Starting phenix.real_space_refine on Mon Mar 25 10:02:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kf5_22843/03_2024/7kf5_22843.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kf5_22843/03_2024/7kf5_22843.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kf5_22843/03_2024/7kf5_22843.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kf5_22843/03_2024/7kf5_22843.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kf5_22843/03_2024/7kf5_22843.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kf5_22843/03_2024/7kf5_22843.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.165 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 108 5.16 5 C 15300 2.51 5 N 3957 2.21 5 O 4290 1.98 5 H 24414 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 7": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 13": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 37": "OD1" <-> "OD2" Residue "A ASP 41": "OD1" <-> "OD2" Residue "A GLU 62": "OE1" <-> "OE2" Residue "A PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 90": "OD1" <-> "OD2" Residue "A TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 99": "OD1" <-> "OD2" Residue "A TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 107": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 109": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 112": "OE1" <-> "OE2" Residue "A TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 141": "OE1" <-> "OE2" Residue "A TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 146": "OD1" <-> "OD2" Residue "A ARG 147": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 152": "OD1" <-> "OD2" Residue "A ASP 155": "OD1" <-> "OD2" Residue "A ARG 157": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 161": "OD1" <-> "OD2" Residue "A PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 173": "OD1" <-> "OD2" Residue "A GLU 176": "OE1" <-> "OE2" Residue "A GLU 186": "OE1" <-> "OE2" Residue "A GLU 205": "OE1" <-> "OE2" Residue "A GLU 223": "OE1" <-> "OE2" Residue "A GLU 226": "OE1" <-> "OE2" Residue "A GLU 228": "OE1" <-> "OE2" Residue "A TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 232": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 252": "OE1" <-> "OE2" Residue "A TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 260": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 272": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 283": "OE1" <-> "OE2" Residue "A ARG 292": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 298": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 306": "OD1" <-> "OD2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A GLU 320": "OE1" <-> "OE2" Residue "A TYR 325": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 327": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 336": "OD1" <-> "OD2" Residue "A GLU 345": "OE1" <-> "OE2" Residue "A PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 361": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 405": "OD1" <-> "OD2" Residue "A GLU 412": "OE1" <-> "OE2" Residue "A ARG 417": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 419": "OE1" <-> "OE2" Residue "A ASP 427": "OD1" <-> "OD2" Residue "A GLU 445": "OE1" <-> "OE2" Residue "A PHE 465": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 468": "OE1" <-> "OE2" Residue "A ARG 473": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 475": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 480": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 503": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 519": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 520": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 523": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 560": "OE1" <-> "OE2" Residue "A GLU 567": "OE1" <-> "OE2" Residue "A TYR 572": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 604": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 606": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 647": "OE1" <-> "OE2" Residue "A GLU 648": "OE1" <-> "OE2" Residue "A ASP 650": "OD1" <-> "OD2" Residue "A ARG 654": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 671": "OD1" <-> "OD2" Residue "A ASP 694": "OD1" <-> "OD2" Residue "A GLU 698": "OE1" <-> "OE2" Residue "A GLU 701": "OE1" <-> "OE2" Residue "A ARG 705": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 717": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 719": "OE1" <-> "OE2" Residue "A ARG 722": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 727": "OE1" <-> "OE2" Residue "A ARG 730": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 735": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 746": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 761": "OE1" <-> "OE2" Residue "A ARG 765": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 766": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 771": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 772": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 777": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 778": "OD1" <-> "OD2" Residue "A ARG 784": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 800": "OD1" <-> "OD2" Residue "A ASP 803": "OD1" <-> "OD2" Residue "A GLU 816": "OE1" <-> "OE2" Residue "A ARG 819": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 829": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 831": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 832": "OD1" <-> "OD2" Residue "A ASP 839": "OD1" <-> "OD2" Residue "A GLU 846": "OE1" <-> "OE2" Residue "A PHE 858": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 862": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 867": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 884": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 891": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 892": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 893": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 896": "OE1" <-> "OE2" Residue "A PHE 930": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 947": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 949": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 971": "OE1" <-> "OE2" Residue "A ARG 982": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 1007": "OE1" <-> "OE2" Residue "A ARG 1011": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 1035": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 7": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 13": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 37": "OD1" <-> "OD2" Residue "B ASP 41": "OD1" <-> "OD2" Residue "B GLU 62": "OE1" <-> "OE2" Residue "B PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 90": "OD1" <-> "OD2" Residue "B TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 99": "OD1" <-> "OD2" Residue "B TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 107": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 109": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 112": "OE1" <-> "OE2" Residue "B TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 141": "OE1" <-> "OE2" Residue "B ASP 146": "OD1" <-> "OD2" Residue "B ARG 147": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 152": "OD1" <-> "OD2" Residue "B ASP 155": "OD1" <-> "OD2" Residue "B ARG 157": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 161": "OD1" <-> "OD2" Residue "B PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 173": "OD1" <-> "OD2" Residue "B GLU 176": "OE1" <-> "OE2" Residue "B GLU 186": "OE1" <-> "OE2" Residue "B GLU 205": "OE1" <-> "OE2" Residue "B GLU 223": "OE1" <-> "OE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B GLU 228": "OE1" <-> "OE2" Residue "B TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 232": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 252": "OE1" <-> "OE2" Residue "B TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 260": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 272": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 283": "OE1" <-> "OE2" Residue "B ARG 292": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 298": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 306": "OD1" <-> "OD2" Residue "B GLU 309": "OE1" <-> "OE2" Residue "B GLU 320": "OE1" <-> "OE2" Residue "B TYR 325": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 327": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 336": "OD1" <-> "OD2" Residue "B GLU 345": "OE1" <-> "OE2" Residue "B PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 361": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 405": "OD1" <-> "OD2" Residue "B GLU 412": "OE1" <-> "OE2" Residue "B ARG 417": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 419": "OE1" <-> "OE2" Residue "B ASP 427": "OD1" <-> "OD2" Residue "B GLU 445": "OE1" <-> "OE2" Residue "B PHE 465": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 468": "OE1" <-> "OE2" Residue "B ARG 473": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 475": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 480": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 503": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 519": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 520": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 523": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 560": "OE1" <-> "OE2" Residue "B GLU 567": "OE1" <-> "OE2" Residue "B TYR 572": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 604": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 606": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 647": "OE1" <-> "OE2" Residue "B GLU 648": "OE1" <-> "OE2" Residue "B ASP 650": "OD1" <-> "OD2" Residue "B ARG 654": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 671": "OD1" <-> "OD2" Residue "B ASP 694": "OD1" <-> "OD2" Residue "B GLU 698": "OE1" <-> "OE2" Residue "B GLU 701": "OE1" <-> "OE2" Residue "B ARG 705": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 717": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 719": "OE1" <-> "OE2" Residue "B ARG 722": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 727": "OE1" <-> "OE2" Residue "B ARG 730": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 735": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 746": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 761": "OE1" <-> "OE2" Residue "B ARG 765": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 766": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 771": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 772": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 777": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 778": "OD1" <-> "OD2" Residue "B ARG 784": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 800": "OD1" <-> "OD2" Residue "B ASP 803": "OD1" <-> "OD2" Residue "B GLU 816": "OE1" <-> "OE2" Residue "B ARG 819": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 829": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 831": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 832": "OD1" <-> "OD2" Residue "B ASP 839": "OD1" <-> "OD2" Residue "B GLU 846": "OE1" <-> "OE2" Residue "B PHE 858": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 862": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 867": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 884": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 891": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 892": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 893": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 896": "OE1" <-> "OE2" Residue "B PHE 930": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 947": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 949": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 971": "OE1" <-> "OE2" Residue "B ARG 982": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 1007": "OE1" <-> "OE2" Residue "B ARG 1011": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 1035": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 7": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 13": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 37": "OD1" <-> "OD2" Residue "C ASP 41": "OD1" <-> "OD2" Residue "C GLU 62": "OE1" <-> "OE2" Residue "C PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 90": "OD1" <-> "OD2" Residue "C TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 99": "OD1" <-> "OD2" Residue "C TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 107": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 109": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 112": "OE1" <-> "OE2" Residue "C TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 141": "OE1" <-> "OE2" Residue "C ASP 146": "OD1" <-> "OD2" Residue "C ARG 147": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ASP 152": "OD1" <-> "OD2" Residue "C ASP 155": "OD1" <-> "OD2" Residue "C ARG 157": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ASP 161": "OD1" <-> "OD2" Residue "C PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 173": "OD1" <-> "OD2" Residue "C GLU 176": "OE1" <-> "OE2" Residue "C GLU 186": "OE1" <-> "OE2" Residue "C GLU 205": "OE1" <-> "OE2" Residue "C GLU 223": "OE1" <-> "OE2" Residue "C GLU 226": "OE1" <-> "OE2" Residue "C GLU 228": "OE1" <-> "OE2" Residue "C TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 232": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 252": "OE1" <-> "OE2" Residue "C TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 260": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 272": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 283": "OE1" <-> "OE2" Residue "C ARG 292": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 298": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ASP 306": "OD1" <-> "OD2" Residue "C GLU 309": "OE1" <-> "OE2" Residue "C GLU 320": "OE1" <-> "OE2" Residue "C TYR 325": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 327": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ASP 336": "OD1" <-> "OD2" Residue "C GLU 345": "OE1" <-> "OE2" Residue "C PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 361": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ASP 405": "OD1" <-> "OD2" Residue "C GLU 412": "OE1" <-> "OE2" Residue "C ARG 417": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 419": "OE1" <-> "OE2" Residue "C ASP 427": "OD1" <-> "OD2" Residue "C GLU 445": "OE1" <-> "OE2" Residue "C PHE 465": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 468": "OE1" <-> "OE2" Residue "C ARG 473": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 475": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 480": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 503": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 519": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 520": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 523": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 560": "OE1" <-> "OE2" Residue "C GLU 567": "OE1" <-> "OE2" Residue "C TYR 572": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 604": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 606": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 647": "OE1" <-> "OE2" Residue "C GLU 648": "OE1" <-> "OE2" Residue "C ASP 650": "OD1" <-> "OD2" Residue "C ARG 654": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ASP 671": "OD1" <-> "OD2" Residue "C ASP 694": "OD1" <-> "OD2" Residue "C GLU 698": "OE1" <-> "OE2" Residue "C GLU 701": "OE1" <-> "OE2" Residue "C ARG 705": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 717": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 719": "OE1" <-> "OE2" Residue "C ARG 722": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 727": "OE1" <-> "OE2" Residue "C ARG 730": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 735": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 746": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 761": "OE1" <-> "OE2" Residue "C ARG 765": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 766": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 771": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 772": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 777": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ASP 778": "OD1" <-> "OD2" Residue "C ARG 784": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ASP 800": "OD1" <-> "OD2" Residue "C ASP 803": "OD1" <-> "OD2" Residue "C GLU 816": "OE1" <-> "OE2" Residue "C ARG 819": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 829": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 831": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ASP 832": "OD1" <-> "OD2" Residue "C ASP 839": "OD1" <-> "OD2" Residue "C GLU 846": "OE1" <-> "OE2" Residue "C PHE 858": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 862": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 867": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 884": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 891": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 892": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 893": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 896": "OE1" <-> "OE2" Residue "C PHE 930": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 947": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 949": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 971": "OE1" <-> "OE2" Residue "C ARG 982": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 1007": "OE1" <-> "OE2" Residue "C ARG 1011": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 1035": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 48069 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 16023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1025, 16023 Classifications: {'peptide': 1025} Link IDs: {'PTRANS': 53, 'TRANS': 971} Chain breaks: 1 Chain: "B" Number of atoms: 16023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1025, 16023 Classifications: {'peptide': 1025} Link IDs: {'PTRANS': 53, 'TRANS': 971} Chain breaks: 1 Chain: "C" Number of atoms: 16023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1025, 16023 Classifications: {'peptide': 1025} Link IDs: {'PTRANS': 53, 'TRANS': 971} Chain breaks: 1 Time building chain proxies: 19.92, per 1000 atoms: 0.41 Number of scatterers: 48069 At special positions: 0 Unit cell: (123.12, 123.12, 151.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 108 16.00 O 4290 8.00 N 3957 7.00 C 15300 6.00 H 24414 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 39.39 Conformation dependent library (CDL) restraints added in 4.6 seconds 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5688 Finding SS restraints... Secondary structure from input PDB file: 114 helices and 24 sheets defined 58.5% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.75 Creating SS restraints... Processing helix chain 'A' and resid 6 through 12 removed outlier: 4.368A pdb=" N ASN A 12 " --> pdb=" O ARG A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 33 removed outlier: 3.714A pdb=" N VAL A 16 " --> pdb=" O ASN A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 65 Processing helix chain 'A' and resid 65 through 74 removed outlier: 3.606A pdb=" N LEU A 74 " --> pdb=" O THR A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 119 removed outlier: 4.007A pdb=" N ARG A 107 " --> pdb=" O PRO A 103 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU A 112 " --> pdb=" O SER A 108 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR A 113 " --> pdb=" O ARG A 109 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLY A 119 " --> pdb=" O ASN A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 136 No H-bonds generated for 'chain 'A' and resid 134 through 136' Processing helix chain 'A' and resid 152 through 168 removed outlier: 3.654A pdb=" N LEU A 156 " --> pdb=" O ASP A 152 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG A 157 " --> pdb=" O LEU A 153 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER A 158 " --> pdb=" O ALA A 154 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LYS A 165 " --> pdb=" O ASP A 161 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N TYR A 166 " --> pdb=" O TRP A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 200 removed outlier: 3.786A pdb=" N TYR A 199 " --> pdb=" O ARG A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 211 Processing helix chain 'A' and resid 296 through 311 removed outlier: 4.114A pdb=" N VAL A 300 " --> pdb=" O ASN A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 358 Processing helix chain 'A' and resid 359 through 368 Processing helix chain 'A' and resid 368 through 385 removed outlier: 3.861A pdb=" N LEU A 372 " --> pdb=" O ILE A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 425 removed outlier: 5.037A pdb=" N GLY A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ALA A 402 " --> pdb=" O ILE A 398 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N ALA A 406 " --> pdb=" O ALA A 402 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ALA A 407 " --> pdb=" O MET A 403 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N MET A 410 " --> pdb=" O ALA A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 462 removed outlier: 3.814A pdb=" N VAL A 446 " --> pdb=" O ALA A 442 " (cutoff:3.500A) Proline residue: A 448 - end of helix Processing helix chain 'A' and resid 463 through 467 removed outlier: 3.555A pdb=" N THR A 466 " --> pdb=" O PRO A 463 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A 467 " --> pdb=" O ILE A 464 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 463 through 467' Processing helix chain 'A' and resid 469 through 496 Proline residue: A 477 - end of helix Processing helix chain 'A' and resid 496 through 504 Processing helix chain 'A' and resid 517 through 535 Proline residue: A 527 - end of helix removed outlier: 3.795A pdb=" N TRP A 535 " --> pdb=" O LYS A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 549 removed outlier: 3.888A pdb=" N THR A 539 " --> pdb=" O TRP A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 557 removed outlier: 3.867A pdb=" N LEU A 554 " --> pdb=" O VAL A 550 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ASN A 555 " --> pdb=" O LEU A 551 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N LYS A 556 " --> pdb=" O TRP A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 597 Processing helix chain 'A' and resid 641 through 653 Processing helix chain 'A' and resid 664 through 675 Processing helix chain 'A' and resid 689 through 705 removed outlier: 3.640A pdb=" N ARG A 705 " --> pdb=" O GLU A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 736 Processing helix chain 'A' and resid 739 through 749 removed outlier: 4.402A pdb=" N PHE A 746 " --> pdb=" O ASP A 742 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N VAL A 747 " --> pdb=" O VAL A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 777 removed outlier: 3.816A pdb=" N TRP A 776 " --> pdb=" O PRO A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 779 through 784 Processing helix chain 'A' and resid 832 through 847 removed outlier: 3.692A pdb=" N VAL A 836 " --> pdb=" O ASP A 832 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 892 removed outlier: 3.701A pdb=" N VAL A 876 " --> pdb=" O LEU A 872 " (cutoff:3.500A) Proline residue: A 877 - end of helix removed outlier: 3.502A pdb=" N ALA A 890 " --> pdb=" O LEU A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 902 Processing helix chain 'A' and resid 903 through 919 removed outlier: 3.697A pdb=" N ALA A 907 " --> pdb=" O SER A 903 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 955 removed outlier: 4.232A pdb=" N GLY A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL A 936 " --> pdb=" O ALA A 932 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL A 955 " --> pdb=" O ALA A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 976 removed outlier: 3.550A pdb=" N ASP A 970 " --> pdb=" O GLU A 966 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU A 971 " --> pdb=" O GLN A 967 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU A 973 " --> pdb=" O LEU A 969 " (cutoff:3.500A) Processing helix chain 'A' and resid 980 through 994 removed outlier: 4.097A pdb=" N LYS A 984 " --> pdb=" O ARG A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 995 through 1001 Processing helix chain 'A' and resid 1005 through 1040 removed outlier: 4.090A pdb=" N MET A1009 " --> pdb=" O GLY A1005 " (cutoff:3.500A) Proline residue: A1015 - end of helix removed outlier: 3.776A pdb=" N ILE A1021 " --> pdb=" O ILE A1017 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N THR A1022 " --> pdb=" O GLY A1018 " (cutoff:3.500A) Proline residue: A1024 - end of helix removed outlier: 4.298A pdb=" N PHE A1029 " --> pdb=" O LEU A1025 " (cutoff:3.500A) Proline residue: A1032 - end of helix Processing helix chain 'B' and resid 6 through 12 removed outlier: 4.367A pdb=" N ASN B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 33 removed outlier: 3.713A pdb=" N VAL B 16 " --> pdb=" O ASN B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 65 Processing helix chain 'B' and resid 65 through 74 removed outlier: 3.605A pdb=" N LEU B 74 " --> pdb=" O THR B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 119 removed outlier: 4.005A pdb=" N ARG B 107 " --> pdb=" O PRO B 103 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU B 112 " --> pdb=" O SER B 108 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR B 113 " --> pdb=" O ARG B 109 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLY B 119 " --> pdb=" O ASN B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 136 No H-bonds generated for 'chain 'B' and resid 134 through 136' Processing helix chain 'B' and resid 152 through 168 removed outlier: 3.654A pdb=" N LEU B 156 " --> pdb=" O ASP B 152 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG B 157 " --> pdb=" O LEU B 153 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER B 158 " --> pdb=" O ALA B 154 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LYS B 165 " --> pdb=" O ASP B 161 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N TYR B 166 " --> pdb=" O TRP B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 200 removed outlier: 3.786A pdb=" N TYR B 199 " --> pdb=" O ARG B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 211 Processing helix chain 'B' and resid 296 through 311 removed outlier: 4.114A pdb=" N VAL B 300 " --> pdb=" O ASN B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 358 Processing helix chain 'B' and resid 359 through 368 Processing helix chain 'B' and resid 368 through 385 removed outlier: 3.861A pdb=" N LEU B 372 " --> pdb=" O ILE B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 425 removed outlier: 5.037A pdb=" N GLY B 401 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ALA B 402 " --> pdb=" O ILE B 398 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N ALA B 406 " --> pdb=" O ALA B 402 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ALA B 407 " --> pdb=" O MET B 403 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N MET B 410 " --> pdb=" O ALA B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 462 removed outlier: 3.813A pdb=" N VAL B 446 " --> pdb=" O ALA B 442 " (cutoff:3.500A) Proline residue: B 448 - end of helix Processing helix chain 'B' and resid 463 through 467 removed outlier: 3.558A pdb=" N THR B 466 " --> pdb=" O PRO B 463 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU B 467 " --> pdb=" O ILE B 464 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 463 through 467' Processing helix chain 'B' and resid 469 through 496 Proline residue: B 477 - end of helix Processing helix chain 'B' and resid 496 through 504 Processing helix chain 'B' and resid 517 through 535 Proline residue: B 527 - end of helix removed outlier: 3.798A pdb=" N TRP B 535 " --> pdb=" O LYS B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 549 removed outlier: 3.888A pdb=" N THR B 539 " --> pdb=" O TRP B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 550 through 557 removed outlier: 3.869A pdb=" N LEU B 554 " --> pdb=" O VAL B 550 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ASN B 555 " --> pdb=" O LEU B 551 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LYS B 556 " --> pdb=" O TRP B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 597 Processing helix chain 'B' and resid 641 through 653 Processing helix chain 'B' and resid 664 through 675 Processing helix chain 'B' and resid 689 through 705 removed outlier: 3.638A pdb=" N ARG B 705 " --> pdb=" O GLU B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 736 Processing helix chain 'B' and resid 739 through 749 removed outlier: 4.402A pdb=" N PHE B 746 " --> pdb=" O ASP B 742 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N VAL B 747 " --> pdb=" O VAL B 743 " (cutoff:3.500A) Processing helix chain 'B' and resid 773 through 777 removed outlier: 3.815A pdb=" N TRP B 776 " --> pdb=" O PRO B 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 779 through 784 Processing helix chain 'B' and resid 832 through 847 removed outlier: 3.692A pdb=" N VAL B 836 " --> pdb=" O ASP B 832 " (cutoff:3.500A) Processing helix chain 'B' and resid 861 through 892 removed outlier: 3.701A pdb=" N VAL B 876 " --> pdb=" O LEU B 872 " (cutoff:3.500A) Proline residue: B 877 - end of helix removed outlier: 3.502A pdb=" N ALA B 890 " --> pdb=" O LEU B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 893 through 902 Processing helix chain 'B' and resid 903 through 919 removed outlier: 3.698A pdb=" N ALA B 907 " --> pdb=" O SER B 903 " (cutoff:3.500A) Processing helix chain 'B' and resid 923 through 955 removed outlier: 4.230A pdb=" N GLY B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL B 936 " --> pdb=" O ALA B 932 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL B 955 " --> pdb=" O ALA B 951 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 976 removed outlier: 3.550A pdb=" N ASP B 970 " --> pdb=" O GLU B 966 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU B 971 " --> pdb=" O GLN B 967 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU B 973 " --> pdb=" O LEU B 969 " (cutoff:3.500A) Processing helix chain 'B' and resid 980 through 994 removed outlier: 4.096A pdb=" N LYS B 984 " --> pdb=" O ARG B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 995 through 1001 Processing helix chain 'B' and resid 1005 through 1040 removed outlier: 4.091A pdb=" N MET B1009 " --> pdb=" O GLY B1005 " (cutoff:3.500A) Proline residue: B1015 - end of helix removed outlier: 3.776A pdb=" N ILE B1021 " --> pdb=" O ILE B1017 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N THR B1022 " --> pdb=" O GLY B1018 " (cutoff:3.500A) Proline residue: B1024 - end of helix removed outlier: 4.298A pdb=" N PHE B1029 " --> pdb=" O LEU B1025 " (cutoff:3.500A) Proline residue: B1032 - end of helix Processing helix chain 'C' and resid 6 through 12 removed outlier: 4.367A pdb=" N ASN C 12 " --> pdb=" O ARG C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 33 removed outlier: 3.715A pdb=" N VAL C 16 " --> pdb=" O ASN C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 65 Processing helix chain 'C' and resid 65 through 74 removed outlier: 3.607A pdb=" N LEU C 74 " --> pdb=" O THR C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 119 removed outlier: 4.005A pdb=" N ARG C 107 " --> pdb=" O PRO C 103 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU C 112 " --> pdb=" O SER C 108 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR C 113 " --> pdb=" O ARG C 109 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLY C 119 " --> pdb=" O ASN C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 136 No H-bonds generated for 'chain 'C' and resid 134 through 136' Processing helix chain 'C' and resid 152 through 168 removed outlier: 3.654A pdb=" N LEU C 156 " --> pdb=" O ASP C 152 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG C 157 " --> pdb=" O LEU C 153 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER C 158 " --> pdb=" O ALA C 154 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LYS C 165 " --> pdb=" O ASP C 161 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N TYR C 166 " --> pdb=" O TRP C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 200 removed outlier: 3.787A pdb=" N TYR C 199 " --> pdb=" O ARG C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 211 Processing helix chain 'C' and resid 296 through 311 removed outlier: 4.116A pdb=" N VAL C 300 " --> pdb=" O ASN C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 358 Processing helix chain 'C' and resid 359 through 368 Processing helix chain 'C' and resid 368 through 385 removed outlier: 3.860A pdb=" N LEU C 372 " --> pdb=" O ILE C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 425 removed outlier: 5.037A pdb=" N GLY C 401 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ALA C 402 " --> pdb=" O ILE C 398 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N ALA C 406 " --> pdb=" O ALA C 402 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ALA C 407 " --> pdb=" O MET C 403 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N MET C 410 " --> pdb=" O ALA C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 462 removed outlier: 3.814A pdb=" N VAL C 446 " --> pdb=" O ALA C 442 " (cutoff:3.500A) Proline residue: C 448 - end of helix Processing helix chain 'C' and resid 463 through 467 removed outlier: 3.558A pdb=" N THR C 466 " --> pdb=" O PRO C 463 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU C 467 " --> pdb=" O ILE C 464 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 463 through 467' Processing helix chain 'C' and resid 469 through 496 Proline residue: C 477 - end of helix Processing helix chain 'C' and resid 496 through 504 Processing helix chain 'C' and resid 517 through 535 Proline residue: C 527 - end of helix removed outlier: 3.797A pdb=" N TRP C 535 " --> pdb=" O LYS C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 535 through 549 removed outlier: 3.888A pdb=" N THR C 539 " --> pdb=" O TRP C 535 " (cutoff:3.500A) Processing helix chain 'C' and resid 550 through 557 removed outlier: 3.866A pdb=" N LEU C 554 " --> pdb=" O VAL C 550 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ASN C 555 " --> pdb=" O LEU C 551 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N LYS C 556 " --> pdb=" O TRP C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 597 Processing helix chain 'C' and resid 641 through 653 Processing helix chain 'C' and resid 664 through 675 Processing helix chain 'C' and resid 689 through 705 removed outlier: 3.640A pdb=" N ARG C 705 " --> pdb=" O GLU C 701 " (cutoff:3.500A) Processing helix chain 'C' and resid 729 through 736 Processing helix chain 'C' and resid 739 through 749 removed outlier: 4.403A pdb=" N PHE C 746 " --> pdb=" O ASP C 742 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N VAL C 747 " --> pdb=" O VAL C 743 " (cutoff:3.500A) Processing helix chain 'C' and resid 773 through 777 removed outlier: 3.817A pdb=" N TRP C 776 " --> pdb=" O PRO C 773 " (cutoff:3.500A) Processing helix chain 'C' and resid 779 through 784 Processing helix chain 'C' and resid 832 through 847 removed outlier: 3.693A pdb=" N VAL C 836 " --> pdb=" O ASP C 832 " (cutoff:3.500A) Processing helix chain 'C' and resid 861 through 892 removed outlier: 3.701A pdb=" N VAL C 876 " --> pdb=" O LEU C 872 " (cutoff:3.500A) Proline residue: C 877 - end of helix removed outlier: 3.501A pdb=" N ALA C 890 " --> pdb=" O LEU C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 893 through 902 Processing helix chain 'C' and resid 903 through 919 removed outlier: 3.698A pdb=" N ALA C 907 " --> pdb=" O SER C 903 " (cutoff:3.500A) Processing helix chain 'C' and resid 923 through 955 removed outlier: 4.231A pdb=" N GLY C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL C 936 " --> pdb=" O ALA C 932 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL C 955 " --> pdb=" O ALA C 951 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 976 removed outlier: 3.550A pdb=" N ASP C 970 " --> pdb=" O GLU C 966 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU C 971 " --> pdb=" O GLN C 967 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU C 973 " --> pdb=" O LEU C 969 " (cutoff:3.500A) Processing helix chain 'C' and resid 980 through 994 removed outlier: 4.098A pdb=" N LYS C 984 " --> pdb=" O ARG C 980 " (cutoff:3.500A) Processing helix chain 'C' and resid 995 through 1001 Processing helix chain 'C' and resid 1005 through 1040 removed outlier: 4.091A pdb=" N MET C1009 " --> pdb=" O GLY C1005 " (cutoff:3.500A) Proline residue: C1015 - end of helix removed outlier: 3.775A pdb=" N ILE C1021 " --> pdb=" O ILE C1017 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N THR C1022 " --> pdb=" O GLY C1018 " (cutoff:3.500A) Proline residue: C1024 - end of helix removed outlier: 4.298A pdb=" N PHE C1029 " --> pdb=" O LEU C1025 " (cutoff:3.500A) Proline residue: C1032 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 127 through 129 Processing sheet with id=AA2, first strand: chain 'A' and resid 174 through 180 removed outlier: 4.161A pdb=" N ALA A 285 " --> pdb=" O LEU A 144 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TYR A 140 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N LEU A 291 " --> pdb=" O TRP A 138 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N TRP A 138 " --> pdb=" O LEU A 291 " (cutoff:3.500A) removed outlier: 8.746A pdb=" N ILE A 139 " --> pdb=" O ASP A 326 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ASP A 326 " --> pdb=" O ILE A 139 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLU A 141 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 263 through 269 removed outlier: 7.144A pdb=" N LYS A 185 " --> pdb=" O PRO A 767 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N ASN A 769 " --> pdb=" O LYS A 185 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N TYR A 187 " --> pdb=" O ASN A 769 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N ARG A 771 " --> pdb=" O TYR A 187 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N VAL A 189 " --> pdb=" O ARG A 771 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 221 through 223 removed outlier: 6.367A pdb=" N ARG B 722 " --> pdb=" O GLU A 228 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N MET A 230 " --> pdb=" O ARG B 722 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ILE B 724 " --> pdb=" O MET A 230 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 247 through 249 removed outlier: 7.454A pdb=" N VAL A 257 " --> pdb=" O LEU A 248 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 274 through 277 removed outlier: 3.667A pdb=" N ARG A 604 " --> pdb=" O GLN A 629 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE A 606 " --> pdb=" O THR A 627 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 712 through 715 removed outlier: 4.403A pdb=" N ILE A 681 " --> pdb=" O ILE A 826 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY A 682 " --> pdb=" O SER A 859 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 802 through 809 removed outlier: 7.202A pdb=" N ARG A 722 " --> pdb=" O MET C 230 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 788 through 789 Processing sheet with id=AB1, first strand: chain 'B' and resid 127 through 129 Processing sheet with id=AB2, first strand: chain 'B' and resid 174 through 180 removed outlier: 4.160A pdb=" N ALA B 285 " --> pdb=" O LEU B 144 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TYR B 140 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N LEU B 291 " --> pdb=" O TRP B 138 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N TRP B 138 " --> pdb=" O LEU B 291 " (cutoff:3.500A) removed outlier: 8.748A pdb=" N ILE B 139 " --> pdb=" O ASP B 326 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ASP B 326 " --> pdb=" O ILE B 139 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N GLU B 141 " --> pdb=" O THR B 324 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 263 through 269 removed outlier: 7.144A pdb=" N LYS B 185 " --> pdb=" O PRO B 767 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N ASN B 769 " --> pdb=" O LYS B 185 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N TYR B 187 " --> pdb=" O ASN B 769 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N ARG B 771 " --> pdb=" O TYR B 187 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N VAL B 189 " --> pdb=" O ARG B 771 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 221 through 223 removed outlier: 6.325A pdb=" N ARG C 722 " --> pdb=" O GLU B 228 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N MET B 230 " --> pdb=" O ARG C 722 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ILE C 724 " --> pdb=" O MET B 230 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 247 through 249 removed outlier: 7.453A pdb=" N VAL B 257 " --> pdb=" O LEU B 248 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 274 through 277 removed outlier: 3.669A pdb=" N ARG B 604 " --> pdb=" O GLN B 629 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE B 606 " --> pdb=" O THR B 627 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 712 through 715 removed outlier: 4.403A pdb=" N ILE B 681 " --> pdb=" O ILE B 826 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY B 682 " --> pdb=" O SER B 859 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 788 through 789 Processing sheet with id=AB9, first strand: chain 'C' and resid 127 through 129 Processing sheet with id=AC1, first strand: chain 'C' and resid 174 through 180 removed outlier: 4.160A pdb=" N ALA C 285 " --> pdb=" O LEU C 144 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TYR C 140 " --> pdb=" O VAL C 289 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N LEU C 291 " --> pdb=" O TRP C 138 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N TRP C 138 " --> pdb=" O LEU C 291 " (cutoff:3.500A) removed outlier: 8.748A pdb=" N ILE C 139 " --> pdb=" O ASP C 326 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ASP C 326 " --> pdb=" O ILE C 139 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLU C 141 " --> pdb=" O THR C 324 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 263 through 269 removed outlier: 7.145A pdb=" N LYS C 185 " --> pdb=" O PRO C 767 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N ASN C 769 " --> pdb=" O LYS C 185 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N TYR C 187 " --> pdb=" O ASN C 769 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N ARG C 771 " --> pdb=" O TYR C 187 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N VAL C 189 " --> pdb=" O ARG C 771 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 247 through 249 removed outlier: 7.454A pdb=" N VAL C 257 " --> pdb=" O LEU C 248 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 274 through 277 removed outlier: 3.667A pdb=" N ARG C 604 " --> pdb=" O GLN C 629 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE C 606 " --> pdb=" O THR C 627 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 712 through 715 removed outlier: 4.401A pdb=" N ILE C 681 " --> pdb=" O ILE C 826 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY C 682 " --> pdb=" O SER C 859 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 788 through 789 1395 hydrogen bonds defined for protein. 4122 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: 19.85 Time building geometry restraints manager: 40.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 24408 1.03 - 1.23: 9 1.23 - 1.42: 9603 1.42 - 1.62: 14328 1.62 - 1.81: 210 Bond restraints: 48558 Sorted by residual: bond pdb=" N VAL C 876 " pdb=" CA VAL C 876 " ideal model delta sigma weight residual 1.461 1.503 -0.041 1.23e-02 6.61e+03 1.13e+01 bond pdb=" N VAL B 876 " pdb=" CA VAL B 876 " ideal model delta sigma weight residual 1.461 1.502 -0.041 1.23e-02 6.61e+03 1.11e+01 bond pdb=" N LEU B 224 " pdb=" CA LEU B 224 " ideal model delta sigma weight residual 1.455 1.496 -0.041 1.25e-02 6.40e+03 1.06e+01 bond pdb=" N LEU C 224 " pdb=" CA LEU C 224 " ideal model delta sigma weight residual 1.455 1.496 -0.041 1.25e-02 6.40e+03 1.06e+01 bond pdb=" N VAL A 876 " pdb=" CA VAL A 876 " ideal model delta sigma weight residual 1.461 1.501 -0.040 1.23e-02 6.61e+03 1.05e+01 ... (remaining 48553 not shown) Histogram of bond angle deviations from ideal: 100.31 - 107.11: 1131 107.11 - 113.91: 60024 113.91 - 120.70: 15894 120.70 - 127.50: 11013 127.50 - 134.30: 315 Bond angle restraints: 88377 Sorted by residual: angle pdb=" CA ASN A 12 " pdb=" C ASN A 12 " pdb=" O ASN A 12 " ideal model delta sigma weight residual 122.63 118.01 4.62 1.29e+00 6.01e-01 1.28e+01 angle pdb=" CA ASN C 12 " pdb=" C ASN C 12 " pdb=" O ASN C 12 " ideal model delta sigma weight residual 122.63 118.07 4.56 1.29e+00 6.01e-01 1.25e+01 angle pdb=" CA ASN B 12 " pdb=" C ASN B 12 " pdb=" O ASN B 12 " ideal model delta sigma weight residual 122.63 118.12 4.51 1.29e+00 6.01e-01 1.22e+01 angle pdb=" C ARG C 722 " pdb=" CA ARG C 722 " pdb=" CB ARG C 722 " ideal model delta sigma weight residual 109.75 104.17 5.58 1.65e+00 3.67e-01 1.14e+01 angle pdb=" CA PHE B 356 " pdb=" C PHE B 356 " pdb=" O PHE B 356 " ideal model delta sigma weight residual 120.70 117.37 3.33 1.03e+00 9.43e-01 1.04e+01 ... (remaining 88372 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 20126 17.78 - 35.56: 1712 35.56 - 53.34: 622 53.34 - 71.12: 145 71.12 - 88.90: 30 Dihedral angle restraints: 22635 sinusoidal: 12519 harmonic: 10116 Sorted by residual: dihedral pdb=" CD ARG B 232 " pdb=" NE ARG B 232 " pdb=" CZ ARG B 232 " pdb=" NH1 ARG B 232 " ideal model delta sinusoidal sigma weight residual 0.00 79.75 -79.75 1 1.00e+01 1.00e-02 7.89e+01 dihedral pdb=" CD ARG A 232 " pdb=" NE ARG A 232 " pdb=" CZ ARG A 232 " pdb=" NH1 ARG A 232 " ideal model delta sinusoidal sigma weight residual 0.00 75.73 -75.73 1 1.00e+01 1.00e-02 7.23e+01 dihedral pdb=" CD ARG C 232 " pdb=" NE ARG C 232 " pdb=" CZ ARG C 232 " pdb=" NH1 ARG C 232 " ideal model delta sinusoidal sigma weight residual 0.00 71.57 -71.57 1 1.00e+01 1.00e-02 6.56e+01 ... (remaining 22632 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 3018 0.042 - 0.083: 582 0.083 - 0.125: 253 0.125 - 0.166: 47 0.166 - 0.208: 3 Chirality restraints: 3903 Sorted by residual: chirality pdb=" CB VAL A 876 " pdb=" CA VAL A 876 " pdb=" CG1 VAL A 876 " pdb=" CG2 VAL A 876 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CB VAL B 876 " pdb=" CA VAL B 876 " pdb=" CG1 VAL B 876 " pdb=" CG2 VAL B 876 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CB VAL C 876 " pdb=" CA VAL C 876 " pdb=" CG1 VAL C 876 " pdb=" CG2 VAL C 876 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 3900 not shown) Planarity restraints: 7050 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 722 " 0.748 9.50e-02 1.11e+02 3.23e-01 1.01e+03 pdb=" NE ARG B 722 " 0.133 2.00e-02 2.50e+03 pdb=" CZ ARG B 722 " 0.032 2.00e-02 2.50e+03 pdb=" NH1 ARG B 722 " 0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG B 722 " -0.046 2.00e-02 2.50e+03 pdb="HH11 ARG B 722 " -0.424 2.00e-02 2.50e+03 pdb="HH12 ARG B 722 " 0.406 2.00e-02 2.50e+03 pdb="HH21 ARG B 722 " -0.032 2.00e-02 2.50e+03 pdb="HH22 ARG B 722 " -0.112 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 722 " 0.767 9.50e-02 1.11e+02 3.26e-01 9.92e+02 pdb=" NE ARG C 722 " 0.122 2.00e-02 2.50e+03 pdb=" CZ ARG C 722 " 0.027 2.00e-02 2.50e+03 pdb=" NH1 ARG C 722 " 0.012 2.00e-02 2.50e+03 pdb=" NH2 ARG C 722 " -0.047 2.00e-02 2.50e+03 pdb="HH11 ARG C 722 " -0.414 2.00e-02 2.50e+03 pdb="HH12 ARG C 722 " 0.406 2.00e-02 2.50e+03 pdb="HH21 ARG C 722 " -0.014 2.00e-02 2.50e+03 pdb="HH22 ARG C 722 " -0.126 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 722 " -0.719 9.50e-02 1.11e+02 3.08e-01 8.99e+02 pdb=" NE ARG A 722 " -0.120 2.00e-02 2.50e+03 pdb=" CZ ARG A 722 " -0.028 2.00e-02 2.50e+03 pdb=" NH1 ARG A 722 " -0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG A 722 " 0.045 2.00e-02 2.50e+03 pdb="HH11 ARG A 722 " 0.395 2.00e-02 2.50e+03 pdb="HH12 ARG A 722 " -0.385 2.00e-02 2.50e+03 pdb="HH21 ARG A 722 " 0.016 2.00e-02 2.50e+03 pdb="HH22 ARG A 722 " 0.121 2.00e-02 2.50e+03 ... (remaining 7047 not shown) Histogram of nonbonded interaction distances: 1.08 - 1.78: 94 1.78 - 2.49: 34032 2.49 - 3.19: 146312 3.19 - 3.90: 187789 3.90 - 4.60: 298080 Nonbonded interactions: 666307 Sorted by model distance: nonbonded pdb=" HB2 SER A 220 " pdb=" HA2 GLY B 752 " model vdw 1.079 2.440 nonbonded pdb=" HA2 GLY A 752 " pdb=" HB2 SER C 220 " model vdw 1.126 2.440 nonbonded pdb=" HB2 SER B 220 " pdb=" HA2 GLY C 752 " model vdw 1.131 2.440 nonbonded pdb=" HE1 TRP A 636 " pdb=" HB2 MET A 640 " model vdw 1.251 2.270 nonbonded pdb=" HE1 TRP C 636 " pdb=" HB2 MET C 640 " model vdw 1.252 2.270 ... (remaining 666302 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.660 Extract box with map and model: 3.340 Check model and map are aligned: 0.640 Set scattering table: 0.370 Process input model: 145.140 Find NCS groups from input model: 1.800 Set up NCS constraints: 0.160 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: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 155.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 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 : 0.003 0.041 24144 Z= 0.189 Angle : 0.555 5.887 32877 Z= 0.330 Chirality : 0.042 0.208 3903 Planarity : 0.017 0.485 4137 Dihedral : 15.928 88.898 8802 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.24 % Allowed : 9.68 % Favored : 90.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.14), residues: 3063 helix: -0.42 (0.12), residues: 1659 sheet: -2.33 (0.22), residues: 417 loop : -3.00 (0.17), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 636 HIS 0.004 0.001 HIS C 526 PHE 0.009 0.001 PHE B 85 TYR 0.006 0.001 TYR C 113 ARG 0.010 0.001 ARG B 819 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 884 residues out of total 2532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 878 time to evaluate : 4.005 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: A 7 ARG cc_start: 0.8196 (mtt-85) cc_final: 0.7747 (mtt90) REVERT: A 238 GLN cc_start: 0.7145 (mm-40) cc_final: 0.6656 (mm-40) REVERT: A 283 GLU cc_start: 0.8541 (mt-10) cc_final: 0.8049 (mt-10) REVERT: A 337 ASN cc_start: 0.7722 (t0) cc_final: 0.7496 (t0) REVERT: A 494 ILE cc_start: 0.8394 (tp) cc_final: 0.8114 (tp) REVERT: A 597 MET cc_start: 0.8497 (mmm) cc_final: 0.8288 (tpt) REVERT: A 755 MET cc_start: 0.7838 (ttp) cc_final: 0.7551 (ttp) REVERT: A 916 TRP cc_start: 0.8539 (t60) cc_final: 0.8053 (t-100) REVERT: B 7 ARG cc_start: 0.8178 (mtt-85) cc_final: 0.7691 (mtt90) REVERT: B 238 GLN cc_start: 0.7294 (mm-40) cc_final: 0.6876 (mm-40) REVERT: B 311 LEU cc_start: 0.8374 (mp) cc_final: 0.8174 (mp) REVERT: B 342 LEU cc_start: 0.8476 (mt) cc_final: 0.8271 (mt) REVERT: B 494 ILE cc_start: 0.8357 (tp) cc_final: 0.8029 (tp) REVERT: B 623 MET cc_start: 0.7906 (ttt) cc_final: 0.7602 (ttm) REVERT: C 321 ILE cc_start: 0.8939 (mt) cc_final: 0.8411 (mt) REVERT: C 337 ASN cc_start: 0.7852 (t0) cc_final: 0.7532 (t0) REVERT: C 342 LEU cc_start: 0.8413 (mt) cc_final: 0.8207 (mt) REVERT: C 435 ARG cc_start: 0.7263 (ttp80) cc_final: 0.6523 (ttt180) REVERT: C 467 LEU cc_start: 0.7604 (mt) cc_final: 0.7368 (mt) REVERT: C 491 LEU cc_start: 0.7899 (tp) cc_final: 0.7509 (mm) outliers start: 6 outliers final: 4 residues processed: 883 average time/residue: 0.8582 time to fit residues: 1161.0860 Evaluate side-chains 699 residues out of total 2532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 695 time to evaluate : 3.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 722 ARG Chi-restraints excluded: chain B residue 722 ARG Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 722 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 10.0000 chunk 231 optimal weight: 10.0000 chunk 128 optimal weight: 6.9990 chunk 79 optimal weight: 7.9990 chunk 156 optimal weight: 7.9990 chunk 123 optimal weight: 8.9990 chunk 239 optimal weight: 9.9990 chunk 92 optimal weight: 9.9990 chunk 145 optimal weight: 7.9990 chunk 178 optimal weight: 10.0000 chunk 277 optimal weight: 5.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN A 359 HIS A 590 GLN A 744 GLN A 959 ASN B 244 ASN B 359 HIS B 590 GLN B 744 GLN B 817 ASN B 959 ASN C 115 ASN C 116 GLN C 359 HIS C 590 GLN C 744 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 24144 Z= 0.445 Angle : 0.760 8.053 32877 Z= 0.396 Chirality : 0.047 0.185 3903 Planarity : 0.006 0.077 4137 Dihedral : 4.678 49.299 3308 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 3.83 % Allowed : 16.15 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.15), residues: 3063 helix: 0.23 (0.13), residues: 1713 sheet: -2.00 (0.22), residues: 474 loop : -2.69 (0.19), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A1039 HIS 0.007 0.001 HIS A 425 PHE 0.023 0.002 PHE B 346 TYR 0.023 0.002 TYR B 53 ARG 0.021 0.001 ARG C 232 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 894 residues out of total 2532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 797 time to evaluate : 3.888 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: A 33 ASN cc_start: 0.8420 (t0) cc_final: 0.8108 (t0) REVERT: A 238 GLN cc_start: 0.7448 (mm110) cc_final: 0.6929 (mm-40) REVERT: A 597 MET cc_start: 0.8339 (mmm) cc_final: 0.8136 (tpt) REVERT: A 859 SER cc_start: 0.8523 (t) cc_final: 0.8109 (t) REVERT: A 916 TRP cc_start: 0.8652 (t60) cc_final: 0.8298 (t-100) REVERT: B 238 GLN cc_start: 0.7643 (mm110) cc_final: 0.7325 (mm-40) REVERT: B 281 GLU cc_start: 0.8241 (mp0) cc_final: 0.7803 (mp0) REVERT: B 617 ASP cc_start: 0.8458 (t0) cc_final: 0.8248 (t0) REVERT: B 623 MET cc_start: 0.8073 (ttt) cc_final: 0.7570 (ttm) REVERT: B 635 GLN cc_start: 0.7151 (OUTLIER) cc_final: 0.6802 (mt0) REVERT: B 663 VAL cc_start: 0.9232 (OUTLIER) cc_final: 0.8985 (m) REVERT: B 751 VAL cc_start: 0.8499 (t) cc_final: 0.8269 (t) REVERT: C 80 LYS cc_start: 0.7660 (ttpp) cc_final: 0.7391 (ttpp) REVERT: C 321 ILE cc_start: 0.9003 (mt) cc_final: 0.8763 (mt) REVERT: C 332 ASP cc_start: 0.8150 (m-30) cc_final: 0.7853 (m-30) REVERT: C 346 PHE cc_start: 0.8481 (t80) cc_final: 0.8277 (t80) REVERT: C 435 ARG cc_start: 0.7704 (ttp80) cc_final: 0.6638 (ttt180) REVERT: C 569 ASP cc_start: 0.7962 (OUTLIER) cc_final: 0.7592 (p0) REVERT: C 617 ASP cc_start: 0.8423 (t0) cc_final: 0.8184 (t0) REVERT: C 751 VAL cc_start: 0.8506 (t) cc_final: 0.8270 (t) REVERT: C 859 SER cc_start: 0.8687 (t) cc_final: 0.8295 (t) REVERT: C 878 MET cc_start: 0.7711 (mtm) cc_final: 0.7497 (mtm) outliers start: 97 outliers final: 64 residues processed: 850 average time/residue: 0.8415 time to fit residues: 1105.4618 Evaluate side-chains 807 residues out of total 2532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 740 time to evaluate : 3.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 229 TYR Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 722 ARG Chi-restraints excluded: chain A residue 759 THR Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 804 ILE Chi-restraints excluded: chain A residue 959 ASN Chi-restraints excluded: chain A residue 1002 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 387 ASN Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 569 ASP Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 635 GLN Chi-restraints excluded: chain B residue 641 THR Chi-restraints excluded: chain B residue 645 ILE Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 668 ASN Chi-restraints excluded: chain B residue 722 ARG Chi-restraints excluded: chain B residue 759 THR Chi-restraints excluded: chain B residue 760 VAL Chi-restraints excluded: chain B residue 808 THR Chi-restraints excluded: chain B residue 876 VAL Chi-restraints excluded: chain B residue 959 ASN Chi-restraints excluded: chain B residue 1002 THR Chi-restraints excluded: chain B residue 1027 SER Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 229 TYR Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 368 ILE Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 569 ASP Chi-restraints excluded: chain C residue 580 ILE Chi-restraints excluded: chain C residue 641 THR Chi-restraints excluded: chain C residue 645 ILE Chi-restraints excluded: chain C residue 722 ARG Chi-restraints excluded: chain C residue 759 THR Chi-restraints excluded: chain C residue 807 SER Chi-restraints excluded: chain C residue 815 THR Chi-restraints excluded: chain C residue 1027 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 154 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 231 optimal weight: 5.9990 chunk 189 optimal weight: 7.9990 chunk 76 optimal weight: 0.0000 chunk 278 optimal weight: 5.9990 chunk 300 optimal weight: 1.9990 chunk 247 optimal weight: 6.9990 chunk 276 optimal weight: 0.8980 chunk 94 optimal weight: 4.9990 chunk 223 optimal weight: 5.9990 overall best weight: 2.1790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 116 GLN C 116 GLN C 413 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.3735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 24144 Z= 0.188 Angle : 0.556 5.926 32877 Z= 0.285 Chirality : 0.041 0.154 3903 Planarity : 0.004 0.060 4137 Dihedral : 4.281 46.481 3308 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.80 % Allowed : 20.93 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.16), residues: 3063 helix: 0.79 (0.13), residues: 1707 sheet: -1.67 (0.23), residues: 471 loop : -2.45 (0.19), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 162 HIS 0.003 0.001 HIS A 526 PHE 0.012 0.001 PHE B 85 TYR 0.016 0.001 TYR B 736 ARG 0.005 0.000 ARG C 109 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 820 residues out of total 2532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 749 time to evaluate : 2.829 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: A 33 ASN cc_start: 0.8255 (t0) cc_final: 0.8020 (t0) REVERT: A 104 TYR cc_start: 0.8271 (m-80) cc_final: 0.7915 (m-80) REVERT: A 195 ARG cc_start: 0.6764 (mtm180) cc_final: 0.6371 (mtm180) REVERT: A 238 GLN cc_start: 0.7607 (mm110) cc_final: 0.7152 (mm-40) REVERT: A 326 ASP cc_start: 0.8215 (t0) cc_final: 0.7859 (t0) REVERT: A 441 ASP cc_start: 0.6959 (m-30) cc_final: 0.6743 (m-30) REVERT: A 667 ARG cc_start: 0.8921 (tpp-160) cc_final: 0.8501 (tpp-160) REVERT: A 859 SER cc_start: 0.8505 (t) cc_final: 0.8119 (t) REVERT: A 916 TRP cc_start: 0.8667 (t60) cc_final: 0.8177 (t-100) REVERT: B 161 ASP cc_start: 0.8507 (m-30) cc_final: 0.7633 (m-30) REVERT: B 281 GLU cc_start: 0.8093 (mp0) cc_final: 0.7692 (mp0) REVERT: B 623 MET cc_start: 0.8002 (ttt) cc_final: 0.7591 (ttm) REVERT: B 635 GLN cc_start: 0.7072 (OUTLIER) cc_final: 0.6761 (mt0) REVERT: B 663 VAL cc_start: 0.9207 (OUTLIER) cc_final: 0.8943 (m) REVERT: B 751 VAL cc_start: 0.8521 (t) cc_final: 0.8305 (t) REVERT: C 80 LYS cc_start: 0.7612 (ttpp) cc_final: 0.7385 (ttpp) REVERT: C 332 ASP cc_start: 0.8174 (m-30) cc_final: 0.7822 (m-30) REVERT: C 337 ASN cc_start: 0.7819 (t0) cc_final: 0.7519 (t0) REVERT: C 569 ASP cc_start: 0.7695 (OUTLIER) cc_final: 0.7461 (p0) REVERT: C 751 VAL cc_start: 0.8507 (t) cc_final: 0.8280 (t) REVERT: C 859 SER cc_start: 0.8518 (t) cc_final: 0.8111 (t) REVERT: C 916 TRP cc_start: 0.8579 (t60) cc_final: 0.8072 (t-100) REVERT: C 939 GLU cc_start: 0.8453 (tm-30) cc_final: 0.7927 (tm-30) REVERT: C 944 MET cc_start: 0.8624 (tpt) cc_final: 0.8377 (tpt) outliers start: 71 outliers final: 57 residues processed: 782 average time/residue: 0.8315 time to fit residues: 1016.8013 Evaluate side-chains 794 residues out of total 2532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 734 time to evaluate : 3.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 229 TYR Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 769 ASN Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 1002 THR Chi-restraints excluded: chain A residue 1025 LEU Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 387 ASN Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 566 ASN Chi-restraints excluded: chain B residue 569 ASP Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain B residue 635 GLN Chi-restraints excluded: chain B residue 642 MET Chi-restraints excluded: chain B residue 645 ILE Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 808 THR Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 1002 THR Chi-restraints excluded: chain B residue 1025 LEU Chi-restraints excluded: chain B residue 1027 SER Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 229 TYR Chi-restraints excluded: chain C residue 266 GLN Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 368 ILE Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 569 ASP Chi-restraints excluded: chain C residue 622 GLU Chi-restraints excluded: chain C residue 642 MET Chi-restraints excluded: chain C residue 645 ILE Chi-restraints excluded: chain C residue 722 ARG Chi-restraints excluded: chain C residue 815 THR Chi-restraints excluded: chain C residue 1002 THR Chi-restraints excluded: chain C residue 1027 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 275 optimal weight: 10.0000 chunk 209 optimal weight: 1.9990 chunk 144 optimal weight: 8.9990 chunk 30 optimal weight: 6.9990 chunk 132 optimal weight: 8.9990 chunk 186 optimal weight: 8.9990 chunk 279 optimal weight: 7.9990 chunk 295 optimal weight: 6.9990 chunk 145 optimal weight: 3.9990 chunk 264 optimal weight: 3.9990 chunk 79 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 ASN B 337 ASN C 244 ASN C 817 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.4416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 24144 Z= 0.303 Angle : 0.612 6.692 32877 Z= 0.318 Chirality : 0.043 0.170 3903 Planarity : 0.005 0.090 4137 Dihedral : 4.145 47.862 3298 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 4.19 % Allowed : 20.66 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.16), residues: 3063 helix: 0.89 (0.13), residues: 1704 sheet: -1.65 (0.23), residues: 471 loop : -2.30 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 535 HIS 0.004 0.001 HIS A 245 PHE 0.025 0.001 PHE C 480 TYR 0.019 0.001 TYR A 736 ARG 0.003 0.001 ARG C 147 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 844 residues out of total 2532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 738 time to evaluate : 3.506 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: A 33 ASN cc_start: 0.8277 (t0) cc_final: 0.8018 (t0) REVERT: A 109 ARG cc_start: 0.8665 (mmp80) cc_final: 0.8276 (mmm160) REVERT: A 238 GLN cc_start: 0.7842 (mm110) cc_final: 0.7473 (mm-40) REVERT: A 592 THR cc_start: 0.8953 (OUTLIER) cc_final: 0.8622 (p) REVERT: A 617 ASP cc_start: 0.8305 (t0) cc_final: 0.8105 (t0) REVERT: A 859 SER cc_start: 0.8636 (t) cc_final: 0.8247 (t) REVERT: A 916 TRP cc_start: 0.8721 (t60) cc_final: 0.8322 (t-100) REVERT: B 158 SER cc_start: 0.8558 (t) cc_final: 0.8255 (m) REVERT: B 216 GLU cc_start: 0.6819 (OUTLIER) cc_final: 0.5787 (tm-30) REVERT: B 345 GLU cc_start: 0.8722 (mt-10) cc_final: 0.8251 (tt0) REVERT: B 567 GLU cc_start: 0.8914 (pm20) cc_final: 0.8227 (pm20) REVERT: B 592 THR cc_start: 0.8650 (OUTLIER) cc_final: 0.8271 (p) REVERT: B 642 MET cc_start: 0.7244 (OUTLIER) cc_final: 0.6967 (ttm) REVERT: B 663 VAL cc_start: 0.9207 (OUTLIER) cc_final: 0.8952 (m) REVERT: B 871 LYS cc_start: 0.8325 (mmtt) cc_final: 0.8109 (mmmt) REVERT: B 876 VAL cc_start: 0.9122 (OUTLIER) cc_final: 0.8921 (t) REVERT: B 917 TRP cc_start: 0.8503 (t-100) cc_final: 0.8296 (t-100) REVERT: C 80 LYS cc_start: 0.7805 (ttpp) cc_final: 0.7574 (ttpp) REVERT: C 332 ASP cc_start: 0.8150 (m-30) cc_final: 0.7727 (m-30) REVERT: C 337 ASN cc_start: 0.7891 (t0) cc_final: 0.7545 (t0) REVERT: C 567 GLU cc_start: 0.8909 (pm20) cc_final: 0.8114 (pm20) REVERT: C 569 ASP cc_start: 0.7796 (OUTLIER) cc_final: 0.7514 (p0) REVERT: C 588 MET cc_start: 0.7443 (tpt) cc_final: 0.7221 (tpt) REVERT: C 592 THR cc_start: 0.8786 (OUTLIER) cc_final: 0.8578 (p) REVERT: C 642 MET cc_start: 0.7041 (OUTLIER) cc_final: 0.6833 (ttm) REVERT: C 755 MET cc_start: 0.7821 (ttp) cc_final: 0.7515 (ttp) REVERT: C 859 SER cc_start: 0.8613 (t) cc_final: 0.8216 (t) REVERT: C 888 TYR cc_start: 0.8851 (t80) cc_final: 0.8634 (t80) REVERT: C 901 ILE cc_start: 0.9204 (tt) cc_final: 0.8951 (tt) REVERT: C 916 TRP cc_start: 0.8636 (t60) cc_final: 0.8233 (t-100) outliers start: 106 outliers final: 72 residues processed: 786 average time/residue: 0.8855 time to fit residues: 1087.8386 Evaluate side-chains 790 residues out of total 2532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 709 time to evaluate : 3.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 229 TYR Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 566 ASN Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 759 THR Chi-restraints excluded: chain A residue 769 ASN Chi-restraints excluded: chain A residue 804 ILE Chi-restraints excluded: chain A residue 807 SER Chi-restraints excluded: chain A residue 881 MET Chi-restraints excluded: chain A residue 1002 THR Chi-restraints excluded: chain A residue 1010 SER Chi-restraints excluded: chain A residue 1027 SER Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 387 ASN Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 566 ASN Chi-restraints excluded: chain B residue 569 ASP Chi-restraints excluded: chain B residue 592 THR Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain B residue 642 MET Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 668 ASN Chi-restraints excluded: chain B residue 804 ILE Chi-restraints excluded: chain B residue 807 SER Chi-restraints excluded: chain B residue 808 THR Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 876 VAL Chi-restraints excluded: chain B residue 881 MET Chi-restraints excluded: chain B residue 1002 THR Chi-restraints excluded: chain B residue 1010 SER Chi-restraints excluded: chain B residue 1026 LEU Chi-restraints excluded: chain B residue 1027 SER Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 229 TYR Chi-restraints excluded: chain C residue 266 GLN Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 566 ASN Chi-restraints excluded: chain C residue 569 ASP Chi-restraints excluded: chain C residue 592 THR Chi-restraints excluded: chain C residue 622 GLU Chi-restraints excluded: chain C residue 642 MET Chi-restraints excluded: chain C residue 722 ARG Chi-restraints excluded: chain C residue 759 THR Chi-restraints excluded: chain C residue 804 ILE Chi-restraints excluded: chain C residue 807 SER Chi-restraints excluded: chain C residue 815 THR Chi-restraints excluded: chain C residue 881 MET Chi-restraints excluded: chain C residue 1002 THR Chi-restraints excluded: chain C residue 1027 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 246 optimal weight: 10.0000 chunk 167 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 chunk 220 optimal weight: 6.9990 chunk 122 optimal weight: 10.0000 chunk 252 optimal weight: 9.9990 chunk 204 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 151 optimal weight: 0.8980 chunk 265 optimal weight: 6.9990 chunk 74 optimal weight: 7.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.4776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 24144 Z= 0.256 Angle : 0.581 6.011 32877 Z= 0.300 Chirality : 0.042 0.187 3903 Planarity : 0.004 0.051 4137 Dihedral : 4.143 47.128 3298 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.99 % Allowed : 21.88 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.16), residues: 3063 helix: 1.01 (0.13), residues: 1707 sheet: -1.49 (0.23), residues: 465 loop : -2.18 (0.20), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 535 HIS 0.003 0.001 HIS C 423 PHE 0.011 0.001 PHE C 85 TYR 0.016 0.001 TYR B 484 ARG 0.007 0.000 ARG C 829 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 831 residues out of total 2532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 730 time to evaluate : 3.584 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: A 33 ASN cc_start: 0.8287 (t0) cc_final: 0.8006 (t0) REVERT: A 109 ARG cc_start: 0.8671 (mmp80) cc_final: 0.8227 (mmm160) REVERT: A 194 GLN cc_start: 0.7020 (mm110) cc_final: 0.6762 (mm110) REVERT: A 216 GLU cc_start: 0.6952 (OUTLIER) cc_final: 0.6421 (tt0) REVERT: A 238 GLN cc_start: 0.7862 (mm110) cc_final: 0.7513 (mm-40) REVERT: A 441 ASP cc_start: 0.6957 (m-30) cc_final: 0.6709 (m-30) REVERT: A 592 THR cc_start: 0.8909 (OUTLIER) cc_final: 0.8600 (p) REVERT: A 617 ASP cc_start: 0.8313 (t0) cc_final: 0.8099 (t0) REVERT: A 859 SER cc_start: 0.8621 (t) cc_final: 0.8294 (t) REVERT: A 916 TRP cc_start: 0.8741 (t60) cc_final: 0.8274 (t-100) REVERT: B 158 SER cc_start: 0.8552 (t) cc_final: 0.8346 (m) REVERT: B 345 GLU cc_start: 0.8706 (mt-10) cc_final: 0.8156 (tt0) REVERT: B 567 GLU cc_start: 0.8922 (pm20) cc_final: 0.8108 (pm20) REVERT: B 592 THR cc_start: 0.8653 (OUTLIER) cc_final: 0.8297 (p) REVERT: B 623 MET cc_start: 0.8059 (ttt) cc_final: 0.7713 (ttm) REVERT: B 625 GLU cc_start: 0.7658 (tt0) cc_final: 0.7455 (tt0) REVERT: B 663 VAL cc_start: 0.9206 (OUTLIER) cc_final: 0.8946 (m) REVERT: B 876 VAL cc_start: 0.9125 (OUTLIER) cc_final: 0.8859 (t) REVERT: B 917 TRP cc_start: 0.8451 (t-100) cc_final: 0.8240 (t-100) REVERT: C 80 LYS cc_start: 0.7834 (ttpp) cc_final: 0.7605 (ttpp) REVERT: C 158 SER cc_start: 0.8589 (t) cc_final: 0.8269 (m) REVERT: C 295 LYS cc_start: 0.9109 (mmtt) cc_final: 0.8909 (mmtt) REVERT: C 332 ASP cc_start: 0.8200 (m-30) cc_final: 0.7825 (m-30) REVERT: C 337 ASN cc_start: 0.7848 (t0) cc_final: 0.7507 (t0) REVERT: C 567 GLU cc_start: 0.8898 (pm20) cc_final: 0.8029 (pm20) REVERT: C 569 ASP cc_start: 0.7801 (OUTLIER) cc_final: 0.7529 (p0) REVERT: C 588 MET cc_start: 0.7493 (tpt) cc_final: 0.7248 (tpt) REVERT: C 592 THR cc_start: 0.8845 (OUTLIER) cc_final: 0.8575 (p) REVERT: C 642 MET cc_start: 0.7240 (OUTLIER) cc_final: 0.6786 (ttm) REVERT: C 722 ARG cc_start: 0.7989 (OUTLIER) cc_final: 0.7654 (mtt90) REVERT: C 755 MET cc_start: 0.7721 (ttp) cc_final: 0.7354 (ttp) REVERT: C 829 ARG cc_start: 0.8335 (mtm-85) cc_final: 0.8113 (mtm-85) REVERT: C 859 SER cc_start: 0.8565 (t) cc_final: 0.8190 (t) REVERT: C 901 ILE cc_start: 0.9167 (tt) cc_final: 0.8915 (tt) REVERT: C 916 TRP cc_start: 0.8691 (t60) cc_final: 0.8250 (t-100) outliers start: 101 outliers final: 73 residues processed: 771 average time/residue: 0.8796 time to fit residues: 1055.3435 Evaluate side-chains 803 residues out of total 2532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 721 time to evaluate : 3.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 566 ASN Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 722 ARG Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 804 ILE Chi-restraints excluded: chain A residue 881 MET Chi-restraints excluded: chain A residue 1002 THR Chi-restraints excluded: chain A residue 1010 SER Chi-restraints excluded: chain A residue 1025 LEU Chi-restraints excluded: chain A residue 1027 SER Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 387 ASN Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 566 ASN Chi-restraints excluded: chain B residue 569 ASP Chi-restraints excluded: chain B residue 592 THR Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 668 ASN Chi-restraints excluded: chain B residue 722 ARG Chi-restraints excluded: chain B residue 807 SER Chi-restraints excluded: chain B residue 808 THR Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 876 VAL Chi-restraints excluded: chain B residue 881 MET Chi-restraints excluded: chain B residue 998 ILE Chi-restraints excluded: chain B residue 1002 THR Chi-restraints excluded: chain B residue 1010 SER Chi-restraints excluded: chain B residue 1027 SER Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 266 GLN Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 566 ASN Chi-restraints excluded: chain C residue 569 ASP Chi-restraints excluded: chain C residue 592 THR Chi-restraints excluded: chain C residue 622 GLU Chi-restraints excluded: chain C residue 642 MET Chi-restraints excluded: chain C residue 722 ARG Chi-restraints excluded: chain C residue 804 ILE Chi-restraints excluded: chain C residue 807 SER Chi-restraints excluded: chain C residue 815 THR Chi-restraints excluded: chain C residue 881 MET Chi-restraints excluded: chain C residue 942 VAL Chi-restraints excluded: chain C residue 1002 THR Chi-restraints excluded: chain C residue 1025 LEU Chi-restraints excluded: chain C residue 1027 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 99 optimal weight: 8.9990 chunk 266 optimal weight: 9.9990 chunk 58 optimal weight: 6.9990 chunk 173 optimal weight: 9.9990 chunk 73 optimal weight: 10.0000 chunk 296 optimal weight: 7.9990 chunk 245 optimal weight: 10.0000 chunk 137 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 97 optimal weight: 8.9990 chunk 155 optimal weight: 10.0000 overall best weight: 8.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 ASN B 87 GLN B 214 ASN B 296 ASN C 87 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.5536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 24144 Z= 0.494 Angle : 0.720 7.315 32877 Z= 0.383 Chirality : 0.047 0.194 3903 Planarity : 0.006 0.089 4137 Dihedral : 4.683 47.364 3298 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 4.98 % Allowed : 22.55 % Favored : 72.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.92 % 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: -0.98 (0.15), residues: 3063 helix: 0.49 (0.13), residues: 1716 sheet: -1.51 (0.24), residues: 474 loop : -2.30 (0.20), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 535 HIS 0.007 0.002 HIS C 359 PHE 0.029 0.002 PHE A 480 TYR 0.019 0.002 TYR B 484 ARG 0.005 0.001 ARG A 980 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 879 residues out of total 2532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 753 time to evaluate : 3.832 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: A 5 ILE cc_start: 0.6018 (tp) cc_final: 0.5774 (tp) REVERT: A 33 ASN cc_start: 0.8285 (t0) cc_final: 0.7987 (t0) REVERT: A 109 ARG cc_start: 0.8741 (mmp80) cc_final: 0.8256 (mmm160) REVERT: A 173 ASP cc_start: 0.8245 (OUTLIER) cc_final: 0.7944 (t0) REVERT: A 216 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.6885 (tt0) REVERT: A 238 GLN cc_start: 0.7931 (mm110) cc_final: 0.7633 (mm-40) REVERT: A 245 HIS cc_start: 0.7488 (m-70) cc_final: 0.7215 (m-70) REVERT: A 299 GLU cc_start: 0.7872 (mt-10) cc_final: 0.7668 (mt-10) REVERT: A 499 ILE cc_start: 0.8968 (mt) cc_final: 0.8697 (mt) REVERT: A 769 ASN cc_start: 0.8417 (OUTLIER) cc_final: 0.8090 (t0) REVERT: A 859 SER cc_start: 0.8605 (t) cc_final: 0.8091 (t) REVERT: A 875 MET cc_start: 0.8035 (ttp) cc_final: 0.7825 (ttp) REVERT: B 5 ILE cc_start: 0.5804 (tp) cc_final: 0.5591 (tp) REVERT: B 158 SER cc_start: 0.8777 (t) cc_final: 0.8538 (m) REVERT: B 192 ASP cc_start: 0.7135 (t0) cc_final: 0.6673 (m-30) REVERT: B 216 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.6621 (tm-30) REVERT: B 283 GLU cc_start: 0.8763 (mt-10) cc_final: 0.8338 (mt-10) REVERT: B 567 GLU cc_start: 0.8898 (pm20) cc_final: 0.8180 (pm20) REVERT: B 570 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8795 (pt) REVERT: B 591 LYS cc_start: 0.8495 (ptpp) cc_final: 0.8288 (ptpp) REVERT: B 663 VAL cc_start: 0.9222 (OUTLIER) cc_final: 0.8961 (m) REVERT: B 876 VAL cc_start: 0.9165 (OUTLIER) cc_final: 0.8894 (t) REVERT: B 917 TRP cc_start: 0.8534 (t-100) cc_final: 0.8334 (t-100) REVERT: B 939 GLU cc_start: 0.8864 (tm-30) cc_final: 0.8661 (tm-30) REVERT: C 5 ILE cc_start: 0.6040 (tp) cc_final: 0.5830 (tp) REVERT: C 80 LYS cc_start: 0.8068 (ttpp) cc_final: 0.7837 (ttpp) REVERT: C 132 ASP cc_start: 0.8510 (t0) cc_final: 0.8297 (t0) REVERT: C 158 SER cc_start: 0.8729 (t) cc_final: 0.8519 (m) REVERT: C 216 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.6430 (tm-30) REVERT: C 332 ASP cc_start: 0.8220 (m-30) cc_final: 0.7856 (m-30) REVERT: C 337 ASN cc_start: 0.7921 (t0) cc_final: 0.7554 (t0) REVERT: C 345 GLU cc_start: 0.8742 (mt-10) cc_final: 0.8389 (tt0) REVERT: C 567 GLU cc_start: 0.8876 (pm20) cc_final: 0.8394 (pm20) REVERT: C 569 ASP cc_start: 0.8178 (OUTLIER) cc_final: 0.7895 (p0) REVERT: C 588 MET cc_start: 0.7661 (tpt) cc_final: 0.7382 (tpt) REVERT: C 592 THR cc_start: 0.8971 (OUTLIER) cc_final: 0.8617 (p) REVERT: C 859 SER cc_start: 0.8614 (t) cc_final: 0.8086 (t) REVERT: C 901 ILE cc_start: 0.9262 (tt) cc_final: 0.9018 (tt) REVERT: C 916 TRP cc_start: 0.8724 (t60) cc_final: 0.8298 (t60) outliers start: 126 outliers final: 100 residues processed: 808 average time/residue: 0.8781 time to fit residues: 1104.0210 Evaluate side-chains 846 residues out of total 2532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 736 time to evaluate : 4.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 566 ASN Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 668 ASN Chi-restraints excluded: chain A residue 722 ARG Chi-restraints excluded: chain A residue 769 ASN Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 804 ILE Chi-restraints excluded: chain A residue 807 SER Chi-restraints excluded: chain A residue 815 THR Chi-restraints excluded: chain A residue 854 THR Chi-restraints excluded: chain A residue 881 MET Chi-restraints excluded: chain A residue 942 VAL Chi-restraints excluded: chain A residue 1002 THR Chi-restraints excluded: chain A residue 1010 SER Chi-restraints excluded: chain A residue 1025 LEU Chi-restraints excluded: chain A residue 1027 SER Chi-restraints excluded: chain A residue 1031 ILE Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 173 ASP Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain B residue 266 GLN Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 387 ASN Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 569 ASP Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 592 THR Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 668 ASN Chi-restraints excluded: chain B residue 722 ARG Chi-restraints excluded: chain B residue 800 ASP Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 804 ILE Chi-restraints excluded: chain B residue 807 SER Chi-restraints excluded: chain B residue 808 THR Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 876 VAL Chi-restraints excluded: chain B residue 881 MET Chi-restraints excluded: chain B residue 942 VAL Chi-restraints excluded: chain B residue 998 ILE Chi-restraints excluded: chain B residue 1002 THR Chi-restraints excluded: chain B residue 1010 SER Chi-restraints excluded: chain B residue 1025 LEU Chi-restraints excluded: chain B residue 1026 LEU Chi-restraints excluded: chain B residue 1027 SER Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 108 SER Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 266 GLN Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 566 ASN Chi-restraints excluded: chain C residue 569 ASP Chi-restraints excluded: chain C residue 592 THR Chi-restraints excluded: chain C residue 622 GLU Chi-restraints excluded: chain C residue 722 ARG Chi-restraints excluded: chain C residue 743 VAL Chi-restraints excluded: chain C residue 759 THR Chi-restraints excluded: chain C residue 801 VAL Chi-restraints excluded: chain C residue 804 ILE Chi-restraints excluded: chain C residue 807 SER Chi-restraints excluded: chain C residue 815 THR Chi-restraints excluded: chain C residue 881 MET Chi-restraints excluded: chain C residue 942 VAL Chi-restraints excluded: chain C residue 1002 THR Chi-restraints excluded: chain C residue 1027 SER Chi-restraints excluded: chain C residue 1031 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 285 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 chunk 168 optimal weight: 0.8980 chunk 216 optimal weight: 2.9990 chunk 167 optimal weight: 3.9990 chunk 249 optimal weight: 0.8980 chunk 165 optimal weight: 4.9990 chunk 294 optimal weight: 5.9990 chunk 184 optimal weight: 9.9990 chunk 179 optimal weight: 10.0000 chunk 136 optimal weight: 6.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 214 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.5602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24144 Z= 0.214 Angle : 0.587 6.009 32877 Z= 0.303 Chirality : 0.042 0.154 3903 Planarity : 0.005 0.058 4137 Dihedral : 4.346 47.426 3298 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.63 % Allowed : 24.49 % Favored : 71.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.28 % 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: -0.52 (0.16), residues: 3063 helix: 0.95 (0.13), residues: 1698 sheet: -1.50 (0.24), residues: 462 loop : -2.15 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 535 HIS 0.003 0.001 HIS C 423 PHE 0.018 0.001 PHE A 475 TYR 0.011 0.001 TYR B 140 ARG 0.006 0.000 ARG C 109 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 845 residues out of total 2532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 753 time to evaluate : 3.520 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: A 5 ILE cc_start: 0.6124 (tp) cc_final: 0.5889 (tp) REVERT: A 33 ASN cc_start: 0.8244 (t0) cc_final: 0.7964 (t0) REVERT: A 161 ASP cc_start: 0.8646 (m-30) cc_final: 0.7841 (m-30) REVERT: A 173 ASP cc_start: 0.8257 (OUTLIER) cc_final: 0.7738 (t0) REVERT: A 238 GLN cc_start: 0.7920 (mm110) cc_final: 0.7627 (mm-40) REVERT: A 245 HIS cc_start: 0.7341 (m-70) cc_final: 0.6953 (m-70) REVERT: A 283 GLU cc_start: 0.8637 (mt-10) cc_final: 0.8410 (mt-10) REVERT: A 499 ILE cc_start: 0.8972 (mt) cc_final: 0.8698 (mt) REVERT: A 570 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8872 (pt) REVERT: A 769 ASN cc_start: 0.8468 (t0) cc_final: 0.8107 (t0) REVERT: A 859 SER cc_start: 0.8563 (t) cc_final: 0.8224 (t) REVERT: B 158 SER cc_start: 0.8579 (t) cc_final: 0.8378 (m) REVERT: B 173 ASP cc_start: 0.8228 (OUTLIER) cc_final: 0.7960 (t0) REVERT: B 271 MET cc_start: 0.7580 (tpp) cc_final: 0.7118 (tpt) REVERT: B 345 GLU cc_start: 0.8728 (mt-10) cc_final: 0.8390 (tt0) REVERT: B 567 GLU cc_start: 0.8910 (pm20) cc_final: 0.8009 (pm20) REVERT: B 591 LYS cc_start: 0.8316 (ptpp) cc_final: 0.8085 (ptpp) REVERT: B 592 THR cc_start: 0.8695 (OUTLIER) cc_final: 0.8302 (p) REVERT: B 634 GLU cc_start: 0.7866 (pm20) cc_final: 0.7587 (pm20) REVERT: B 663 VAL cc_start: 0.9201 (OUTLIER) cc_final: 0.8942 (m) REVERT: B 819 ARG cc_start: 0.7453 (mtt180) cc_final: 0.7106 (mtm-85) REVERT: B 876 VAL cc_start: 0.9150 (OUTLIER) cc_final: 0.8893 (t) REVERT: C 5 ILE cc_start: 0.6140 (tp) cc_final: 0.5921 (tp) REVERT: C 80 LYS cc_start: 0.7989 (ttpp) cc_final: 0.7753 (ttpp) REVERT: C 158 SER cc_start: 0.8561 (t) cc_final: 0.8351 (m) REVERT: C 295 LYS cc_start: 0.9029 (mmtm) cc_final: 0.8690 (mmtp) REVERT: C 332 ASP cc_start: 0.8150 (m-30) cc_final: 0.7879 (m-30) REVERT: C 337 ASN cc_start: 0.7784 (t0) cc_final: 0.7428 (t0) REVERT: C 566 ASN cc_start: 0.8847 (OUTLIER) cc_final: 0.8475 (t0) REVERT: C 567 GLU cc_start: 0.8884 (pm20) cc_final: 0.8241 (pm20) REVERT: C 569 ASP cc_start: 0.7963 (OUTLIER) cc_final: 0.7725 (p0) REVERT: C 588 MET cc_start: 0.7538 (tpt) cc_final: 0.7276 (tpt) REVERT: C 592 THR cc_start: 0.8789 (OUTLIER) cc_final: 0.8487 (p) REVERT: C 594 LYS cc_start: 0.7435 (tptt) cc_final: 0.7210 (tppt) REVERT: C 663 VAL cc_start: 0.9203 (m) cc_final: 0.8988 (m) REVERT: C 755 MET cc_start: 0.7561 (ttp) cc_final: 0.7118 (ttp) REVERT: C 859 SER cc_start: 0.8595 (t) cc_final: 0.8269 (t) REVERT: C 916 TRP cc_start: 0.8725 (t60) cc_final: 0.8313 (t-100) outliers start: 92 outliers final: 76 residues processed: 789 average time/residue: 0.8453 time to fit residues: 1028.3581 Evaluate side-chains 827 residues out of total 2532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 742 time to evaluate : 3.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 358 TRP Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 566 ASN Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 722 ARG Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 804 ILE Chi-restraints excluded: chain A residue 807 SER Chi-restraints excluded: chain A residue 881 MET Chi-restraints excluded: chain A residue 1002 THR Chi-restraints excluded: chain A residue 1025 LEU Chi-restraints excluded: chain A residue 1027 SER Chi-restraints excluded: chain A residue 1031 ILE Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 173 ASP Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 358 TRP Chi-restraints excluded: chain B residue 383 PHE Chi-restraints excluded: chain B residue 387 ASN Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 569 ASP Chi-restraints excluded: chain B residue 592 THR Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 668 ASN Chi-restraints excluded: chain B residue 722 ARG Chi-restraints excluded: chain B residue 808 THR Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 876 VAL Chi-restraints excluded: chain B residue 881 MET Chi-restraints excluded: chain B residue 942 VAL Chi-restraints excluded: chain B residue 1002 THR Chi-restraints excluded: chain B residue 1010 SER Chi-restraints excluded: chain B residue 1025 LEU Chi-restraints excluded: chain B residue 1026 LEU Chi-restraints excluded: chain B residue 1027 SER Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 266 GLN Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 383 PHE Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 566 ASN Chi-restraints excluded: chain C residue 569 ASP Chi-restraints excluded: chain C residue 592 THR Chi-restraints excluded: chain C residue 622 GLU Chi-restraints excluded: chain C residue 801 VAL Chi-restraints excluded: chain C residue 881 MET Chi-restraints excluded: chain C residue 942 VAL Chi-restraints excluded: chain C residue 1002 THR Chi-restraints excluded: chain C residue 1025 LEU Chi-restraints excluded: chain C residue 1027 SER Chi-restraints excluded: chain C residue 1031 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 182 optimal weight: 6.9990 chunk 117 optimal weight: 8.9990 chunk 176 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 187 optimal weight: 7.9990 chunk 200 optimal weight: 2.9990 chunk 145 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 chunk 231 optimal weight: 1.9990 chunk 268 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.5685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24144 Z= 0.203 Angle : 0.566 5.981 32877 Z= 0.290 Chirality : 0.041 0.226 3903 Planarity : 0.004 0.050 4137 Dihedral : 4.083 29.236 3294 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.28 % Allowed : 24.92 % Favored : 71.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.16), residues: 3063 helix: 1.19 (0.13), residues: 1698 sheet: -1.44 (0.24), residues: 447 loop : -2.04 (0.20), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 535 HIS 0.002 0.001 HIS C 245 PHE 0.015 0.001 PHE B 163 TYR 0.009 0.001 TYR B 229 ARG 0.007 0.000 ARG B 109 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 828 residues out of total 2532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 745 time to evaluate : 3.493 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: A 5 ILE cc_start: 0.5819 (tp) cc_final: 0.5595 (tp) REVERT: A 33 ASN cc_start: 0.8213 (t0) cc_final: 0.7954 (t0) REVERT: A 161 ASP cc_start: 0.8578 (m-30) cc_final: 0.7829 (m-30) REVERT: A 173 ASP cc_start: 0.8179 (OUTLIER) cc_final: 0.7653 (t0) REVERT: A 238 GLN cc_start: 0.7914 (mm110) cc_final: 0.7637 (mm-40) REVERT: A 245 HIS cc_start: 0.7219 (m-70) cc_final: 0.6957 (m-70) REVERT: A 283 GLU cc_start: 0.8614 (mt-10) cc_final: 0.8375 (mt-10) REVERT: A 499 ILE cc_start: 0.8970 (mt) cc_final: 0.8700 (mt) REVERT: A 592 THR cc_start: 0.8591 (t) cc_final: 0.8371 (p) REVERT: A 722 ARG cc_start: 0.7733 (OUTLIER) cc_final: 0.7277 (mtm-85) REVERT: A 769 ASN cc_start: 0.8455 (t0) cc_final: 0.8063 (t0) REVERT: A 859 SER cc_start: 0.8564 (t) cc_final: 0.8152 (t) REVERT: B 158 SER cc_start: 0.8545 (t) cc_final: 0.8315 (m) REVERT: B 161 ASP cc_start: 0.8627 (m-30) cc_final: 0.7793 (m-30) REVERT: B 173 ASP cc_start: 0.8185 (OUTLIER) cc_final: 0.7905 (t0) REVERT: B 271 MET cc_start: 0.7581 (tpp) cc_final: 0.7122 (tpt) REVERT: B 283 GLU cc_start: 0.8718 (mt-10) cc_final: 0.8302 (mt-10) REVERT: B 567 GLU cc_start: 0.8918 (pm20) cc_final: 0.7898 (pm20) REVERT: B 592 THR cc_start: 0.8736 (OUTLIER) cc_final: 0.8298 (p) REVERT: B 623 MET cc_start: 0.8008 (ttt) cc_final: 0.7561 (ttm) REVERT: B 663 VAL cc_start: 0.9173 (OUTLIER) cc_final: 0.8915 (m) REVERT: B 819 ARG cc_start: 0.7482 (mtt180) cc_final: 0.7127 (mtm-85) REVERT: B 875 MET cc_start: 0.8083 (ttp) cc_final: 0.7732 (ttp) REVERT: B 876 VAL cc_start: 0.9142 (OUTLIER) cc_final: 0.8911 (t) REVERT: C 5 ILE cc_start: 0.6104 (tp) cc_final: 0.5871 (tp) REVERT: C 80 LYS cc_start: 0.7971 (ttpp) cc_final: 0.7753 (ttpp) REVERT: C 158 SER cc_start: 0.8545 (t) cc_final: 0.8330 (m) REVERT: C 161 ASP cc_start: 0.8582 (m-30) cc_final: 0.8072 (m-30) REVERT: C 295 LYS cc_start: 0.9046 (mmtm) cc_final: 0.8705 (mmtp) REVERT: C 332 ASP cc_start: 0.8209 (m-30) cc_final: 0.7956 (m-30) REVERT: C 337 ASN cc_start: 0.7759 (t0) cc_final: 0.7408 (t0) REVERT: C 567 GLU cc_start: 0.8885 (pm20) cc_final: 0.8404 (pm20) REVERT: C 569 ASP cc_start: 0.7930 (OUTLIER) cc_final: 0.7663 (p0) REVERT: C 570 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8672 (pt) REVERT: C 588 MET cc_start: 0.7546 (tpt) cc_final: 0.7264 (tpt) REVERT: C 592 THR cc_start: 0.8804 (OUTLIER) cc_final: 0.8463 (p) REVERT: C 594 LYS cc_start: 0.7398 (tptt) cc_final: 0.7197 (tppt) REVERT: C 755 MET cc_start: 0.7574 (ttp) cc_final: 0.7117 (ttp) REVERT: C 859 SER cc_start: 0.8680 (t) cc_final: 0.8307 (t) REVERT: C 873 LYS cc_start: 0.8732 (tttt) cc_final: 0.8336 (ttmt) REVERT: C 916 TRP cc_start: 0.8697 (t60) cc_final: 0.8311 (t-100) outliers start: 83 outliers final: 67 residues processed: 781 average time/residue: 0.8605 time to fit residues: 1047.9426 Evaluate side-chains 805 residues out of total 2532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 729 time to evaluate : 3.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 358 TRP Chi-restraints excluded: chain A residue 383 PHE Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 668 ASN Chi-restraints excluded: chain A residue 722 ARG Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 804 ILE Chi-restraints excluded: chain A residue 807 SER Chi-restraints excluded: chain A residue 881 MET Chi-restraints excluded: chain A residue 1002 THR Chi-restraints excluded: chain A residue 1010 SER Chi-restraints excluded: chain A residue 1025 LEU Chi-restraints excluded: chain A residue 1027 SER Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 173 ASP Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 358 TRP Chi-restraints excluded: chain B residue 383 PHE Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 569 ASP Chi-restraints excluded: chain B residue 592 THR Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 668 ASN Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 807 SER Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 876 VAL Chi-restraints excluded: chain B residue 881 MET Chi-restraints excluded: chain B residue 1002 THR Chi-restraints excluded: chain B residue 1010 SER Chi-restraints excluded: chain B residue 1025 LEU Chi-restraints excluded: chain B residue 1027 SER Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 266 GLN Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 569 ASP Chi-restraints excluded: chain C residue 570 LEU Chi-restraints excluded: chain C residue 592 THR Chi-restraints excluded: chain C residue 622 GLU Chi-restraints excluded: chain C residue 743 VAL Chi-restraints excluded: chain C residue 759 THR Chi-restraints excluded: chain C residue 801 VAL Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 881 MET Chi-restraints excluded: chain C residue 1002 THR Chi-restraints excluded: chain C residue 1027 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 282 optimal weight: 10.0000 chunk 257 optimal weight: 10.0000 chunk 274 optimal weight: 10.0000 chunk 165 optimal weight: 4.9990 chunk 119 optimal weight: 3.9990 chunk 215 optimal weight: 7.9990 chunk 84 optimal weight: 10.0000 chunk 248 optimal weight: 8.9990 chunk 259 optimal weight: 0.8980 chunk 273 optimal weight: 0.8980 chunk 180 optimal weight: 9.9990 overall best weight: 3.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.5822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 24144 Z= 0.240 Angle : 0.573 5.967 32877 Z= 0.295 Chirality : 0.042 0.152 3903 Planarity : 0.005 0.047 4137 Dihedral : 4.083 29.741 3294 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.32 % Allowed : 25.00 % Favored : 71.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.16), residues: 3063 helix: 1.21 (0.13), residues: 1701 sheet: -1.45 (0.24), residues: 462 loop : -2.04 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 535 HIS 0.002 0.001 HIS A 359 PHE 0.017 0.001 PHE C 163 TYR 0.008 0.001 TYR B 140 ARG 0.007 0.000 ARG B 109 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 823 residues out of total 2532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 739 time to evaluate : 3.517 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: A 5 ILE cc_start: 0.5843 (tp) cc_final: 0.5614 (tp) REVERT: A 33 ASN cc_start: 0.8179 (t0) cc_final: 0.7928 (t0) REVERT: A 161 ASP cc_start: 0.8566 (m-30) cc_final: 0.7799 (m-30) REVERT: A 238 GLN cc_start: 0.7902 (mm110) cc_final: 0.7633 (mm-40) REVERT: A 245 HIS cc_start: 0.7276 (m-70) cc_final: 0.7041 (m-70) REVERT: A 283 GLU cc_start: 0.8618 (mt-10) cc_final: 0.8373 (mt-10) REVERT: A 499 ILE cc_start: 0.8955 (mt) cc_final: 0.8690 (mt) REVERT: A 592 THR cc_start: 0.8606 (t) cc_final: 0.8358 (p) REVERT: A 722 ARG cc_start: 0.7771 (OUTLIER) cc_final: 0.7337 (mtm-85) REVERT: A 769 ASN cc_start: 0.8496 (OUTLIER) cc_final: 0.8103 (t0) REVERT: A 859 SER cc_start: 0.8588 (t) cc_final: 0.8181 (t) REVERT: B 158 SER cc_start: 0.8563 (t) cc_final: 0.8341 (m) REVERT: B 161 ASP cc_start: 0.8643 (m-30) cc_final: 0.7802 (m-30) REVERT: B 173 ASP cc_start: 0.8221 (OUTLIER) cc_final: 0.7965 (t0) REVERT: B 211 ASP cc_start: 0.7559 (p0) cc_final: 0.7115 (p0) REVERT: B 271 MET cc_start: 0.7603 (tpp) cc_final: 0.7128 (tpt) REVERT: B 283 GLU cc_start: 0.8724 (mt-10) cc_final: 0.8425 (mt-10) REVERT: B 345 GLU cc_start: 0.8728 (mt-10) cc_final: 0.8395 (tt0) REVERT: B 567 GLU cc_start: 0.8867 (pm20) cc_final: 0.7911 (pm20) REVERT: B 592 THR cc_start: 0.8780 (OUTLIER) cc_final: 0.8310 (p) REVERT: B 623 MET cc_start: 0.8019 (ttt) cc_final: 0.7525 (ttm) REVERT: B 663 VAL cc_start: 0.9179 (OUTLIER) cc_final: 0.8921 (m) REVERT: B 819 ARG cc_start: 0.7496 (mtt180) cc_final: 0.7136 (mtm-85) REVERT: B 875 MET cc_start: 0.8140 (ttp) cc_final: 0.7816 (ttp) REVERT: B 896 GLU cc_start: 0.7253 (OUTLIER) cc_final: 0.6739 (mp0) REVERT: C 5 ILE cc_start: 0.5889 (tp) cc_final: 0.5640 (tp) REVERT: C 132 ASP cc_start: 0.8376 (t0) cc_final: 0.8062 (t0) REVERT: C 158 SER cc_start: 0.8558 (t) cc_final: 0.8351 (m) REVERT: C 161 ASP cc_start: 0.8607 (m-30) cc_final: 0.8082 (m-30) REVERT: C 332 ASP cc_start: 0.8229 (m-30) cc_final: 0.7972 (m-30) REVERT: C 337 ASN cc_start: 0.7761 (t0) cc_final: 0.7413 (t0) REVERT: C 567 GLU cc_start: 0.8773 (pm20) cc_final: 0.8243 (pm20) REVERT: C 569 ASP cc_start: 0.7983 (OUTLIER) cc_final: 0.7710 (p0) REVERT: C 570 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8701 (pt) REVERT: C 588 MET cc_start: 0.7573 (tpt) cc_final: 0.7297 (tpt) REVERT: C 592 THR cc_start: 0.8825 (OUTLIER) cc_final: 0.8458 (p) REVERT: C 594 LYS cc_start: 0.7461 (tptt) cc_final: 0.7250 (tptt) REVERT: C 755 MET cc_start: 0.7528 (ttp) cc_final: 0.7056 (ttp) REVERT: C 859 SER cc_start: 0.8682 (t) cc_final: 0.8312 (t) REVERT: C 873 LYS cc_start: 0.8725 (tttt) cc_final: 0.8351 (ttmt) REVERT: C 916 TRP cc_start: 0.8698 (t60) cc_final: 0.8331 (t-100) outliers start: 84 outliers final: 72 residues processed: 778 average time/residue: 0.8389 time to fit residues: 1004.4468 Evaluate side-chains 815 residues out of total 2532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 734 time to evaluate : 3.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 358 TRP Chi-restraints excluded: chain A residue 383 PHE Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 566 ASN Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 668 ASN Chi-restraints excluded: chain A residue 722 ARG Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 769 ASN Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 807 SER Chi-restraints excluded: chain A residue 881 MET Chi-restraints excluded: chain A residue 1002 THR Chi-restraints excluded: chain A residue 1010 SER Chi-restraints excluded: chain A residue 1025 LEU Chi-restraints excluded: chain A residue 1027 SER Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 173 ASP Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 383 PHE Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 569 ASP Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 592 THR Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 668 ASN Chi-restraints excluded: chain B residue 722 ARG Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 807 SER Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 881 MET Chi-restraints excluded: chain B residue 896 GLU Chi-restraints excluded: chain B residue 1002 THR Chi-restraints excluded: chain B residue 1010 SER Chi-restraints excluded: chain B residue 1025 LEU Chi-restraints excluded: chain B residue 1027 SER Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 266 GLN Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 569 ASP Chi-restraints excluded: chain C residue 570 LEU Chi-restraints excluded: chain C residue 592 THR Chi-restraints excluded: chain C residue 622 GLU Chi-restraints excluded: chain C residue 743 VAL Chi-restraints excluded: chain C residue 759 THR Chi-restraints excluded: chain C residue 796 ILE Chi-restraints excluded: chain C residue 801 VAL Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 881 MET Chi-restraints excluded: chain C residue 1002 THR Chi-restraints excluded: chain C residue 1027 SER Chi-restraints excluded: chain C residue 1031 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 290 optimal weight: 8.9990 chunk 177 optimal weight: 4.9990 chunk 137 optimal weight: 8.9990 chunk 202 optimal weight: 5.9990 chunk 304 optimal weight: 0.8980 chunk 280 optimal weight: 10.0000 chunk 242 optimal weight: 8.9990 chunk 25 optimal weight: 0.4980 chunk 187 optimal weight: 6.9990 chunk 148 optimal weight: 0.9990 chunk 192 optimal weight: 3.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.5873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24144 Z= 0.184 Angle : 0.554 5.947 32877 Z= 0.282 Chirality : 0.041 0.189 3903 Planarity : 0.004 0.052 4137 Dihedral : 3.985 29.443 3294 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 3.08 % Allowed : 25.12 % Favored : 71.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.16), residues: 3063 helix: 1.34 (0.13), residues: 1701 sheet: -1.39 (0.24), residues: 462 loop : -1.99 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 162 HIS 0.002 0.000 HIS A 526 PHE 0.015 0.001 PHE B 163 TYR 0.010 0.001 TYR B 484 ARG 0.008 0.000 ARG B 109 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 819 residues out of total 2532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 741 time to evaluate : 3.577 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: A 5 ILE cc_start: 0.5845 (tp) cc_final: 0.5568 (tp) REVERT: A 33 ASN cc_start: 0.8054 (t0) cc_final: 0.7813 (t0) REVERT: A 238 GLN cc_start: 0.7910 (mm110) cc_final: 0.7624 (mm-40) REVERT: A 245 HIS cc_start: 0.7260 (m-70) cc_final: 0.7010 (m-70) REVERT: A 283 GLU cc_start: 0.8616 (mt-10) cc_final: 0.8371 (mt-10) REVERT: A 499 ILE cc_start: 0.8959 (mt) cc_final: 0.8694 (mt) REVERT: A 592 THR cc_start: 0.8593 (t) cc_final: 0.8369 (p) REVERT: A 722 ARG cc_start: 0.7714 (OUTLIER) cc_final: 0.7322 (mtm-85) REVERT: A 859 SER cc_start: 0.8564 (t) cc_final: 0.8286 (t) REVERT: B 161 ASP cc_start: 0.8624 (m-30) cc_final: 0.7821 (m-30) REVERT: B 173 ASP cc_start: 0.8111 (OUTLIER) cc_final: 0.7834 (t0) REVERT: B 211 ASP cc_start: 0.7560 (p0) cc_final: 0.7127 (p0) REVERT: B 271 MET cc_start: 0.7602 (tpp) cc_final: 0.7118 (tpt) REVERT: B 345 GLU cc_start: 0.8676 (mt-10) cc_final: 0.8323 (tt0) REVERT: B 567 GLU cc_start: 0.8861 (pm20) cc_final: 0.7860 (pm20) REVERT: B 592 THR cc_start: 0.8743 (OUTLIER) cc_final: 0.8286 (p) REVERT: B 623 MET cc_start: 0.8013 (ttt) cc_final: 0.7535 (ttm) REVERT: B 663 VAL cc_start: 0.9187 (OUTLIER) cc_final: 0.8929 (m) REVERT: B 819 ARG cc_start: 0.7495 (mtt180) cc_final: 0.7136 (mtm-85) REVERT: B 875 MET cc_start: 0.8094 (ttp) cc_final: 0.7783 (ttp) REVERT: C 5 ILE cc_start: 0.5886 (tp) cc_final: 0.5636 (tp) REVERT: C 158 SER cc_start: 0.8505 (t) cc_final: 0.8304 (m) REVERT: C 161 ASP cc_start: 0.8534 (m-30) cc_final: 0.8016 (m-30) REVERT: C 332 ASP cc_start: 0.8199 (m-30) cc_final: 0.7936 (m-30) REVERT: C 337 ASN cc_start: 0.7687 (t0) cc_final: 0.7339 (t0) REVERT: C 567 GLU cc_start: 0.8790 (pm20) cc_final: 0.8249 (pm20) REVERT: C 569 ASP cc_start: 0.7982 (OUTLIER) cc_final: 0.7705 (p0) REVERT: C 570 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8666 (pt) REVERT: C 592 THR cc_start: 0.8803 (OUTLIER) cc_final: 0.8451 (p) REVERT: C 755 MET cc_start: 0.7516 (ttp) cc_final: 0.7049 (ttp) REVERT: C 859 SER cc_start: 0.8667 (t) cc_final: 0.8422 (t) REVERT: C 873 LYS cc_start: 0.8708 (tttt) cc_final: 0.8337 (ttmt) REVERT: C 916 TRP cc_start: 0.8691 (t60) cc_final: 0.8323 (t-100) outliers start: 78 outliers final: 68 residues processed: 775 average time/residue: 0.8606 time to fit residues: 1030.3151 Evaluate side-chains 798 residues out of total 2532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 723 time to evaluate : 3.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 358 TRP Chi-restraints excluded: chain A residue 383 PHE Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 566 ASN Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 722 ARG Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 807 SER Chi-restraints excluded: chain A residue 881 MET Chi-restraints excluded: chain A residue 1002 THR Chi-restraints excluded: chain A residue 1010 SER Chi-restraints excluded: chain A residue 1025 LEU Chi-restraints excluded: chain A residue 1027 SER Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 173 ASP Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 358 TRP Chi-restraints excluded: chain B residue 383 PHE Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 569 ASP Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 592 THR Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 668 ASN Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 807 SER Chi-restraints excluded: chain B residue 808 THR Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 881 MET Chi-restraints excluded: chain B residue 1002 THR Chi-restraints excluded: chain B residue 1010 SER Chi-restraints excluded: chain B residue 1025 LEU Chi-restraints excluded: chain B residue 1027 SER Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 266 GLN Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 569 ASP Chi-restraints excluded: chain C residue 570 LEU Chi-restraints excluded: chain C residue 592 THR Chi-restraints excluded: chain C residue 622 GLU Chi-restraints excluded: chain C residue 743 VAL Chi-restraints excluded: chain C residue 801 VAL Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 881 MET Chi-restraints excluded: chain C residue 1002 THR Chi-restraints excluded: chain C residue 1027 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 9.9990 chunk 74 optimal weight: 0.9980 chunk 223 optimal weight: 8.9990 chunk 35 optimal weight: 8.9990 chunk 67 optimal weight: 10.0000 chunk 243 optimal weight: 5.9990 chunk 101 optimal weight: 6.9990 chunk 249 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 44 optimal weight: 7.9990 chunk 213 optimal weight: 6.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.151617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.127554 restraints weight = 103566.934| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.75 r_work: 0.3160 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.6061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 24144 Z= 0.307 Angle : 0.601 6.029 32877 Z= 0.312 Chirality : 0.042 0.157 3903 Planarity : 0.005 0.047 4137 Dihedral : 4.123 29.869 3294 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 3.75 % Allowed : 24.76 % Favored : 71.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.16), residues: 3063 helix: 1.18 (0.13), residues: 1704 sheet: -1.30 (0.24), residues: 453 loop : -2.07 (0.20), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 535 HIS 0.004 0.001 HIS C 245 PHE 0.017 0.001 PHE C 163 TYR 0.010 0.001 TYR C 974 ARG 0.009 0.001 ARG B 109 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15375.09 seconds wall clock time: 269 minutes 2.59 seconds (16142.59 seconds total)