVERT: B 2108 ASP cc_start: 0.9558 (t70) cc_final: 0.9263 (m-30) REVERT: B 2111 MET cc_start: 0.8981 (mmm) cc_final: 0.8500 (mmm) REVERT: B 2238 ILE cc_start: 0.9669 (tt) cc_final: 0.9417 (tp) REVERT: B 2260 TRP cc_start: 0.8479 (p90) cc_final: 0.7256 (p90) REVERT: B 2279 MET cc_start: 0.8677 (ttt) cc_final: 0.8475 (ttt) REVERT: B 2318 ARG cc_start: 0.9527 (mtt-85) cc_final: 0.9148 (ttm110) REVERT: B 2356 MET cc_start: 0.7722 (mmp) cc_final: 0.7480 (mmm) REVERT: B 2364 ASP cc_start: 0.9258 (t0) cc_final: 0.9019 (p0) REVERT: B 2422 GLN cc_start: 0.8817 (tm-30) cc_final: 0.8541 (tm-30) REVERT: B 2523 MET cc_start: 0.9459 (mmp) cc_final: 0.9163 (mmm) REVERT: B 2719 ASP cc_start: 0.8792 (t0) cc_final: 0.8538 (t70) REVERT: B 2775 MET cc_start: 0.8528 (mtm) cc_final: 0.8083 (mtm) REVERT: B 2860 MET cc_start: 0.8771 (mmm) cc_final: 0.8229 (mtm) REVERT: B 2869 MET cc_start: 0.9223 (mtp) cc_final: 0.8958 (mtm) REVERT: B 2912 ASP cc_start: 0.8801 (t0) cc_final: 0.8239 (p0) REVERT: B 2947 MET cc_start: 0.8917 (tpt) cc_final: 0.8602 (tpt) REVERT: B 2955 GLU cc_start: 0.8984 (tt0) cc_final: 0.8764 (pt0) REVERT: B 3068 GLU cc_start: 0.7954 (pm20) cc_final: 0.7632 (pm20) REVERT: B 3493 GLU cc_start: 0.9030 (mp0) cc_final: 0.8774 (mp0) REVERT: B 3508 LYS cc_start: 0.9306 (tptm) cc_final: 0.8953 (mptt) REVERT: B 3737 GLU cc_start: 0.9447 (mt-10) cc_final: 0.9183 (mm-30) REVERT: B 3767 MET cc_start: 0.8681 (tmm) cc_final: 0.8124 (tmm) REVERT: B 3978 GLU cc_start: 0.8628 (tt0) cc_final: 0.8099 (tm-30) REVERT: B 4040 MET cc_start: 0.8262 (ttt) cc_final: 0.7921 (tpt) REVERT: B 4043 ASN cc_start: 0.9342 (m-40) cc_final: 0.9091 (m-40) REVERT: B 4121 ASP cc_start: 0.8622 (t0) cc_final: 0.8234 (m-30) REVERT: B 4159 MET cc_start: 0.8624 (mmm) cc_final: 0.7376 (mmm) REVERT: B 4352 GLU cc_start: 0.9060 (tm-30) cc_final: 0.8747 (tm-30) REVERT: B 4356 MET cc_start: 0.9614 (tpp) cc_final: 0.8934 (tpp) REVERT: B 4385 GLU cc_start: 0.9653 (mm-30) cc_final: 0.9405 (mp0) REVERT: B 4431 ASP cc_start: 0.8885 (t0) cc_final: 0.8642 (t0) REVERT: B 4456 GLN cc_start: 0.9281 (mt0) cc_final: 0.9003 (tt0) REVERT: C 893 GLU cc_start: 0.9576 (mt-10) cc_final: 0.8764 (tm-30) REVERT: C 1085 MET cc_start: 0.9201 (mmp) cc_final: 0.8964 (mmm) REVERT: C 1162 ARG cc_start: 0.9325 (tmt170) cc_final: 0.9040 (tpt90) REVERT: C 1164 MET cc_start: 0.9544 (tpt) cc_final: 0.9313 (tpp) REVERT: C 1240 MET cc_start: 0.9407 (mtm) cc_final: 0.8913 (ptm) REVERT: C 1268 ASP cc_start: 0.9158 (m-30) cc_final: 0.8694 (t0) REVERT: C 1367 TYR cc_start: 0.8396 (m-80) cc_final: 0.7915 (m-80) REVERT: C 1433 MET cc_start: 0.8956 (mtt) cc_final: 0.8380 (mtp) REVERT: C 1438 MET cc_start: 0.9658 (mmm) cc_final: 0.9281 (mmm) REVERT: C 1510 LEU cc_start: 0.9208 (tt) cc_final: 0.8970 (tt) REVERT: C 1561 MET cc_start: 0.9315 (tmm) cc_final: 0.9051 (tmm) REVERT: C 2001 MET cc_start: 0.9282 (mmp) cc_final: 0.9015 (mmm) REVERT: C 2128 MET cc_start: 0.9295 (ptp) cc_final: 0.8984 (ppp) REVERT: C 2191 LEU cc_start: 0.9609 (tp) cc_final: 0.9342 (tp) REVERT: C 2243 GLU cc_start: 0.9388 (tp30) cc_final: 0.8566 (tm-30) REVERT: C 2452 MET cc_start: 0.9166 (mpp) cc_final: 0.8873 (mpp) REVERT: C 2512 ILE cc_start: 0.8946 (pt) cc_final: 0.8679 (mp) REVERT: C 2521 GLU cc_start: 0.9550 (pm20) cc_final: 0.9171 (tm-30) REVERT: C 2788 VAL cc_start: 0.6069 (t) cc_final: 0.5813 (t) REVERT: C 2937 TYR cc_start: 0.9152 (m-80) cc_final: 0.8460 (m-80) REVERT: C 2965 MET cc_start: 0.8017 (ptp) cc_final: 0.7462 (mtp) REVERT: C 3050 GLU cc_start: 0.8902 (tt0) cc_final: 0.8684 (pt0) REVERT: C 3069 MET cc_start: 0.9741 (mmp) cc_final: 0.9363 (mmm) REVERT: C 3150 MET cc_start: 0.9383 (ttm) cc_final: 0.9114 (tmm) REVERT: C 3195 TYR cc_start: 0.9380 (t80) cc_final: 0.9087 (t80) REVERT: C 3623 MET cc_start: 0.8833 (tpp) cc_final: 0.8612 (tpp) REVERT: C 3958 ASN cc_start: 0.9142 (m110) cc_final: 0.8745 (p0) REVERT: C 4165 MET cc_start: 0.8930 (mpp) cc_final: 0.7971 (mpp) REVERT: D 248 MET cc_start: 0.6547 (mmt) cc_final: 0.5116 (tpt) REVERT: E 116 VAL cc_start: 0.8493 (t) cc_final: 0.8029 (p) REVERT: G 145 LEU cc_start: 0.7638 (tp) cc_final: 0.7341 (tp) REVERT: L 107 LEU cc_start: 0.5855 (pp) cc_final: 0.5529 (pp) REVERT: N 22 LYS cc_start: 0.7593 (mmmt) cc_final: 0.7288 (mmmt) outliers start: 3 outliers final: 2 residues processed: 1419 average time/residue: 1.0546 time to fit residues: 2628.2600 Evaluate side-chains 1099 residues out of total 14031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1097 time to evaluate : 9.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1553 random chunks: chunk 505 optimal weight: 2.9990 chunk 1351 optimal weight: 5.9990 chunk 296 optimal weight: 2.9990 chunk 881 optimal weight: 6.9990 chunk 370 optimal weight: 9.9990 chunk 1502 optimal weight: 5.9990 chunk 1247 optimal weight: 1.9990 chunk 695 optimal weight: 20.0000 chunk 124 optimal weight: 8.9990 chunk 497 optimal weight: 10.0000 chunk 788 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 741 ASN ** A 755 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1079 HIS A1205 GLN ** A1486 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1693 GLN ** A2220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3956 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4067 HIS ** A4448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4603 ASN B 431 ASN ** B 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 832 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1062 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1079 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1524 ASN B1807 GLN ** B2139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2203 ASN ** B2214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2736 HIS ** B2758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2871 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3053 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3081 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3086 HIS ** B3238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3746 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3810 GLN ** B3820 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3888 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 826 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2074 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2743 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3004 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3178 ASN ** C3547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3631 GLN ** C3654 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3682 GLN ** C3858 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 153 HIS ** D 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 220 ASN ** E 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6309 moved from start: 0.5634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 121585 Z= 0.222 Angle : 0.508 14.025 164623 Z= 0.275 Chirality : 0.036 0.228 18615 Planarity : 0.003 0.061 21279 Dihedral : 5.022 105.557 16700 Min Nonbonded Distance : 1.752 Molprobity Statistics. All-atom Clashscore : 60.11 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.44 % Favored : 95.31 % Rotamer: Outliers : 0.03 % Allowed : 1.36 % Favored : 98.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.03 % Twisted Proline : 0.00 % 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: 1.77 (0.07), residues: 15467 helix: 2.70 (0.05), residues: 8660 sheet: -0.03 (0.13), residues: 1428 loop : -1.13 (0.08), residues: 5379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A 659 HIS 0.023 0.001 HIS B2258 PHE 0.047 0.001 PHE J 51 TYR 0.020 0.001 TYR B2059 ARG 0.011 0.000 ARG A 636 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 30934 Ramachandran restraints generated. 15467 Oldfield, 0 Emsley, 15467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 30934 Ramachandran restraints generated. 15467 Oldfield, 0 Emsley, 15467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue SER 3 is missing expected H atoms. Skipping. Residue VAL 5 is missing expected H atoms. Skipping. Residue MET 6 is missing expected H atoms. Skipping. Residue LEU 8 is missing expected H atoms. Skipping. Residue SER 9 is missing expected H atoms. Skipping. Residue ILE 13 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue ALA 19 is missing expected H atoms. Skipping. Residue SER 21 is missing expected H atoms. Skipping. Residue TYR 23 is missing expected H atoms. Skipping. Residue LEU 28 is missing expected H atoms. Skipping. Residue ALA 30 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue VAL 33 is missing expected H atoms. Skipping. Residue SER 34 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue LEU 38 is missing expected H atoms. Skipping. Residue ALA 39 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue SER 48 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Residue MET 55 is missing expected H atoms. Skipping. Residue ILE 56 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Residue VAL 59 is missing expected H atoms. Skipping. Residue LYS 62 is missing expected H atoms. Skipping. Residue THR 64 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue ILE 67 is missing expected H atoms. Skipping. Residue LYS 68 is missing expected H atoms. Skipping. Residue SER 70 is missing expected H atoms. Skipping. Residue LEU 73 is missing expected H atoms. Skipping. Residue ILE 75 is missing expected H atoms. Skipping. Residue TYR 76 is missing expected H atoms. Skipping. Residue TYR 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue ALA 82 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Evaluate side-chains 1345 residues out of total 14031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1342 time to evaluate : 10.296 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1204 LYS cc_start: 0.6663 (mttt) cc_final: 0.5039 (mtmt) REVERT: A 1550 LYS cc_start: 0.6421 (ptpt) cc_final: 0.6008 (ptmt) REVERT: A 1552 MET cc_start: 0.5245 (ttt) cc_final: 0.4833 (ttt) REVERT: A 1665 GLU cc_start: 0.8378 (tm-30) cc_final: 0.8094 (tm-30) REVERT: A 1713 GLU cc_start: 0.9202 (tt0) cc_final: 0.8893 (tp30) REVERT: A 1750 MET cc_start: 0.9332 (tpt) cc_final: 0.8992 (tpt) REVERT: A 1761 MET cc_start: 0.9216 (tpt) cc_final: 0.8552 (tpp) REVERT: A 1770 GLU cc_start: 0.8850 (mm-30) cc_final: 0.8635 (mt-10) REVERT: A 1814 ILE cc_start: 0.9368 (mp) cc_final: 0.8981 (tp) REVERT: A 1843 GLU cc_start: 0.8619 (tm-30) cc_final: 0.8414 (tm-30) REVERT: A 1907 MET cc_start: 0.9417 (mmt) cc_final: 0.9168 (mmp) REVERT: A 1984 GLN cc_start: 0.8100 (tm-30) cc_final: 0.7703 (tm-30) REVERT: A 2035 GLU cc_start: 0.9104 (tt0) cc_final: 0.8875 (tm-30) REVERT: A 2036 GLU cc_start: 0.9423 (mt-10) cc_final: 0.9133 (mt-10) REVERT: A 2123 GLU cc_start: 0.9471 (tm-30) cc_final: 0.8822 (tp30) REVERT: A 2264 MET cc_start: 0.8536 (ttp) cc_final: 0.7468 (ttt) REVERT: A 2268 CYS cc_start: 0.8710 (t) cc_final: 0.8432 (t) REVERT: A 2348 MET cc_start: 0.8851 (mmt) cc_final: 0.8538 (tpp) REVERT: A 2488 SER cc_start: 0.8468 (p) cc_final: 0.8205 (p) REVERT: A 2536 GLU cc_start: 0.8677 (tt0) cc_final: 0.8388 (mt-10) REVERT: A 2590 MET cc_start: 0.8908 (mtt) cc_final: 0.8657 (mmm) REVERT: A 2602 MET cc_start: 0.8965 (mpp) cc_final: 0.8686 (mpp) REVERT: A 2634 MET cc_start: 0.8723 (mmm) cc_final: 0.8490 (mmm) REVERT: A 2657 PHE cc_start: 0.8765 (m-80) cc_final: 0.8389 (m-80) REVERT: A 2831 ARG cc_start: 0.9314 (mmm160) cc_final: 0.8415 (tpp80) REVERT: A 2837 MET cc_start: 0.8700 (ttm) cc_final: 0.7712 (tmm) REVERT: A 2858 GLN cc_start: 0.8317 (mm110) cc_final: 0.7754 (mt0) REVERT: A 2877 THR cc_start: 0.9403 (m) cc_final: 0.9080 (p) REVERT: A 2949 ASN cc_start: 0.9251 (m-40) cc_final: 0.8874 (p0) REVERT: A 2993 ASP cc_start: 0.9482 (t0) cc_final: 0.9177 (m-30) REVERT: A 3453 PHE cc_start: 0.8638 (t80) cc_final: 0.8216 (t80) REVERT: A 3477 MET cc_start: 0.8729 (mmm) cc_final: 0.8388 (mmm) REVERT: A 3502 GLU cc_start: 0.9609 (mm-30) cc_final: 0.9204 (tp30) REVERT: A 3510 LYS cc_start: 0.8798 (tptm) cc_final: 0.8480 (tptp) REVERT: A 3581 GLU cc_start: 0.9119 (tt0) cc_final: 0.8795 (pt0) REVERT: A 3590 MET cc_start: 0.9411 (ppp) cc_final: 0.9149 (ppp) REVERT: A 3609 ASN cc_start: 0.9557 (p0) cc_final: 0.9284 (t0) REVERT: A 3633 SER cc_start: 0.9266 (m) cc_final: 0.8993 (p) REVERT: A 3671 GLU cc_start: 0.8933 (tt0) cc_final: 0.8479 (pt0) REVERT: A 3680 ASP cc_start: 0.9454 (m-30) cc_final: 0.9177 (t0) REVERT: A 3725 GLU cc_start: 0.9360 (tt0) cc_final: 0.9030 (tm-30) REVERT: A 3746 GLN cc_start: 0.9003 (mt0) cc_final: 0.8693 (mt0) REVERT: A 3794 LEU cc_start: 0.7730 (mt) cc_final: 0.7490 (tp) REVERT: A 3841 ILE cc_start: 0.8923 (tt) cc_final: 0.8522 (pt) REVERT: A 3905 ASN cc_start: 0.9204 (m-40) cc_final: 0.8901 (t0) REVERT: A 4015 GLU cc_start: 0.8646 (mm-30) cc_final: 0.8334 (mp0) REVERT: A 4019 MET cc_start: 0.9161 (mmm) cc_final: 0.8322 (tpp) REVERT: A 4096 GLU cc_start: 0.8352 (tm-30) cc_final: 0.8054 (tm-30) REVERT: A 4177 MET cc_start: 0.9009 (mmm) cc_final: 0.8770 (tpp) REVERT: A 4209 ASP cc_start: 0.8934 (t0) cc_final: 0.8660 (t0) REVERT: A 4221 GLU cc_start: 0.9027 (mt-10) cc_final: 0.8650 (tp30) REVERT: A 4232 ASP cc_start: 0.9214 (m-30) cc_final: 0.8324 (p0) REVERT: A 4295 GLU cc_start: 0.9315 (tt0) cc_final: 0.8850 (tm-30) REVERT: A 4317 GLU cc_start: 0.8608 (mp0) cc_final: 0.8279 (mp0) REVERT: A 4388 ASP cc_start: 0.9274 (m-30) cc_final: 0.8979 (t0) REVERT: A 4405 GLU cc_start: 0.9631 (tt0) cc_final: 0.9207 (tm-30) REVERT: A 4572 MET cc_start: 0.8677 (ttt) cc_final: 0.8247 (tpp) REVERT: B 547 LEU cc_start: 0.7864 (mt) cc_final: 0.7629 (mt) REVERT: B 1765 GLU cc_start: 0.9441 (tt0) cc_final: 0.9154 (mm-30) REVERT: B 1794 ASP cc_start: 0.9014 (t0) cc_final: 0.8426 (t70) REVERT: B 1953 ASP cc_start: 0.9345 (t0) cc_final: 0.8637 (p0) REVERT: B 2004 MET cc_start: 0.8032 (ttm) cc_final: 0.6910 (tmm) REVERT: B 2080 LYS cc_start: 0.9434 (ttpt) cc_final: 0.9125 (tptp) REVERT: B 2096 MET cc_start: 0.8669 (tmm) cc_final: 0.8391 (tmm) REVERT: B 2108 ASP cc_start: 0.9568 (t70) cc_final: 0.9280 (m-30) REVERT: B 2238 ILE cc_start: 0.9670 (tt) cc_final: 0.9439 (tp) REVERT: B 2318 ARG cc_start: 0.9527 (mtt-85) cc_final: 0.9165 (ttm110) REVERT: B 2422 GLN cc_start: 0.8772 (tm-30) cc_final: 0.8501 (tm-30) REVERT: B 2523 MET cc_start: 0.9465 (mmp) cc_final: 0.9150 (mmm) REVERT: B 2676 MET cc_start: 0.8978 (mmm) cc_final: 0.8724 (mmm) REVERT: B 2775 MET cc_start: 0.8433 (mtm) cc_final: 0.8033 (mtm) REVERT: B 2860 MET cc_start: 0.8891 (mmm) cc_final: 0.8180 (mtm) REVERT: B 2912 ASP cc_start: 0.8873 (t0) cc_final: 0.8536 (t0) REVERT: B 2947 MET cc_start: 0.8849 (tpt) cc_final: 0.8553 (tpt) REVERT: B 2955 GLU cc_start: 0.8939 (tt0) cc_final: 0.8731 (pt0) REVERT: B 3029 MET cc_start: 0.9434 (tmm) cc_final: 0.9212 (tmm) REVERT: B 3068 GLU cc_start: 0.7798 (pm20) cc_final: 0.7457 (pm20) REVERT: B 3660 MET cc_start: 0.9249 (mpp) cc_final: 0.8898 (mpp) REVERT: B 3767 MET cc_start: 0.8577 (tmm) cc_final: 0.8131 (tmm) REVERT: B 3978 GLU cc_start: 0.8634 (tt0) cc_final: 0.8100 (tm-30) REVERT: B 4043 ASN cc_start: 0.9419 (m-40) cc_final: 0.9163 (m110) REVERT: B 4121 ASP cc_start: 0.8658 (t0) cc_final: 0.8206 (m-30) REVERT: B 4159 MET cc_start: 0.8681 (mmm) cc_final: 0.7362 (mmm) REVERT: B 4352 GLU cc_start: 0.9053 (tm-30) cc_final: 0.8691 (tm-30) REVERT: B 4356 MET cc_start: 0.9605 (tpp) cc_final: 0.8890 (tpp) REVERT: B 4385 GLU cc_start: 0.9658 (mm-30) cc_final: 0.9414 (mp0) REVERT: B 4431 ASP cc_start: 0.8904 (t0) cc_final: 0.8677 (t0) REVERT: B 4440 MET cc_start: 0.8132 (mmp) cc_final: 0.7664 (mmp) REVERT: B 4456 GLN cc_start: 0.9315 (mt0) cc_final: 0.9014 (tt0) REVERT: C 893 GLU cc_start: 0.9567 (mt-10) cc_final: 0.8736 (tm-30) REVERT: C 913 MET cc_start: 0.8736 (mmt) cc_final: 0.7809 (mtp) REVERT: C 1085 MET cc_start: 0.9275 (mmp) cc_final: 0.9015 (mmm) REVERT: C 1107 MET cc_start: 0.6836 (mmm) cc_final: 0.6420 (mmm) REVERT: C 1162 ARG cc_start: 0.9325 (tmt170) cc_final: 0.9041 (tpt90) REVERT: C 1164 MET cc_start: 0.9562 (tpt) cc_final: 0.9323 (tpp) REVERT: C 1240 MET cc_start: 0.9426 (mtm) cc_final: 0.8916 (ptm) REVERT: C 1268 ASP cc_start: 0.9196 (m-30) cc_final: 0.8714 (t0) REVERT: C 1386 TYR cc_start: 0.8783 (m-10) cc_final: 0.8582 (m-80) REVERT: C 1433 MET cc_start: 0.8967 (mtt) cc_final: 0.8388 (mtt) REVERT: C 1438 MET cc_start: 0.9671 (mmm) cc_final: 0.9397 (mmp) REVERT: C 1510 LEU cc_start: 0.9239 (tt) cc_final: 0.8983 (tt) REVERT: C 1561 MET cc_start: 0.9325 (tmm) cc_final: 0.9078 (tmm) REVERT: C 1683 MET cc_start: 0.8068 (mtp) cc_final: 0.7722 (mtt) REVERT: C 1726 TYR cc_start: 0.9221 (t80) cc_final: 0.9016 (t80) REVERT: C 2001 MET cc_start: 0.9303 (mmp) cc_final: 0.8992 (mmm) REVERT: C 2128 MET cc_start: 0.9322 (ptp) cc_final: 0.8954 (ppp) REVERT: C 2191 LEU cc_start: 0.9638 (tp) cc_final: 0.9382 (tp) REVERT: C 2452 MET cc_start: 0.9185 (mpp) cc_final: 0.8787 (mpp) REVERT: C 2521 GLU cc_start: 0.9559 (pm20) cc_final: 0.9210 (tm-30) REVERT: C 2937 TYR cc_start: 0.9181 (m-80) cc_final: 0.8472 (m-80) REVERT: C 3050 GLU cc_start: 0.9023 (tt0) cc_final: 0.8752 (pt0) REVERT: C 3069 MET cc_start: 0.9757 (mmp) cc_final: 0.9362 (mmm) REVERT: C 3150 MET cc_start: 0.9417 (ttm) cc_final: 0.9069 (tmm) REVERT: C 3195 TYR cc_start: 0.9424 (t80) cc_final: 0.9132 (t80) REVERT: C 3623 MET cc_start: 0.8808 (tpp) cc_final: 0.8599 (tpp) REVERT: C 3958 ASN cc_start: 0.9072 (m110) cc_final: 0.8706 (p0) REVERT: C 4165 MET cc_start: 0.9007 (mpp) cc_final: 0.8033 (mpp) REVERT: E 116 VAL cc_start: 0.8630 (t) cc_final: 0.7755 (p) REVERT: G 116 ASP cc_start: 0.7341 (m-30) cc_final: 0.7112 (m-30) REVERT: H 60 ILE cc_start: 0.6006 (tt) cc_final: 0.5256 (tt) REVERT: L 42 ILE cc_start: 0.8313 (pt) cc_final: 0.8066 (pt) outliers start: 3 outliers final: 2 residues processed: 1345 average time/residue: 1.0237 time to fit residues: 2417.7822 Evaluate side-chains 1040 residues out of total 14031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1038 time to evaluate : 10.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1553 random chunks: chunk 1448 optimal weight: 5.9990 chunk 169 optimal weight: 6.9990 chunk 856 optimal weight: 3.9990 chunk 1097 optimal weight: 6.9990 chunk 850 optimal weight: 9.9990 chunk 1264 optimal weight: 7.9990 chunk 839 optimal weight: 10.0000 chunk 1496 optimal weight: 5.9990 chunk 936 optimal weight: 40.0000 chunk 912 optimal weight: 5.9990 chunk 691 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 900 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1047 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1080 ASN A1221 ASN ** A1444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1486 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2373 GLN ** A2425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3956 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 761 ASN ** B 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 816 GLN ** B 832 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1062 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1079 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1956 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2203 ASN ** B2307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2871 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3053 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3265 GLN ** B3362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3584 GLN ** B3604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3746 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3820 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3875 GLN ** B3888 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B4346 GLN B4417 ASN ** C 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 826 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 995 HIS ** C1274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1572 HIS ** C1655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1765 ASN ** C2074 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2743 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2920 GLN ** C3004 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3178 ASN ** C3547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3654 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3858 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C4102 HIS ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 450 HIS ** E 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 71 HIS ** J 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 104 ASN ** O 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6449 moved from start: 0.6279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 121585 Z= 0.317 Angle : 0.642 20.195 164623 Z= 0.345 Chirality : 0.039 0.238 18615 Planarity : 0.004 0.072 21279 Dihedral : 5.323 107.642 16700 Min Nonbonded Distance : 1.696 Molprobity Statistics. All-atom Clashscore : 71.28 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.51 % Favored : 94.21 % Rotamer: Outliers : 0.02 % Allowed : 1.55 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.03 % 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: 1.02 (0.07), residues: 15467 helix: 2.04 (0.05), residues: 8660 sheet: -0.32 (0.13), residues: 1485 loop : -1.37 (0.08), residues: 5322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP B 644 HIS 0.012 0.002 HIS E 261 PHE 0.044 0.002 PHE B1556 TYR 0.050 0.002 TYR E 262 ARG 0.031 0.001 ARG B 709 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 30934 Ramachandran restraints generated. 15467 Oldfield, 0 Emsley, 15467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 30934 Ramachandran restraints generated. 15467 Oldfield, 0 Emsley, 15467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue SER 3 is missing expected H atoms. Skipping. Residue VAL 5 is missing expected H atoms. Skipping. Residue MET 6 is missing expected H atoms. Skipping. Residue LEU 8 is missing expected H atoms. Skipping. Residue SER 9 is missing expected H atoms. Skipping. Residue ILE 13 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue ALA 19 is missing expected H atoms. Skipping. Residue SER 21 is missing expected H atoms. Skipping. Residue TYR 23 is missing expected H atoms. Skipping. Residue LEU 28 is missing expected H atoms. Skipping. Residue ALA 30 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue VAL 33 is missing expected H atoms. Skipping. Residue SER 34 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue LEU 38 is missing expected H atoms. Skipping. Residue ALA 39 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue SER 48 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Residue MET 55 is missing expected H atoms. Skipping. Residue ILE 56 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Residue VAL 59 is missing expected H atoms. Skipping. Residue LYS 62 is missing expected H atoms. Skipping. Residue THR 64 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue ILE 67 is missing expected H atoms. Skipping. Residue LYS 68 is missing expected H atoms. Skipping. Residue SER 70 is missing expected H atoms. Skipping. Residue LEU 73 is missing expected H atoms. Skipping. Residue ILE 75 is missing expected H atoms. Skipping. Residue TYR 76 is missing expected H atoms. Skipping. Residue TYR 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue ALA 82 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Evaluate side-chains 1269 residues out of total 14031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1267 time to evaluate : 10.217 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1665 GLU cc_start: 0.8399 (tm-30) cc_final: 0.8181 (tm-30) REVERT: A 1713 GLU cc_start: 0.9249 (tt0) cc_final: 0.8979 (tm-30) REVERT: A 1750 MET cc_start: 0.9311 (tpt) cc_final: 0.9004 (tpt) REVERT: A 1770 GLU cc_start: 0.8959 (mm-30) cc_final: 0.8706 (mt-10) REVERT: A 1814 ILE cc_start: 0.9312 (mp) cc_final: 0.8958 (tp) REVERT: A 2035 GLU cc_start: 0.9106 (tt0) cc_final: 0.8858 (tm-30) REVERT: A 2036 GLU cc_start: 0.9404 (mt-10) cc_final: 0.9162 (mt-10) REVERT: A 2072 MET cc_start: 0.9176 (tmm) cc_final: 0.8928 (tmm) REVERT: A 2196 MET cc_start: 0.8881 (ttp) cc_final: 0.8319 (ptm) REVERT: A 2264 MET cc_start: 0.8438 (ttp) cc_final: 0.7430 (ttt) REVERT: A 2348 MET cc_start: 0.9023 (mmt) cc_final: 0.8714 (tpp) REVERT: A 2536 GLU cc_start: 0.8697 (tt0) cc_final: 0.8415 (mt-10) REVERT: A 2554 MET cc_start: 0.8959 (mmt) cc_final: 0.8566 (mmm) REVERT: A 2590 MET cc_start: 0.8877 (mtt) cc_final: 0.8573 (mmm) REVERT: A 2641 GLU cc_start: 0.9303 (tm-30) cc_final: 0.9069 (tm-30) REVERT: A 2657 PHE cc_start: 0.8557 (m-80) cc_final: 0.8183 (m-80) REVERT: A 2683 MET cc_start: 0.8690 (mmp) cc_final: 0.8242 (mmm) REVERT: A 2695 ASN cc_start: 0.8317 (m-40) cc_final: 0.7718 (m-40) REVERT: A 2785 PHE cc_start: 0.8575 (m-10) cc_final: 0.8038 (m-80) REVERT: A 2831 ARG cc_start: 0.9310 (mmm160) cc_final: 0.8410 (tpp80) REVERT: A 2837 MET cc_start: 0.8887 (ttm) cc_final: 0.7963 (tmm) REVERT: A 2858 GLN cc_start: 0.8397 (mm110) cc_final: 0.7866 (mt0) REVERT: A 2946 GLU cc_start: 0.8347 (pt0) cc_final: 0.8002 (pp20) REVERT: A 2949 ASN cc_start: 0.9291 (m-40) cc_final: 0.8984 (p0) REVERT: A 2993 ASP cc_start: 0.9519 (t0) cc_final: 0.9196 (m-30) REVERT: A 2998 MET cc_start: 0.9105 (mmm) cc_final: 0.8902 (tpp) REVERT: A 3453 PHE cc_start: 0.8942 (t80) cc_final: 0.8588 (t80) REVERT: A 3477 MET cc_start: 0.8634 (mmm) cc_final: 0.8209 (mmm) REVERT: A 3490 LEU cc_start: 0.9424 (tt) cc_final: 0.9189 (tt) REVERT: A 3502 GLU cc_start: 0.9628 (mm-30) cc_final: 0.9239 (tp30) REVERT: A 3510 LYS cc_start: 0.8811 (tptm) cc_final: 0.8581 (tptp) REVERT: A 3581 GLU cc_start: 0.9122 (tt0) cc_final: 0.8865 (pt0) REVERT: A 3590 MET cc_start: 0.9289 (ppp) cc_final: 0.9023 (ppp) REVERT: A 3633 SER cc_start: 0.9209 (m) cc_final: 0.8952 (p) REVERT: A 3671 GLU cc_start: 0.8893 (tt0) cc_final: 0.8447 (pt0) REVERT: A 3725 GLU cc_start: 0.9377 (tt0) cc_final: 0.9112 (mt-10) REVERT: A 3746 GLN cc_start: 0.9111 (mt0) cc_final: 0.8748 (mt0) REVERT: A 3794 LEU cc_start: 0.8047 (mt) cc_final: 0.7767 (tp) REVERT: A 3841 ILE cc_start: 0.8967 (tt) cc_final: 0.8543 (pt) REVERT: A 3905 ASN cc_start: 0.9245 (m-40) cc_final: 0.8939 (t0) REVERT: A 4010 LYS cc_start: 0.9672 (mptt) cc_final: 0.9449 (mppt) REVERT: A 4015 GLU cc_start: 0.8703 (mm-30) cc_final: 0.8366 (mp0) REVERT: A 4177 MET cc_start: 0.8998 (mmm) cc_final: 0.8762 (tpp) REVERT: A 4221 GLU cc_start: 0.9210 (mt-10) cc_final: 0.8762 (mm-30) REVERT: A 4232 ASP cc_start: 0.9226 (m-30) cc_final: 0.8505 (p0) REVERT: A 4295 GLU cc_start: 0.9361 (tt0) cc_final: 0.8921 (tm-30) REVERT: A 4388 ASP cc_start: 0.9334 (m-30) cc_final: 0.9051 (t0) REVERT: A 4405 GLU cc_start: 0.9644 (tt0) cc_final: 0.9221 (tm-30) REVERT: A 4572 MET cc_start: 0.8443 (ttt) cc_final: 0.8166 (tpp) REVERT: B 1794 ASP cc_start: 0.9080 (t0) cc_final: 0.8554 (t70) REVERT: B 2004 MET cc_start: 0.7913 (ttm) cc_final: 0.6935 (tmm) REVERT: B 2080 LYS cc_start: 0.9446 (ttpt) cc_final: 0.9110 (tptp) REVERT: B 2238 ILE cc_start: 0.9676 (tt) cc_final: 0.9457 (tp) REVERT: B 2279 MET cc_start: 0.8712 (ttt) cc_final: 0.7709 (ttp) REVERT: B 2318 ARG cc_start: 0.9571 (mtt-85) cc_final: 0.9116 (mtp85) REVERT: B 2523 MET cc_start: 0.9485 (mmp) cc_final: 0.9144 (mmm) REVERT: B 2775 MET cc_start: 0.8351 (mtm) cc_final: 0.7752 (mtm) REVERT: B 2860 MET cc_start: 0.8848 (mmm) cc_final: 0.8180 (mtm) REVERT: B 2912 ASP cc_start: 0.8931 (t0) cc_final: 0.8579 (t0) REVERT: B 2947 MET cc_start: 0.8776 (tpt) cc_final: 0.8463 (tpt) REVERT: B 3029 MET cc_start: 0.9360 (tmm) cc_final: 0.9067 (tmm) REVERT: B 3068 GLU cc_start: 0.7742 (pm20) cc_final: 0.7391 (pm20) REVERT: B 3239 VAL cc_start: 0.7874 (m) cc_final: 0.7352 (m) REVERT: B 3508 LYS cc_start: 0.9392 (tptm) cc_final: 0.9104 (mttt) REVERT: B 3660 MET cc_start: 0.9187 (mpp) cc_final: 0.8851 (mpp) REVERT: B 3737 GLU cc_start: 0.9412 (mm-30) cc_final: 0.9199 (mm-30) REVERT: B 3767 MET cc_start: 0.8570 (tmm) cc_final: 0.8171 (tmm) REVERT: B 3770 MET cc_start: 0.8869 (ptp) cc_final: 0.7985 (ppp) REVERT: B 4043 ASN cc_start: 0.9527 (m-40) cc_final: 0.9294 (m110) REVERT: B 4121 ASP cc_start: 0.8713 (t0) cc_final: 0.8235 (m-30) REVERT: B 4159 MET cc_start: 0.8744 (mmm) cc_final: 0.7136 (mmm) REVERT: B 4294 GLN cc_start: 0.8624 (tp40) cc_final: 0.8178 (tm-30) REVERT: B 4352 GLU cc_start: 0.9045 (tm-30) cc_final: 0.8760 (tm-30) REVERT: B 4356 MET cc_start: 0.9595 (tpp) cc_final: 0.8983 (tpp) REVERT: B 4385 GLU cc_start: 0.9664 (mm-30) cc_final: 0.9395 (mp0) REVERT: B 4440 MET cc_start: 0.8306 (mmp) cc_final: 0.7865 (mmp) REVERT: C 854 MET cc_start: 0.8263 (ttm) cc_final: 0.7900 (tmm) REVERT: C 1085 MET cc_start: 0.9341 (mmp) cc_final: 0.9017 (mmm) REVERT: C 1162 ARG cc_start: 0.9333 (tmt170) cc_final: 0.9048 (tpt90) REVERT: C 1164 MET cc_start: 0.9571 (tpt) cc_final: 0.9356 (tpp) REVERT: C 1240 MET cc_start: 0.9349 (mtm) cc_final: 0.8821 (ptm) REVERT: C 1268 ASP cc_start: 0.9275 (m-30) cc_final: 0.8821 (t0) REVERT: C 1433 MET cc_start: 0.8984 (mtt) cc_final: 0.8377 (mtt) REVERT: C 1438 MET cc_start: 0.9672 (mmm) cc_final: 0.9172 (mmp) REVERT: C 1509 TYR cc_start: 0.9345 (t80) cc_final: 0.9136 (t80) REVERT: C 1510 LEU cc_start: 0.9203 (tt) cc_final: 0.8993 (tt) REVERT: C 1561 MET cc_start: 0.9321 (tmm) cc_final: 0.9078 (tmm) REVERT: C 1683 MET cc_start: 0.8030 (mtp) cc_final: 0.7689 (mtt) REVERT: C 1726 TYR cc_start: 0.9157 (t80) cc_final: 0.8921 (t80) REVERT: C 1741 MET cc_start: 0.8501 (mpp) cc_final: 0.7631 (mpp) REVERT: C 1765 ASN cc_start: 0.9213 (OUTLIER) cc_final: 0.8598 (p0) REVERT: C 2128 MET cc_start: 0.9374 (ptp) cc_final: 0.8978 (ppp) REVERT: C 2190 MET cc_start: 0.9276 (mtm) cc_final: 0.9001 (mtt) REVERT: C 2191 LEU cc_start: 0.9576 (tp) cc_final: 0.9322 (tp) REVERT: C 2243 GLU cc_start: 0.9439 (tp30) cc_final: 0.8831 (tm-30) REVERT: C 2452 MET cc_start: 0.9249 (mpp) cc_final: 0.8678 (mpp) REVERT: C 2576 LYS cc_start: 0.9220 (tmtt) cc_final: 0.8742 (tptp) REVERT: C 2937 TYR cc_start: 0.9267 (m-80) cc_final: 0.8668 (m-80) REVERT: C 3069 MET cc_start: 0.9752 (mmp) cc_final: 0.9294 (mmm) REVERT: C 3150 MET cc_start: 0.9483 (ttm) cc_final: 0.9140 (tmm) REVERT: C 3195 TYR cc_start: 0.9416 (t80) cc_final: 0.9156 (t80) REVERT: C 3787 MET cc_start: 0.8619 (mmp) cc_final: 0.8400 (mmp) REVERT: C 3958 ASN cc_start: 0.9090 (m110) cc_final: 0.8602 (p0) REVERT: C 3963 MET cc_start: 0.9283 (mtm) cc_final: 0.9082 (mtp) REVERT: C 4033 MET cc_start: 0.9609 (mtt) cc_final: 0.9108 (mtp) REVERT: C 4146 MET cc_start: 0.8694 (mmm) cc_final: 0.8422 (mpp) REVERT: C 4165 MET cc_start: 0.9175 (mpp) cc_final: 0.8306 (mpp) REVERT: D 70 MET cc_start: -0.0558 (mtt) cc_final: -0.1039 (mtt) REVERT: E 116 VAL cc_start: 0.8606 (t) cc_final: 0.8023 (p) REVERT: G 145 LEU cc_start: 0.7242 (tp) cc_final: 0.6965 (tp) REVERT: H 84 LEU cc_start: 0.5946 (mm) cc_final: 0.5574 (mm) REVERT: K 85 LEU cc_start: 0.5441 (tp) cc_final: 0.5216 (tp) REVERT: L 23 PHE cc_start: 0.5086 (t80) cc_final: 0.4877 (t80) REVERT: L 30 LEU cc_start: 0.8279 (pp) cc_final: 0.8069 (pp) REVERT: N 22 LYS cc_start: 0.7627 (mmmt) cc_final: 0.7270 (mmmt) outliers start: 2 outliers final: 0 residues processed: 1268 average time/residue: 1.0247 time to fit residues: 2286.6200 Evaluate side-chains 981 residues out of total 14031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 980 time to evaluate : 10.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1553 random chunks: chunk 926 optimal weight: 0.9980 chunk 597 optimal weight: 2.9990 chunk 893 optimal weight: 9.9990 chunk 450 optimal weight: 50.0000 chunk 294 optimal weight: 4.9990 chunk 289 optimal weight: 6.9990 chunk 951 optimal weight: 120.0000 chunk 1019 optimal weight: 3.9990 chunk 740 optimal weight: 5.9990 chunk 139 optimal weight: 2.9990 chunk 1176 optimal weight: 0.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 741 ASN ** A 755 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 900 ASN ** A 952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1047 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1205 GLN ** A1486 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3772 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3956 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4185 HIS ** A4263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 816 GLN ** B 832 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1062 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1079 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1956 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2203 ASN ** B2214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2343 GLN ** B2635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2871 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2930 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3053 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3746 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3810 GLN ** B3820 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3888 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4175 GLN B4214 ASN ** B4267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 826 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2074 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2129 ASN ** C2197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2743 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2920 GLN ** C3004 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3178 ASN ** C3547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3654 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 196 GLN ** E 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6385 moved from start: 0.6350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 121585 Z= 0.167 Angle : 0.483 16.371 164623 Z= 0.261 Chirality : 0.036 0.179 18615 Planarity : 0.004 0.249 21279 Dihedral : 5.170 148.904 16700 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 63.61 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.44 % Favored : 95.29 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.03 % 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: 1.49 (0.07), residues: 15467 helix: 2.46 (0.05), residues: 8664 sheet: -0.22 (0.13), residues: 1459 loop : -1.21 (0.08), residues: 5344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.075 0.002 TRP B1518 HIS 0.013 0.001 HIS M 39 PHE 0.031 0.001 PHE O 42 TYR 0.028 0.001 TYR A1208 ARG 0.009 0.000 ARG A2697 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 30934 Ramachandran restraints generated. 15467 Oldfield, 0 Emsley, 15467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 30934 Ramachandran restraints generated. 15467 Oldfield, 0 Emsley, 15467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue SER 3 is missing expected H atoms. Skipping. Residue VAL 5 is missing expected H atoms. Skipping. Residue MET 6 is missing expected H atoms. Skipping. Residue LEU 8 is missing expected H atoms. Skipping. Residue SER 9 is missing expected H atoms. Skipping. Residue ILE 13 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue ALA 19 is missing expected H atoms. Skipping. Residue SER 21 is missing expected H atoms. Skipping. Residue TYR 23 is missing expected H atoms. Skipping. Residue LEU 28 is missing expected H atoms. Skipping. Residue ALA 30 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue VAL 33 is missing expected H atoms. Skipping. Residue SER 34 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue LEU 38 is missing expected H atoms. Skipping. Residue ALA 39 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue SER 48 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Residue MET 55 is missing expected H atoms. Skipping. Residue ILE 56 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Residue VAL 59 is missing expected H atoms. Skipping. Residue LYS 62 is missing expected H atoms. Skipping. Residue THR 64 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue ILE 67 is missing expected H atoms. Skipping. Residue LYS 68 is missing expected H atoms. Skipping. Residue SER 70 is missing expected H atoms. Skipping. Residue LEU 73 is missing expected H atoms. Skipping. Residue ILE 75 is missing expected H atoms. Skipping. Residue TYR 76 is missing expected H atoms. Skipping. Residue TYR 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue ALA 82 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Evaluate side-chains 1266 residues out of total 14031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1266 time to evaluate : 10.401 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1550 LYS cc_start: 0.6214 (ptpt) cc_final: 0.5809 (ptmt) REVERT: A 1665 GLU cc_start: 0.8429 (tm-30) cc_final: 0.8213 (tm-30) REVERT: A 1713 GLU cc_start: 0.9219 (tt0) cc_final: 0.8924 (tm-30) REVERT: A 1750 MET cc_start: 0.9248 (tpt) cc_final: 0.8973 (tpt) REVERT: A 1759 GLU cc_start: 0.9510 (mm-30) cc_final: 0.9293 (mp0) REVERT: A 1770 GLU cc_start: 0.8954 (mm-30) cc_final: 0.8695 (mt-10) REVERT: A 1814 ILE cc_start: 0.9356 (mp) cc_final: 0.8995 (tp) REVERT: A 1843 GLU cc_start: 0.8634 (tm-30) cc_final: 0.8384 (tm-30) REVERT: A 2035 GLU cc_start: 0.9077 (tt0) cc_final: 0.8808 (tm-30) REVERT: A 2036 GLU cc_start: 0.9447 (mt-10) cc_final: 0.9198 (mt-10) REVERT: A 2072 MET cc_start: 0.9069 (tmm) cc_final: 0.8803 (tmm) REVERT: A 2123 GLU cc_start: 0.9349 (tm-30) cc_final: 0.9030 (tp30) REVERT: A 2196 MET cc_start: 0.8871 (ttp) cc_final: 0.8271 (ptm) REVERT: A 2264 MET cc_start: 0.8414 (ttp) cc_final: 0.7378 (ttt) REVERT: A 2348 MET cc_start: 0.8955 (mmt) cc_final: 0.8636 (tpp) REVERT: A 2488 SER cc_start: 0.8427 (p) cc_final: 0.8115 (p) REVERT: A 2536 GLU cc_start: 0.8704 (tt0) cc_final: 0.8348 (mt-10) REVERT: A 2554 MET cc_start: 0.8988 (mmt) cc_final: 0.8497 (mmm) REVERT: A 2590 MET cc_start: 0.8921 (mtt) cc_final: 0.8577 (mmm) REVERT: A 2641 GLU cc_start: 0.9283 (tm-30) cc_final: 0.9050 (tm-30) REVERT: A 2657 PHE cc_start: 0.8681 (m-80) cc_final: 0.8288 (m-80) REVERT: A 2683 MET cc_start: 0.8677 (mmp) cc_final: 0.8325 (mmm) REVERT: A 2785 PHE cc_start: 0.8667 (m-10) cc_final: 0.8164 (m-80) REVERT: A 2831 ARG cc_start: 0.9297 (mmm160) cc_final: 0.8418 (tpp80) REVERT: A 2837 MET cc_start: 0.8814 (ttm) cc_final: 0.7873 (tmm) REVERT: A 2858 GLN cc_start: 0.8358 (mm110) cc_final: 0.7785 (mt0) REVERT: A 2946 GLU cc_start: 0.8324 (pt0) cc_final: 0.7960 (pp20) REVERT: A 2949 ASN cc_start: 0.9243 (m-40) cc_final: 0.8887 (p0) REVERT: A 2993 ASP cc_start: 0.9518 (t0) cc_final: 0.9172 (m-30) REVERT: A 2998 MET cc_start: 0.9091 (mmm) cc_final: 0.8818 (tpp) REVERT: A 3113 GLN cc_start: 0.9272 (mt0) cc_final: 0.8927 (mt0) REVERT: A 3453 PHE cc_start: 0.8937 (t80) cc_final: 0.8501 (t80) REVERT: A 3477 MET cc_start: 0.8613 (mmm) cc_final: 0.8255 (mmm) REVERT: A 3502 GLU cc_start: 0.9613 (mm-30) cc_final: 0.9226 (tp30) REVERT: A 3510 LYS cc_start: 0.8849 (tptm) cc_final: 0.8495 (tptp) REVERT: A 3581 GLU cc_start: 0.9163 (tt0) cc_final: 0.8796 (pt0) REVERT: A 3590 MET cc_start: 0.9304 (ppp) cc_final: 0.9025 (ppp) REVERT: A 3633 SER cc_start: 0.9186 (m) cc_final: 0.8921 (p) REVERT: A 3671 GLU cc_start: 0.8922 (tt0) cc_final: 0.8454 (pt0) REVERT: A 3695 LEU cc_start: 0.9536 (tt) cc_final: 0.9235 (tp) REVERT: A 3721 THR cc_start: 0.9450 (p) cc_final: 0.9029 (p) REVERT: A 3725 GLU cc_start: 0.9346 (tt0) cc_final: 0.9141 (pt0) REVERT: A 3746 GLN cc_start: 0.9056 (mt0) cc_final: 0.8718 (mt0) REVERT: A 3794 LEU cc_start: 0.7980 (mt) cc_final: 0.7653 (tp) REVERT: A 3841 ILE cc_start: 0.8868 (tt) cc_final: 0.8520 (pt) REVERT: A 3905 ASN cc_start: 0.9218 (m-40) cc_final: 0.8909 (t0) REVERT: A 4010 LYS cc_start: 0.9663 (mptt) cc_final: 0.9443 (mppt) REVERT: A 4015 GLU cc_start: 0.8685 (mm-30) cc_final: 0.8358 (mp0) REVERT: A 4096 GLU cc_start: 0.8478 (tm-30) cc_final: 0.8129 (tm-30) REVERT: A 4177 MET cc_start: 0.8964 (mmm) cc_final: 0.8728 (tpp) REVERT: A 4221 GLU cc_start: 0.9100 (mt-10) cc_final: 0.8679 (mm-30) REVERT: A 4232 ASP cc_start: 0.9209 (m-30) cc_final: 0.8501 (p0) REVERT: A 4295 GLU cc_start: 0.9355 (tt0) cc_final: 0.8902 (tm-30) REVERT: A 4351 ASN cc_start: 0.7984 (t0) cc_final: 0.7567 (t0) REVERT: A 4388 ASP cc_start: 0.9311 (m-30) cc_final: 0.9009 (t0) REVERT: A 4405 GLU cc_start: 0.9646 (tt0) cc_final: 0.9213 (tm-30) REVERT: A 4572 MET cc_start: 0.8556 (ttt) cc_final: 0.8245 (tpp) REVERT: B 1794 ASP cc_start: 0.9049 (t0) cc_final: 0.8635 (t70) REVERT: B 2004 MET cc_start: 0.7828 (ttm) cc_final: 0.6847 (tmm) REVERT: B 2080 LYS cc_start: 0.9458 (ttpt) cc_final: 0.9128 (tptp) REVERT: B 2095 ASP cc_start: 0.9026 (t0) cc_final: 0.8694 (p0) REVERT: B 2238 ILE cc_start: 0.9596 (tt) cc_final: 0.9340 (tp) REVERT: B 2257 MET cc_start: 0.8884 (ptt) cc_final: 0.8601 (ptt) REVERT: B 2318 ARG cc_start: 0.9564 (mtt-85) cc_final: 0.9260 (mtt-85) REVERT: B 2523 MET cc_start: 0.9502 (mmp) cc_final: 0.9159 (mmm) REVERT: B 2775 MET cc_start: 0.8466 (mtm) cc_final: 0.7707 (mtm) REVERT: B 2860 MET cc_start: 0.8695 (mmm) cc_final: 0.8132 (mtm) REVERT: B 2912 ASP cc_start: 0.8876 (t0) cc_final: 0.8540 (t0) REVERT: B 2947 MET cc_start: 0.8761 (tpt) cc_final: 0.8558 (tpp) REVERT: B 3068 GLU cc_start: 0.7831 (pm20) cc_final: 0.7435 (pm20) REVERT: B 3239 VAL cc_start: 0.7853 (m) cc_final: 0.7320 (m) REVERT: B 3492 ILE cc_start: 0.9369 (mt) cc_final: 0.9152 (mt) REVERT: B 3493 GLU cc_start: 0.9047 (mp0) cc_final: 0.8831 (mp0) REVERT: B 3660 MET cc_start: 0.9227 (mpp) cc_final: 0.8857 (mpp) REVERT: B 3737 GLU cc_start: 0.9374 (mm-30) cc_final: 0.9173 (mm-30) REVERT: B 3767 MET cc_start: 0.8564 (tmm) cc_final: 0.8170 (tmm) REVERT: B 4040 MET cc_start: 0.8127 (tpp) cc_final: 0.7637 (tpt) REVERT: B 4043 ASN cc_start: 0.9556 (m-40) cc_final: 0.9281 (m110) REVERT: B 4121 ASP cc_start: 0.8734 (t0) cc_final: 0.8233 (m-30) REVERT: B 4159 MET cc_start: 0.8646 (mmm) cc_final: 0.7154 (mmm) REVERT: B 4352 GLU cc_start: 0.9054 (tm-30) cc_final: 0.8717 (tm-30) REVERT: B 4356 MET cc_start: 0.9566 (tpp) cc_final: 0.8914 (tpp) REVERT: B 4385 GLU cc_start: 0.9652 (mm-30) cc_final: 0.9411 (mp0) REVERT: C 1085 MET cc_start: 0.9302 (mmp) cc_final: 0.9005 (mmm) REVERT: C 1162 ARG cc_start: 0.9349 (tmt170) cc_final: 0.9054 (tpt90) REVERT: C 1222 MET cc_start: 0.8984 (ttp) cc_final: 0.8245 (ppp) REVERT: C 1240 MET cc_start: 0.9349 (mtm) cc_final: 0.8800 (ptm) REVERT: C 1268 ASP cc_start: 0.9201 (m-30) cc_final: 0.8729 (t0) REVERT: C 1433 MET cc_start: 0.8924 (mtt) cc_final: 0.8286 (mtt) REVERT: C 1438 MET cc_start: 0.9630 (mmm) cc_final: 0.9343 (mmp) REVERT: C 1509 TYR cc_start: 0.9389 (t80) cc_final: 0.9187 (t80) REVERT: C 1561 MET cc_start: 0.9289 (tmm) cc_final: 0.9028 (tmm) REVERT: C 1683 MET cc_start: 0.8010 (mtp) cc_final: 0.7667 (mtt) REVERT: C 1726 TYR cc_start: 0.9134 (t80) cc_final: 0.8913 (t80) REVERT: C 1765 ASN cc_start: 0.9321 (m110) cc_final: 0.8772 (p0) REVERT: C 2128 MET cc_start: 0.9381 (ptp) cc_final: 0.9014 (ppp) REVERT: C 2191 LEU cc_start: 0.9605 (tp) cc_final: 0.9338 (tp) REVERT: C 2243 GLU cc_start: 0.9398 (tp30) cc_final: 0.8791 (tm-30) REVERT: C 2452 MET cc_start: 0.9283 (mpp) cc_final: 0.8815 (mpp) REVERT: C 2521 GLU cc_start: 0.9503 (pm20) cc_final: 0.9209 (tm-30) REVERT: C 2627 LYS cc_start: 0.8893 (tmmt) cc_final: 0.8554 (tmtt) REVERT: C 2937 TYR cc_start: 0.9197 (m-80) cc_final: 0.8465 (m-80) REVERT: C 2965 MET cc_start: 0.8050 (ptp) cc_final: 0.7595 (mtp) REVERT: C 3050 GLU cc_start: 0.9042 (tt0) cc_final: 0.8812 (pt0) REVERT: C 3069 MET cc_start: 0.9700 (mmp) cc_final: 0.9264 (mmm) REVERT: C 3131 LEU cc_start: 0.9048 (tp) cc_final: 0.8730 (tp) REVERT: C 3150 MET cc_start: 0.9462 (ttm) cc_final: 0.9080 (tmm) REVERT: C 3195 TYR cc_start: 0.9445 (t80) cc_final: 0.9127 (t80) REVERT: C 3623 MET cc_start: 0.9151 (tpp) cc_final: 0.8946 (tpp) REVERT: C 3787 MET cc_start: 0.8669 (mmp) cc_final: 0.8445 (mmp) REVERT: C 3958 ASN cc_start: 0.9074 (m110) cc_final: 0.8603 (p0) REVERT: C 4146 MET cc_start: 0.8558 (mmm) cc_final: 0.8290 (mpp) REVERT: C 4165 MET cc_start: 0.9114 (mpp) cc_final: 0.8201 (mpp) REVERT: D 70 MET cc_start: -0.0836 (mtt) cc_final: -0.1337 (mtt) REVERT: D 248 MET cc_start: 0.6096 (mmt) cc_final: 0.5155 (tpt) REVERT: G 116 ASP cc_start: 0.7485 (m-30) cc_final: 0.7253 (m-30) REVERT: G 145 LEU cc_start: 0.7128 (tp) cc_final: 0.6688 (tp) REVERT: H 84 LEU cc_start: 0.5966 (mm) cc_final: 0.5677 (mm) REVERT: J 36 ILE cc_start: 0.7638 (mp) cc_final: 0.7386 (mp) REVERT: K 85 LEU cc_start: 0.5681 (tp) cc_final: 0.5463 (tp) REVERT: L 107 LEU cc_start: 0.6658 (pp) cc_final: 0.6448 (pp) REVERT: M 83 LEU cc_start: 0.5435 (tp) cc_final: 0.5131 (tp) outliers start: 0 outliers final: 0 residues processed: 1266 average time/residue: 1.0094 time to fit residues: 2254.1542 Evaluate side-chains 986 residues out of total 14031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 986 time to evaluate : 10.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1553 random chunks: chunk 1361 optimal weight: 2.9990 chunk 1434 optimal weight: 6.9990 chunk 1308 optimal weight: 30.0000 chunk 1394 optimal weight: 30.0000 chunk 1433 optimal weight: 5.9990 chunk 839 optimal weight: 8.9990 chunk 607 optimal weight: 0.5980 chunk 1095 optimal weight: 9.9990 chunk 428 optimal weight: 4.9990 chunk 1260 optimal weight: 10.0000 chunk 1319 optimal weight: 5.9990 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 852 ASN ** A 952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1047 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1205 GLN A1221 ASN ** A1486 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1951 HIS ** A2220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3956 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 832 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1062 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1079 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1081 GLN ** B1188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1566 ASN ** B1956 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2203 ASN ** B2214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2871 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2913 GLN ** B2930 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3053 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3584 GLN ** B3604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3746 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3810 GLN ** B3820 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3888 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 826 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2074 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2743 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2920 GLN ** C2987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3004 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3178 ASN ** C3547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3654 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3858 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3879 GLN ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6453 moved from start: 0.6658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 121585 Z= 0.249 Angle : 0.551 17.875 164623 Z= 0.295 Chirality : 0.037 0.183 18615 Planarity : 0.004 0.094 21279 Dihedral : 5.259 178.546 16700 Min Nonbonded Distance : 1.740 Molprobity Statistics. All-atom Clashscore : 69.94 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.59 % Favored : 94.12 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.03 % 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: 1.28 (0.07), residues: 15467 helix: 2.29 (0.05), residues: 8658 sheet: -0.32 (0.13), residues: 1470 loop : -1.31 (0.08), residues: 5339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP B1518 HIS 0.014 0.001 HIS B1135 PHE 0.034 0.002 PHE B2055 TYR 0.023 0.002 TYR A2031 ARG 0.009 0.001 ARG A1532 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 30934 Ramachandran restraints generated. 15467 Oldfield, 0 Emsley, 15467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 30934 Ramachandran restraints generated. 15467 Oldfield, 0 Emsley, 15467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue SER 3 is missing expected H atoms. Skipping. Residue VAL 5 is missing expected H atoms. Skipping. Residue MET 6 is missing expected H atoms. Skipping. Residue LEU 8 is missing expected H atoms. Skipping. Residue SER 9 is missing expected H atoms. Skipping. Residue ILE 13 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue ALA 19 is missing expected H atoms. Skipping. Residue SER 21 is missing expected H atoms. Skipping. Residue TYR 23 is missing expected H atoms. Skipping. Residue LEU 28 is missing expected H atoms. Skipping. Residue ALA 30 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue VAL 33 is missing expected H atoms. Skipping. Residue SER 34 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue LEU 38 is missing expected H atoms. Skipping. Residue ALA 39 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue SER 48 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Residue MET 55 is missing expected H atoms. Skipping. Residue ILE 56 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Residue VAL 59 is missing expected H atoms. Skipping. Residue LYS 62 is missing expected H atoms. Skipping. Residue THR 64 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue ILE 67 is missing expected H atoms. Skipping. Residue LYS 68 is missing expected H atoms. Skipping. Residue SER 70 is missing expected H atoms. Skipping. Residue LEU 73 is missing expected H atoms. Skipping. Residue ILE 75 is missing expected H atoms. Skipping. Residue TYR 76 is missing expected H atoms. Skipping. Residue TYR 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue ALA 82 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Evaluate side-chains 1222 residues out of total 14031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1222 time to evaluate : 10.058 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1550 LYS cc_start: 0.6276 (ptpt) cc_final: 0.5739 (ptmt) REVERT: A 1665 GLU cc_start: 0.8426 (tm-30) cc_final: 0.8217 (tm-30) REVERT: A 1713 GLU cc_start: 0.9226 (tt0) cc_final: 0.8923 (tm-30) REVERT: A 1750 MET cc_start: 0.9258 (tpt) cc_final: 0.9013 (tpt) REVERT: A 1759 GLU cc_start: 0.9525 (mm-30) cc_final: 0.9301 (mp0) REVERT: A 1770 GLU cc_start: 0.8940 (mm-30) cc_final: 0.8710 (mt-10) REVERT: A 1814 ILE cc_start: 0.9314 (mp) cc_final: 0.8946 (tp) REVERT: A 2035 GLU cc_start: 0.9069 (tt0) cc_final: 0.8799 (tm-30) REVERT: A 2036 GLU cc_start: 0.9435 (mt-10) cc_final: 0.9183 (mt-10) REVERT: A 2072 MET cc_start: 0.9101 (tmm) cc_final: 0.8781 (tmm) REVERT: A 2075 MET cc_start: 0.8745 (tmm) cc_final: 0.8491 (tmm) REVERT: A 2196 MET cc_start: 0.8884 (ttp) cc_final: 0.8332 (ptm) REVERT: A 2264 MET cc_start: 0.8292 (ttp) cc_final: 0.7196 (ttt) REVERT: A 2348 MET cc_start: 0.8988 (mmt) cc_final: 0.8683 (tpp) REVERT: A 2488 SER cc_start: 0.8378 (p) cc_final: 0.7993 (p) REVERT: A 2536 GLU cc_start: 0.8597 (tt0) cc_final: 0.8264 (mt-10) REVERT: A 2546 GLU cc_start: 0.8863 (mt-10) cc_final: 0.8417 (tt0) REVERT: A 2554 MET cc_start: 0.8945 (mmt) cc_final: 0.8565 (mmm) REVERT: A 2590 MET cc_start: 0.8871 (mtt) cc_final: 0.8539 (mmm) REVERT: A 2641 GLU cc_start: 0.9286 (tm-30) cc_final: 0.9049 (tm-30) REVERT: A 2657 PHE cc_start: 0.8638 (m-80) cc_final: 0.8125 (m-80) REVERT: A 2683 MET cc_start: 0.8661 (mmp) cc_final: 0.8267 (mmm) REVERT: A 2785 PHE cc_start: 0.8793 (m-10) cc_final: 0.8269 (m-80) REVERT: A 2837 MET cc_start: 0.8839 (ttm) cc_final: 0.7871 (tmm) REVERT: A 2858 GLN cc_start: 0.8383 (mm110) cc_final: 0.7788 (mt0) REVERT: A 2946 GLU cc_start: 0.8329 (pt0) cc_final: 0.7975 (pp20) REVERT: A 2949 ASN cc_start: 0.9264 (m-40) cc_final: 0.8906 (p0) REVERT: A 2993 ASP cc_start: 0.9529 (t0) cc_final: 0.9209 (m-30) REVERT: A 2998 MET cc_start: 0.9116 (mmm) cc_final: 0.8896 (mmm) REVERT: A 3453 PHE cc_start: 0.8945 (t80) cc_final: 0.8645 (t80) REVERT: A 3477 MET cc_start: 0.8575 (mmm) cc_final: 0.8193 (mmm) REVERT: A 3502 GLU cc_start: 0.9615 (mm-30) cc_final: 0.9238 (tm-30) REVERT: A 3510 LYS cc_start: 0.8807 (tptm) cc_final: 0.8449 (tptp) REVERT: A 3581 GLU cc_start: 0.9189 (tt0) cc_final: 0.8762 (pt0) REVERT: A 3590 MET cc_start: 0.9261 (ppp) cc_final: 0.9026 (ppp) REVERT: A 3633 SER cc_start: 0.9210 (m) cc_final: 0.9008 (p) REVERT: A 3671 GLU cc_start: 0.8912 (tt0) cc_final: 0.8442 (pt0) REVERT: A 3746 GLN cc_start: 0.9066 (mt0) cc_final: 0.8736 (mt0) REVERT: A 3794 LEU cc_start: 0.8076 (mt) cc_final: 0.7779 (tp) REVERT: A 3841 ILE cc_start: 0.8885 (tt) cc_final: 0.8531 (pt) REVERT: A 3905 ASN cc_start: 0.9237 (m-40) cc_final: 0.8928 (t0) REVERT: A 4003 ASP cc_start: 0.9113 (m-30) cc_final: 0.8858 (m-30) REVERT: A 4010 LYS cc_start: 0.9666 (mptt) cc_final: 0.9443 (mppt) REVERT: A 4012 PHE cc_start: 0.8224 (t80) cc_final: 0.7771 (t80) REVERT: A 4015 GLU cc_start: 0.8774 (mm-30) cc_final: 0.8431 (mp0) REVERT: A 4177 MET cc_start: 0.8982 (mmm) cc_final: 0.8777 (tpp) REVERT: A 4221 GLU cc_start: 0.9216 (mt-10) cc_final: 0.8808 (mm-30) REVERT: A 4232 ASP cc_start: 0.9222 (m-30) cc_final: 0.8511 (p0) REVERT: A 4295 GLU cc_start: 0.9338 (tt0) cc_final: 0.8913 (tm-30) REVERT: A 4388 ASP cc_start: 0.9339 (m-30) cc_final: 0.9048 (t0) REVERT: A 4405 GLU cc_start: 0.9647 (tt0) cc_final: 0.9344 (tm-30) REVERT: B 1794 ASP cc_start: 0.9015 (t0) cc_final: 0.8561 (t70) REVERT: B 2004 MET cc_start: 0.7873 (ttm) cc_final: 0.6905 (tmm) REVERT: B 2080 LYS cc_start: 0.9463 (ttpt) cc_final: 0.9114 (tptp) REVERT: B 2238 ILE cc_start: 0.9588 (tt) cc_final: 0.9328 (tp) REVERT: B 2318 ARG cc_start: 0.9508 (mtt-85) cc_final: 0.9220 (mtt-85) REVERT: B 2523 MET cc_start: 0.9496 (mmp) cc_final: 0.9155 (mmm) REVERT: B 2775 MET cc_start: 0.8442 (mtm) cc_final: 0.7687 (mtm) REVERT: B 2912 ASP cc_start: 0.8901 (t0) cc_final: 0.8550 (t0) REVERT: B 2947 MET cc_start: 0.8759 (tpt) cc_final: 0.8504 (tpp) REVERT: B 3068 GLU cc_start: 0.8003 (pm20) cc_final: 0.7575 (pm20) REVERT: B 3239 VAL cc_start: 0.7854 (m) cc_final: 0.7629 (m) REVERT: B 3437 VAL cc_start: 0.5419 (t) cc_final: 0.5144 (t) REVERT: B 3767 MET cc_start: 0.8431 (tmm) cc_final: 0.8045 (tmm) REVERT: B 3770 MET cc_start: 0.8775 (ptp) cc_final: 0.7995 (ppp) REVERT: B 4040 MET cc_start: 0.8324 (tpp) cc_final: 0.7910 (tpt) REVERT: B 4043 ASN cc_start: 0.9526 (m-40) cc_final: 0.9291 (m110) REVERT: B 4121 ASP cc_start: 0.8828 (t0) cc_final: 0.8314 (m-30) REVERT: B 4159 MET cc_start: 0.8716 (mmm) cc_final: 0.7263 (mmm) REVERT: B 4352 GLU cc_start: 0.9051 (tm-30) cc_final: 0.8738 (tm-30) REVERT: B 4356 MET cc_start: 0.9570 (tpp) cc_final: 0.8989 (tpp) REVERT: B 4385 GLU cc_start: 0.9666 (mm-30) cc_final: 0.9406 (mp0) REVERT: B 4440 MET cc_start: 0.8400 (mmp) cc_final: 0.8013 (mmp) REVERT: B 4489 GLU cc_start: 0.8231 (tt0) cc_final: 0.7703 (mt-10) REVERT: C 854 MET cc_start: 0.8495 (ttp) cc_final: 0.8134 (tmm) REVERT: C 1085 MET cc_start: 0.9338 (mmp) cc_final: 0.9043 (mmp) REVERT: C 1162 ARG cc_start: 0.9345 (tmt170) cc_final: 0.9051 (tpt90) REVERT: C 1222 MET cc_start: 0.9012 (ttp) cc_final: 0.8300 (ppp) REVERT: C 1240 MET cc_start: 0.9327 (mtm) cc_final: 0.8774 (ptm) REVERT: C 1268 ASP cc_start: 0.9263 (m-30) cc_final: 0.8772 (t0) REVERT: C 1433 MET cc_start: 0.8967 (mtt) cc_final: 0.8389 (mtt) REVERT: C 1438 MET cc_start: 0.9635 (mmm) cc_final: 0.9322 (mmp) REVERT: C 1509 TYR cc_start: 0.9366 (t80) cc_final: 0.9135 (t80) REVERT: C 1510 LEU cc_start: 0.9087 (tt) cc_final: 0.8815 (tt) REVERT: C 1561 MET cc_start: 0.9315 (tmm) cc_final: 0.9059 (tmm) REVERT: C 1683 MET cc_start: 0.8027 (mtp) cc_final: 0.7670 (mtt) REVERT: C 1726 TYR cc_start: 0.9066 (t80) cc_final: 0.8795 (t80) REVERT: C 1765 ASN cc_start: 0.9343 (m110) cc_final: 0.9092 (p0) REVERT: C 2128 MET cc_start: 0.9247 (ptp) cc_final: 0.9003 (ppp) REVERT: C 2191 LEU cc_start: 0.9572 (tp) cc_final: 0.9311 (tp) REVERT: C 2243 GLU cc_start: 0.9425 (tp30) cc_final: 0.8811 (tm-30) REVERT: C 2452 MET cc_start: 0.9232 (mpp) cc_final: 0.8584 (mpp) REVERT: C 2521 GLU cc_start: 0.9501 (pm20) cc_final: 0.9295 (pm20) REVERT: C 2894 ASN cc_start: 0.6791 (t0) cc_final: 0.6377 (t0) REVERT: C 2937 TYR cc_start: 0.9257 (m-80) cc_final: 0.8548 (m-10) REVERT: C 2965 MET cc_start: 0.8106 (ptp) cc_final: 0.7612 (mtp) REVERT: C 3050 GLU cc_start: 0.9047 (tt0) cc_final: 0.8841 (pt0) REVERT: C 3069 MET cc_start: 0.9711 (mmp) cc_final: 0.9297 (mmm) REVERT: C 3150 MET cc_start: 0.9446 (ttm) cc_final: 0.9209 (tpp) REVERT: C 3195 TYR cc_start: 0.9440 (t80) cc_final: 0.9138 (t80) REVERT: C 3787 MET cc_start: 0.8708 (mmp) cc_final: 0.8444 (mmp) REVERT: C 3958 ASN cc_start: 0.9085 (m110) cc_final: 0.8688 (p0) REVERT: C 4146 MET cc_start: 0.8678 (mmm) cc_final: 0.8391 (mpp) REVERT: C 4165 MET cc_start: 0.9142 (mpp) cc_final: 0.8254 (mpp) REVERT: D 70 MET cc_start: -0.0459 (mtt) cc_final: -0.0992 (mtt) REVERT: D 248 MET cc_start: 0.6179 (mmt) cc_final: 0.5318 (tpt) REVERT: G 116 ASP cc_start: 0.7643 (m-30) cc_final: 0.7348 (m-30) REVERT: G 145 LEU cc_start: 0.7185 (tp) cc_final: 0.6900 (tp) REVERT: H 6 LYS cc_start: 0.8634 (mmpt) cc_final: 0.8411 (mmmm) REVERT: H 84 LEU cc_start: 0.5983 (mm) cc_final: 0.5588 (mm) REVERT: K 85 LEU cc_start: 0.6159 (tp) cc_final: 0.5918 (tp) outliers start: 0 outliers final: 0 residues processed: 1222 average time/residue: 1.0190 time to fit residues: 2203.0203 Evaluate side-chains 955 residues out of total 14031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 955 time to evaluate : 10.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1553 random chunks: chunk 1389 optimal weight: 8.9990 chunk 915 optimal weight: 7.9990 chunk 1474 optimal weight: 9.9990 chunk 900 optimal weight: 30.0000 chunk 699 optimal weight: 8.9990 chunk 1025 optimal weight: 3.9990 chunk 1547 optimal weight: 8.9990 chunk 1424 optimal weight: 3.9990 chunk 1232 optimal weight: 4.9990 chunk 127 optimal weight: 10.0000 chunk 951 optimal weight: 20.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 968 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1007 GLN ** A1047 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1486 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3238 ASN A3718 ASN ** A3772 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3956 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 832 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 834 ASN ** B 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1062 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1079 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1956 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2203 ASN ** B2307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2871 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2930 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3053 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3584 GLN ** B3604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3674 GLN ** B3714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3746 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3810 GLN ** B3820 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3888 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4175 GLN ** B4267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 826 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2074 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2743 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2961 HIS ** C2987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3004 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3178 ASN ** C3245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3654 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3682 GLN ** C3858 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C4003 GLN ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 220 ASN ** E 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 48 ASN ** I 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6536 moved from start: 0.7092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.104 121585 Z= 0.338 Angle : 0.647 22.013 164623 Z= 0.349 Chirality : 0.039 0.340 18615 Planarity : 0.004 0.137 21279 Dihedral : 5.573 170.278 16700 Min Nonbonded Distance : 1.707 Molprobity Statistics. All-atom Clashscore : 77.62 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.04 % Favored : 93.67 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.03 % 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: 0.65 (0.07), residues: 15467 helix: 1.76 (0.05), residues: 8641 sheet: -0.55 (0.13), residues: 1451 loop : -1.55 (0.08), residues: 5375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.127 0.002 TRP A 659 HIS 0.028 0.002 HIS C2961 PHE 0.047 0.002 PHE A 655 TYR 0.031 0.002 TYR B2059 ARG 0.022 0.001 ARG B2391 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 30934 Ramachandran restraints generated. 15467 Oldfield, 0 Emsley, 15467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 30934 Ramachandran restraints generated. 15467 Oldfield, 0 Emsley, 15467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue ALA 2 is missing expected H atoms. Skipping. Residue SER 3 is missing expected H atoms. Skipping. Residue VAL 5 is missing expected H atoms. Skipping. Residue MET 6 is missing expected H atoms. Skipping. Residue LEU 8 is missing expected H atoms. Skipping. Residue SER 9 is missing expected H atoms. Skipping. Residue ILE 13 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue ALA 19 is missing expected H atoms. Skipping. Residue SER 21 is missing expected H atoms. Skipping. Residue TYR 23 is missing expected H atoms. Skipping. Residue LEU 28 is missing expected H atoms. Skipping. Residue ALA 30 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue VAL 33 is missing expected H atoms. Skipping. Residue SER 34 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue LEU 38 is missing expected H atoms. Skipping. Residue ALA 39 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue SER 48 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Residue MET 55 is missing expected H atoms. Skipping. Residue ILE 56 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Residue VAL 59 is missing expected H atoms. Skipping. Residue LYS 62 is missing expected H atoms. Skipping. Residue THR 64 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue ILE 67 is missing expected H atoms. Skipping. Residue LYS 68 is missing expected H atoms. Skipping. Residue SER 70 is missing expected H atoms. Skipping. Residue LEU 73 is missing expected H atoms. Skipping. Residue ILE 75 is missing expected H atoms. Skipping. Residue TYR 76 is missing expected H atoms. Skipping. Residue TYR 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue ALA 82 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Evaluate side-chains 1187 residues out of total 14031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1187 time to evaluate : 10.230 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1662 ARG cc_start: 0.8821 (ptt-90) cc_final: 0.8433 (tpp-160) REVERT: A 1750 MET cc_start: 0.9244 (tpt) cc_final: 0.9040 (tpt) REVERT: A 1770 GLU cc_start: 0.8954 (mm-30) cc_final: 0.8727 (mt-10) REVERT: A 1814 ILE cc_start: 0.9287 (mp) cc_final: 0.8957 (tp) REVERT: A 1984 GLN cc_start: 0.8021 (tm-30) cc_final: 0.7664 (tm-30) REVERT: A 2035 GLU cc_start: 0.9282 (tt0) cc_final: 0.8929 (tm-30) REVERT: A 2036 GLU cc_start: 0.9409 (mt-10) cc_final: 0.8861 (mt-10) REVERT: A 2072 MET cc_start: 0.9138 (tmm) cc_final: 0.8790 (tmm) REVERT: A 2075 MET cc_start: 0.8765 (tmm) cc_final: 0.8547 (tmm) REVERT: A 2123 GLU cc_start: 0.9259 (tm-30) cc_final: 0.8681 (tp30) REVERT: A 2196 MET cc_start: 0.8834 (ttp) cc_final: 0.8374 (ptm) REVERT: A 2225 LYS cc_start: 0.9039 (pttt) cc_final: 0.8820 (pttt) REVERT: A 2264 MET cc_start: 0.8373 (ttp) cc_final: 0.7398 (ttt) REVERT: A 2348 MET cc_start: 0.9038 (mmt) cc_final: 0.8730 (tpp) REVERT: A 2488 SER cc_start: 0.8392 (p) cc_final: 0.8036 (p) REVERT: A 2536 GLU cc_start: 0.8613 (tt0) cc_final: 0.8296 (mt-10) REVERT: A 2546 GLU cc_start: 0.8872 (mt-10) cc_final: 0.8576 (mt-10) REVERT: A 2554 MET cc_start: 0.9045 (mmt) cc_final: 0.8676 (tmm) REVERT: A 2657 PHE cc_start: 0.8664 (m-80) cc_final: 0.8232 (m-80) REVERT: A 2683 MET cc_start: 0.8776 (mmp) cc_final: 0.8386 (mmm) REVERT: A 2785 PHE cc_start: 0.8711 (m-10) cc_final: 0.8217 (m-80) REVERT: A 2837 MET cc_start: 0.8848 (ttm) cc_final: 0.8056 (tmm) REVERT: A 2858 GLN cc_start: 0.8409 (mm110) cc_final: 0.7783 (mt0) REVERT: A 2946 GLU cc_start: 0.8318 (pt0) cc_final: 0.7911 (pp20) REVERT: A 2949 ASN cc_start: 0.9275 (m-40) cc_final: 0.9020 (p0) REVERT: A 2993 ASP cc_start: 0.9533 (t0) cc_final: 0.9200 (m-30) REVERT: A 3453 PHE cc_start: 0.9016 (t80) cc_final: 0.8709 (t80) REVERT: A 3477 MET cc_start: 0.8509 (mmm) cc_final: 0.8159 (mmm) REVERT: A 3502 GLU cc_start: 0.9609 (mm-30) cc_final: 0.9142 (tp30) REVERT: A 3510 LYS cc_start: 0.8927 (tptm) cc_final: 0.8570 (tptp) REVERT: A 3581 GLU cc_start: 0.9102 (tt0) cc_final: 0.8756 (pt0) REVERT: A 3590 MET cc_start: 0.9248 (ppp) cc_final: 0.8982 (ppp) REVERT: A 3610 VAL cc_start: 0.9315 (t) cc_final: 0.9084 (t) REVERT: A 3633 SER cc_start: 0.9205 (m) cc_final: 0.8993 (p) REVERT: A 3671 GLU cc_start: 0.8951 (tt0) cc_final: 0.8478 (pt0) REVERT: A 3746 GLN cc_start: 0.9080 (mt0) cc_final: 0.8745 (mt0) REVERT: A 3794 LEU cc_start: 0.8499 (mt) cc_final: 0.8169 (tp) REVERT: A 3827 ILE cc_start: 0.9161 (tp) cc_final: 0.8935 (tt) REVERT: A 3841 ILE cc_start: 0.8902 (tt) cc_final: 0.8530 (pt) REVERT: A 3905 ASN cc_start: 0.9265 (m-40) cc_final: 0.8952 (t0) REVERT: A 4003 ASP cc_start: 0.9087 (m-30) cc_final: 0.8811 (m-30) REVERT: A 4010 LYS cc_start: 0.9661 (mptt) cc_final: 0.9434 (mppt) REVERT: A 4012 PHE cc_start: 0.8329 (t80) cc_final: 0.7842 (t80) REVERT: A 4015 GLU cc_start: 0.8775 (mm-30) cc_final: 0.8437 (mp0) REVERT: A 4019 MET cc_start: 0.9300 (tpp) cc_final: 0.8471 (tpp) REVERT: A 4069 ASP cc_start: 0.8692 (m-30) cc_final: 0.8319 (t70) REVERT: A 4221 GLU cc_start: 0.9221 (mt-10) cc_final: 0.8825 (mm-30) REVERT: A 4232 ASP cc_start: 0.9219 (m-30) cc_final: 0.8548 (p0) REVERT: A 4295 GLU cc_start: 0.9406 (tt0) cc_final: 0.8976 (tm-30) REVERT: A 4388 ASP cc_start: 0.9352 (m-30) cc_final: 0.9079 (t0) REVERT: A 4405 GLU cc_start: 0.9644 (tt0) cc_final: 0.9367 (tm-30) REVERT: B 547 LEU cc_start: 0.7785 (mt) cc_final: 0.7424 (mt) REVERT: B 1794 ASP cc_start: 0.9002 (t0) cc_final: 0.8578 (t70) REVERT: B 2004 MET cc_start: 0.7845 (ttm) cc_final: 0.6933 (tmm) REVERT: B 2080 LYS cc_start: 0.9435 (ttpt) cc_final: 0.9081 (tptp) REVERT: B 2238 ILE cc_start: 0.9612 (tt) cc_final: 0.9383 (tp) REVERT: B 2242 MET cc_start: 0.9219 (mmp) cc_final: 0.8986 (mmp) REVERT: B 2260 TRP cc_start: 0.8556 (p90) cc_final: 0.6785 (p90) REVERT: B 2318 ARG cc_start: 0.9582 (mtt-85) cc_final: 0.9101 (mtp85) REVERT: B 2523 MET cc_start: 0.9514 (mmp) cc_final: 0.9157 (mmm) REVERT: B 2775 MET cc_start: 0.8529 (mtm) cc_final: 0.7846 (mtm) REVERT: B 2912 ASP cc_start: 0.8909 (t0) cc_final: 0.8580 (t0) REVERT: B 2947 MET cc_start: 0.8748 (tpt) cc_final: 0.8461 (tpt) REVERT: B 3068 GLU cc_start: 0.7987 (pm20) cc_final: 0.7540 (pm20) REVERT: B 3116 ASP cc_start: 0.9232 (m-30) cc_final: 0.9025 (m-30) REVERT: B 3239 VAL cc_start: 0.7899 (m) cc_final: 0.7654 (m) REVERT: B 3437 VAL cc_start: 0.5806 (t) cc_final: 0.5281 (t) REVERT: B 3508 LYS cc_start: 0.9368 (tptm) cc_final: 0.9119 (mttt) REVERT: B 3660 MET cc_start: 0.9256 (mpp) cc_final: 0.8912 (mpp) REVERT: B 3767 MET cc_start: 0.8452 (tmm) cc_final: 0.8044 (tmm) REVERT: B 3770 MET cc_start: 0.8917 (ptp) cc_final: 0.8119 (ppp) REVERT: B 4040 MET cc_start: 0.8236 (tpp) cc_final: 0.7977 (tpt) REVERT: B 4159 MET cc_start: 0.8861 (mmm) cc_final: 0.7201 (mmm) REVERT: B 4352 GLU cc_start: 0.9148 (tm-30) cc_final: 0.8836 (tm-30) REVERT: B 4356 MET cc_start: 0.9581 (tpp) cc_final: 0.9009 (tpp) REVERT: B 4385 GLU cc_start: 0.9658 (mm-30) cc_final: 0.9424 (mp0) REVERT: B 4440 MET cc_start: 0.8346 (mmp) cc_final: 0.7934 (mmp) REVERT: C 1085 MET cc_start: 0.9363 (mmp) cc_final: 0.8986 (mmm) REVERT: C 1162 ARG cc_start: 0.9299 (tmt170) cc_final: 0.9042 (tpt90) REVERT: C 1240 MET cc_start: 0.9321 (mtm) cc_final: 0.8741 (ptm) REVERT: C 1268 ASP cc_start: 0.9363 (m-30) cc_final: 0.8842 (t0) REVERT: C 1433 MET cc_start: 0.9037 (mtt) cc_final: 0.8482 (mtt) REVERT: C 1438 MET cc_start: 0.9655 (mmm) cc_final: 0.9146 (mmp) REVERT: C 1509 TYR cc_start: 0.9409 (t80) cc_final: 0.9134 (t80) REVERT: C 1510 LEU cc_start: 0.9105 (tt) cc_final: 0.8830 (tt) REVERT: C 1561 MET cc_start: 0.9305 (tmm) cc_final: 0.9063 (tmm) REVERT: C 1656 LYS cc_start: 0.9355 (mmpt) cc_final: 0.8765 (tppt) REVERT: C 1683 MET cc_start: 0.8094 (mtp) cc_final: 0.7757 (mtt) REVERT: C 1726 TYR cc_start: 0.9126 (t80) cc_final: 0.8825 (t80) REVERT: C 1765 ASN cc_start: 0.9368 (m110) cc_final: 0.9158 (p0) REVERT: C 2128 MET cc_start: 0.9329 (ptp) cc_final: 0.8894 (ppp) REVERT: C 2191 LEU cc_start: 0.9551 (tp) cc_final: 0.9291 (tp) REVERT: C 2243 GLU cc_start: 0.9441 (tp30) cc_final: 0.8791 (tm-30) REVERT: C 2452 MET cc_start: 0.9280 (mpp) cc_final: 0.8968 (mpp) REVERT: C 2626 GLU cc_start: 0.7728 (mp0) cc_final: 0.7460 (mp0) REVERT: C 2627 LYS cc_start: 0.8860 (pttp) cc_final: 0.8440 (pttp) REVERT: C 2894 ASN cc_start: 0.7025 (t0) cc_final: 0.6568 (t0) REVERT: C 2937 TYR cc_start: 0.9223 (m-80) cc_final: 0.8499 (m-10) REVERT: C 2965 MET cc_start: 0.8141 (ptp) cc_final: 0.7574 (mtp) REVERT: C 3050 GLU cc_start: 0.9187 (tt0) cc_final: 0.8960 (pt0) REVERT: C 3069 MET cc_start: 0.9720 (mmp) cc_final: 0.9308 (mmm) REVERT: C 3150 MET cc_start: 0.9426 (ttm) cc_final: 0.9039 (tmm) REVERT: C 3195 TYR cc_start: 0.9458 (t80) cc_final: 0.9128 (t80) REVERT: C 3429 GLU cc_start: 0.9554 (mm-30) cc_final: 0.9280 (tp30) REVERT: C 3787 MET cc_start: 0.8608 (mmp) cc_final: 0.8358 (mmp) REVERT: C 3877 GLU cc_start: 0.8679 (tm-30) cc_final: 0.8435 (tm-30) REVERT: C 3892 ASP cc_start: 0.8966 (m-30) cc_final: 0.8704 (m-30) REVERT: C 3958 ASN cc_start: 0.9056 (m110) cc_final: 0.8582 (p0) REVERT: C 3963 MET cc_start: 0.9287 (mtm) cc_final: 0.8999 (mtp) REVERT: C 4165 MET cc_start: 0.9252 (mpp) cc_final: 0.8464 (mpp) REVERT: D 70 MET cc_start: 0.0349 (mtt) cc_final: 0.0096 (mtt) REVERT: G 116 ASP cc_start: 0.7622 (m-30) cc_final: 0.7386 (m-30) REVERT: J 36 ILE cc_start: 0.7568 (mp) cc_final: 0.7356 (mp) REVERT: M 81 CYS cc_start: 0.5044 (m) cc_final: 0.4693 (m) outliers start: 0 outliers final: 0 residues processed: 1187 average time/residue: 1.0330 time to fit residues: 2165.3460 Evaluate side-chains 930 residues out of total 14031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 930 time to evaluate : 10.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1553 random chunks: chunk 755 optimal weight: 5.9990 chunk 978 optimal weight: 0.7980 chunk 1312 optimal weight: 0.8980 chunk 377 optimal weight: 0.2980 chunk 1136 optimal weight: 0.0870 chunk 181 optimal weight: 2.9990 chunk 342 optimal weight: 4.9990 chunk 1233 optimal weight: 5.9990 chunk 516 optimal weight: 0.0980 chunk 1267 optimal weight: 0.8980 chunk 156 optimal weight: 0.4980 overall best weight: 0.3558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1047 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1221 ASN ** A1486 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1666 ASN ** A2220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3772 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3956 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 611 GLN ** B 788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 832 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1062 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1079 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1194 ASN ** B1956 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2139 GLN B2203 ASN ** B2214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2930 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3053 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3081 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3820 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3888 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4175 GLN ** B4267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 826 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2341 HIS ** C2743 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2920 GLN ** C3004 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3178 ASN ** C3547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3654 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3682 GLN ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 196 GLN E 220 ASN ** E 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 HIS ** F 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 109 ASN ** 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 = 0.3429 r_free = 0.3429 target = 0.062349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.050458 restraints weight = 924235.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.051534 restraints weight = 614586.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.052230 restraints weight = 420857.679| |-----------------------------------------------------------------------------| r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.6983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.103 121585 Z= 0.130 Angle : 0.476 12.895 164623 Z= 0.257 Chirality : 0.037 0.377 18615 Planarity : 0.003 0.067 21279 Dihedral : 5.127 161.983 16700 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 63.06 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.29 % Favored : 95.44 % Rotamer: Outliers : 0.01 % Allowed : 0.20 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.03 % 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: 1.54 (0.07), residues: 15467 helix: 2.52 (0.06), residues: 8661 sheet: -0.29 (0.14), residues: 1450 loop : -1.20 (0.08), residues: 5356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.101 0.002 TRP A 659 HIS 0.015 0.001 HIS B1135 PHE 0.031 0.001 PHE O 42 TYR 0.024 0.001 TYR C2824 ARG 0.008 0.000 ARG A1532 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 38658.87 seconds wall clock time: 707 minutes 0.22 seconds (42420.22 seconds total)