Starting phenix.real_space_refine on Sat Feb 17 22:43:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kf7_22845/02_2024/7kf7_22845_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kf7_22845/02_2024/7kf7_22845.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kf7_22845/02_2024/7kf7_22845.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kf7_22845/02_2024/7kf7_22845.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kf7_22845/02_2024/7kf7_22845_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kf7_22845/02_2024/7kf7_22845_updated.pdb" } resolution = 2.8 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 ------------------------------------------------------------------------------- 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= 0.384 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 23451 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians Cu 1 5.60 5 S 108 5.16 5 C 15253 2.51 5 N 3945 2.21 5 O 4275 1.98 5 H 24324 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 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 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 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 14": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 102": "OD1" <-> "OD2" Residue "B ARG 107": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 109": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 132": "OD1" <-> "OD2" Residue "B TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 141": "OE1" <-> "OE2" Residue "B TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 146": "OD1" <-> "OD2" Residue "B ARG 147": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 155": "OD1" <-> "OD2" Residue "B ARG 157": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 167": "OE1" <-> "OE2" Residue "B ASP 173": "OD1" <-> "OD2" Residue "B GLU 176": "OE1" <-> "OE2" Residue "B TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 192": "OD1" <-> "OD2" Residue "B TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 211": "OD1" <-> "OD2" Residue "B ARG 232": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 242": "OD1" <-> "OD2" Residue "B TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 260": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 261": "OD1" <-> "OD2" Residue "B GLU 270": "OE1" <-> "OE2" 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 GLU 309": "OE1" <-> "OE2" Residue "B GLU 320": "OE1" <-> "OE2" Residue "B ARG 327": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 332": "OD1" <-> "OD2" Residue "B ASP 336": "OD1" <-> "OD2" Residue "B ARG 361": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 405": "OD1" <-> "OD2" Residue "B ARG 417": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 419": "OE1" <-> "OE2" Residue "B ASP 441": "OD1" <-> "OD2" Residue "B PHE 480": "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 TYR 525": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 601": "OE1" <-> "OE2" 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 622": "OE1" <-> "OE2" Residue "B GLU 647": "OE1" <-> "OE2" Residue "B ARG 654": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 671": "OD1" <-> "OD2" Residue "B ASP 692": "OD1" <-> "OD2" Residue "B GLU 698": "OE1" <-> "OE2" Residue "B ARG 717": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 722": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 723": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 730": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 731": "OE1" <-> "OE2" Residue "B ARG 735": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 746": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 ARG 777": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 784": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" 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 839": "OD1" <-> "OD2" Residue "B GLU 846": "OE1" <-> "OE2" Residue "B GLU 863": "OE1" <-> "OE2" Residue "B ARG 867": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 884": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 888": "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 GLU 939": "OE1" <-> "OE2" Residue "B ARG 949": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 970": "OD1" <-> "OD2" Residue "B GLU 971": "OE1" <-> "OE2" Residue "B TYR 974": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 PHE 1029": "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 85": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 GLU 128": "OE1" <-> "OE2" Residue "C GLU 141": "OE1" <-> "OE2" Residue "C ASP 146": "OD1" <-> "OD2" Residue "C ARG 147": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 157": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 176": "OE1" <-> "OE2" Residue "C TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 205": "OE1" <-> "OE2" Residue "C GLU 223": "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 ASP 241": "OD1" <-> "OD2" Residue "C ASP 242": "OD1" <-> "OD2" 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 GLU 270": "OE1" <-> "OE2" Residue "C ARG 272": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 277": "OE1" <-> "OE2" Residue "C ARG 292": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 298": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 299": "OE1" <-> "OE2" Residue "C TYR 325": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 326": "OD1" <-> "OD2" Residue "C ARG 327": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 345": "OE1" <-> "OE2" Residue "C PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 361": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 417": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 419": "OE1" <-> "OE2" Residue "C ASP 427": "OD1" <-> "OD2" Residue "C ASP 441": "OD1" <-> "OD2" 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 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 TYR 525": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 569": "OD1" <-> "OD2" Residue "C TYR 572": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 593": "OD1" <-> "OD2" Residue "C ARG 604": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ASP 617": "OD1" <-> "OD2" Residue "C GLU 625": "OE1" <-> "OE2" Residue "C GLU 648": "OE1" <-> "OE2" Residue "C ARG 654": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ASP 671": "OD1" <-> "OD2" Residue "C ASP 692": "OD1" <-> "OD2" Residue "C ASP 694": "OD1" <-> "OD2" Residue "C GLU 698": "OE1" <-> "OE2" Residue "C GLU 702": "OE1" <-> "OE2" Residue "C ARG 705": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 716": "OE1" <-> "OE2" 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 GLU 731": "OE1" <-> "OE2" Residue "C ARG 735": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 736": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 746": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 ARG 784": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 819": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ASP 827": "OD1" <-> "OD2" Residue "C ARG 829": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ASP 830": "OD1" <-> "OD2" Residue "C ARG 831": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 863": "OE1" <-> "OE2" Residue "C GLU 866": "OE1" <-> "OE2" Residue "C ARG 867": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 884": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 888": "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 PHE 906": "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 966": "OE1" <-> "OE2" Residue "C ASP 970": "OD1" <-> "OD2" Residue "C GLU 971": "OE1" <-> "OE2" Residue "C TYR 974": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 982": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" 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: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 47906 Number of models: 1 Model: "" Number of chains: 4 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: 15860 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1015, 15838 Classifications: {'peptide': 1015} Link IDs: {'PTRANS': 52, 'TRANS': 962} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 1015, 15838 Classifications: {'peptide': 1015} Link IDs: {'PTRANS': 52, 'TRANS': 962} Chain breaks: 2 bond proxies already assigned to first conformer: 15973 Chain: "C" Number of atoms: 16022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1025, 16022 Classifications: {'peptide': 1025} Link IDs: {'PTRANS': 53, 'TRANS': 971} Chain breaks: 1 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'CU1': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ALYS B 984 " occ=0.50 ... (42 atoms not shown) pdb=" HZ3BLYS B 984 " occ=0.50 Time building chain proxies: 19.53, per 1000 atoms: 0.41 Number of scatterers: 47906 At special positions: 0 Unit cell: (119.88, 125.28, 152.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cu 1 28.99 S 108 16.00 O 4275 8.00 N 3945 7.00 C 15253 6.00 H 24324 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: 29.60 Conformation dependent library (CDL) restraints added in 4.9 seconds 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5670 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 111 helices and 24 sheets defined 53.1% alpha, 12.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.56 Creating SS restraints... Processing helix chain 'A' and resid 7 through 11 Processing helix chain 'A' and resid 13 through 32 Processing helix chain 'A' and resid 58 through 64 Processing helix chain 'A' and resid 66 through 75 removed outlier: 3.606A pdb=" N LEU A 74 " --> pdb=" O THR A 70 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N SER A 75 " --> pdb=" O THR A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 120 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: 4.152A pdb=" N GLY A 119 " --> pdb=" O ASN A 115 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N LYS A 120 " --> pdb=" O GLN A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 137 No H-bonds generated for 'chain 'A' and resid 135 through 137' Processing helix chain 'A' and resid 153 through 167 removed outlier: 3.705A 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: 4.102A 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 193 through 199 removed outlier: 3.786A pdb=" N TYR A 199 " --> pdb=" O ARG A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 212 removed outlier: 3.789A pdb=" N ALA A 212 " --> pdb=" O SER A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 261 No H-bonds generated for 'chain 'A' and resid 259 through 261' Processing helix chain 'A' and resid 297 through 310 Processing helix chain 'A' and resid 328 through 357 Processing helix chain 'A' and resid 360 through 384 removed outlier: 4.545A pdb=" N SER A 369 " --> pdb=" O VAL A 365 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N LEU A 370 " --> pdb=" O ALA A 366 " (cutoff:3.500A) Proline residue: A 371 - end of helix Processing helix chain 'A' and resid 390 through 424 removed outlier: 5.039A pdb=" N GLY A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ALA A 402 " --> pdb=" O ILE A 398 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N ALA A 406 " --> pdb=" O ALA A 402 " (cutoff:3.500A) removed outlier: 4.454A 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 432 through 466 removed outlier: 3.813A pdb=" N VAL A 446 " --> pdb=" O ALA A 442 " (cutoff:3.500A) Proline residue: A 448 - end of helix Proline residue: A 463 - end of helix removed outlier: 5.323A pdb=" N THR A 466 " --> pdb=" O ILE A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 495 Proline residue: A 477 - end of helix Processing helix chain 'A' and resid 497 through 503 Processing helix chain 'A' and resid 518 through 534 Proline residue: A 527 - end of helix Processing helix chain 'A' and resid 536 through 550 removed outlier: 4.768A pdb=" N VAL A 550 " --> pdb=" O SER A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 555 No H-bonds generated for 'chain 'A' and resid 553 through 555' Processing helix chain 'A' and resid 582 through 598 removed outlier: 3.609A pdb=" N SER A 598 " --> pdb=" O LYS A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 652 Processing helix chain 'A' and resid 665 through 674 Processing helix chain 'A' and resid 690 through 706 removed outlier: 3.639A pdb=" N ARG A 705 " --> pdb=" O GLU A 701 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N THR A 706 " --> pdb=" O GLU A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 735 Processing helix chain 'A' and resid 740 through 748 removed outlier: 4.401A pdb=" N PHE A 746 " --> pdb=" O ASP A 742 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N VAL A 747 " --> pdb=" O VAL A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 774 through 776 No H-bonds generated for 'chain 'A' and resid 774 through 776' Processing helix chain 'A' and resid 780 through 783 No H-bonds generated for 'chain 'A' and resid 780 through 783' Processing helix chain 'A' and resid 833 through 846 Processing helix chain 'A' and resid 861 through 874 Processing helix chain 'A' and resid 876 through 891 removed outlier: 3.501A pdb=" N ALA A 890 " --> pdb=" O LEU A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 918 removed outlier: 4.377A pdb=" N SER A 903 " --> pdb=" O LEU A 899 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N VAL A 904 " --> pdb=" O ILE A 900 " (cutoff:3.500A) Proline residue: A 905 - end of helix Processing helix chain 'A' and resid 924 through 954 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) Processing helix chain 'A' and resid 967 through 977 removed outlier: 3.665A pdb=" N GLU A 971 " --> pdb=" O GLN A 967 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU A 973 " --> pdb=" O LEU A 969 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 999 removed outlier: 3.676A pdb=" N LEU A 995 " --> pdb=" O ILE A 991 " (cutoff:3.500A) Proline residue: A 997 - end of helix Processing helix chain 'A' and resid 1006 through 1039 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 7 through 10 No H-bonds generated for 'chain 'B' and resid 7 through 10' Processing helix chain 'B' and resid 13 through 32 Processing helix chain 'B' and resid 58 through 64 Processing helix chain 'B' and resid 66 through 75 removed outlier: 4.721A pdb=" N SER B 75 " --> pdb=" O THR B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 113 removed outlier: 3.801A pdb=" N TYR B 113 " --> pdb=" O ARG B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 162 Processing helix chain 'B' and resid 164 through 168 Processing helix chain 'B' and resid 193 through 199 Processing helix chain 'B' and resid 203 through 211 Processing helix chain 'B' and resid 240 through 244 Processing helix chain 'B' and resid 297 through 314 removed outlier: 4.595A pdb=" N SER B 313 " --> pdb=" O GLU B 309 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N SER B 314 " --> pdb=" O THR B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 356 Processing helix chain 'B' and resid 361 through 367 Processing helix chain 'B' and resid 369 through 384 removed outlier: 3.602A pdb=" N GLY B 373 " --> pdb=" O SER B 369 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU B 374 " --> pdb=" O LEU B 370 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN B 384 " --> pdb=" O VAL B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 394 Processing helix chain 'B' and resid 396 through 423 removed outlier: 3.694A pdb=" N GLY B 401 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ASP B 405 " --> pdb=" O GLY B 401 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N ALA B 406 " --> pdb=" O ALA B 402 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ALA B 407 " --> pdb=" O MET B 403 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLN B 422 " --> pdb=" O LEU B 418 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N HIS B 423 " --> pdb=" O GLU B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 466 removed outlier: 3.712A pdb=" N SER B 443 " --> pdb=" O ILE B 439 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N VAL B 446 " --> pdb=" O ALA B 442 " (cutoff:3.500A) Proline residue: B 448 - end of helix removed outlier: 4.646A pdb=" N PHE B 461 " --> pdb=" O ILE B 457 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N ILE B 462 " --> pdb=" O THR B 458 " (cutoff:3.500A) Proline residue: B 463 - end of helix Processing helix chain 'B' and resid 470 through 495 Proline residue: B 477 - end of helix Processing helix chain 'B' and resid 497 through 502 Processing helix chain 'B' and resid 518 through 556 Proline residue: B 527 - end of helix removed outlier: 3.537A pdb=" N HIS B 534 " --> pdb=" O LEU B 530 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N TRP B 535 " --> pdb=" O LYS B 531 " (cutoff:3.500A) Proline residue: B 536 - end of helix removed outlier: 4.479A pdb=" N LEU B 551 " --> pdb=" O VAL B 547 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N TRP B 552 " --> pdb=" O LEU B 548 " (cutoff:3.500A) Proline residue: B 553 - end of helix removed outlier: 3.559A pdb=" N LYS B 556 " --> pdb=" O TRP B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 598 removed outlier: 3.613A pdb=" N ALA B 586 " --> pdb=" O ALA B 582 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER B 598 " --> pdb=" O LYS B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 635 No H-bonds generated for 'chain 'B' and resid 633 through 635' Processing helix chain 'B' and resid 642 through 652 Processing helix chain 'B' and resid 665 through 673 Processing helix chain 'B' and resid 690 through 705 removed outlier: 3.864A pdb=" N GLN B 699 " --> pdb=" O ALA B 695 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLU B 702 " --> pdb=" O GLU B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 730 through 736 removed outlier: 4.201A pdb=" N TYR B 736 " --> pdb=" O LYS B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 740 through 749 removed outlier: 3.910A pdb=" N PHE B 746 " --> pdb=" O ASP B 742 " (cutoff:3.500A) Processing helix chain 'B' and resid 774 through 776 No H-bonds generated for 'chain 'B' and resid 774 through 776' Processing helix chain 'B' and resid 780 through 785 removed outlier: 3.885A pdb=" N GLN B 785 " --> pdb=" O GLN B 781 " (cutoff:3.500A) Processing helix chain 'B' and resid 833 through 847 removed outlier: 3.512A pdb=" N VAL B 837 " --> pdb=" O MET B 833 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N HIS B 838 " --> pdb=" O VAL B 834 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASP B 839 " --> pdb=" O SER B 835 " (cutoff:3.500A) Processing helix chain 'B' and resid 861 through 891 removed outlier: 3.923A pdb=" N GLU B 866 " --> pdb=" O GLU B 863 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ASN B 869 " --> pdb=" O GLU B 866 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N VAL B 876 " --> pdb=" O LYS B 873 " (cutoff:3.500A) Proline residue: B 877 - end of helix removed outlier: 4.347A pdb=" N VAL B 885 " --> pdb=" O ILE B 882 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N TYR B 888 " --> pdb=" O VAL B 885 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 918 Proline residue: B 905 - end of helix removed outlier: 4.291A pdb=" N LEU B 914 " --> pdb=" O GLY B 910 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N LEU B 915 " --> pdb=" O GLY B 911 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N TRP B 916 " --> pdb=" O ILE B 912 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N TRP B 917 " --> pdb=" O TRP B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 924 through 952 removed outlier: 3.534A pdb=" N TYR B 947 " --> pdb=" O VAL B 943 " (cutoff:3.500A) Processing helix chain 'B' and resid 955 through 960 removed outlier: 4.158A pdb=" N ASN B 960 " --> pdb=" O SER B 957 " (cutoff:3.500A) Processing helix chain 'B' and resid 967 through 999 removed outlier: 4.411A pdb=" N VAL B 978 " --> pdb=" O HIS B 975 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N LEU B 979 " --> pdb=" O GLY B 976 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL B 981 " --> pdb=" O VAL B 978 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ARG B 982 " --> pdb=" O LEU B 979 " (cutoff:3.500A) Proline residue: B 983 - end of helix removed outlier: 4.442A pdb=" N LEU B 996 " --> pdb=" O ALA B 993 " (cutoff:3.500A) Proline residue: B 997 - end of helix Processing helix chain 'B' and resid 1006 through 1021 Proline residue: B1015 - end of helix removed outlier: 4.412A pdb=" N ILE B1021 " --> pdb=" O ILE B1017 " (cutoff:3.500A) Processing helix chain 'B' and resid 1023 through 1036 removed outlier: 4.793A pdb=" N ILE B1031 " --> pdb=" O SER B1027 " (cutoff:3.500A) Proline residue: B1032 - end of helix Processing helix chain 'C' and resid 7 through 10 No H-bonds generated for 'chain 'C' and resid 7 through 10' Processing helix chain 'C' and resid 13 through 32 Processing helix chain 'C' and resid 58 through 64 Processing helix chain 'C' and resid 67 through 75 removed outlier: 3.640A pdb=" N THR C 72 " --> pdb=" O PRO C 68 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N SER C 75 " --> pdb=" O THR C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 117 removed outlier: 3.649A pdb=" N TYR C 113 " --> pdb=" O ARG C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 137 No H-bonds generated for 'chain 'C' and resid 135 through 137' Processing helix chain 'C' and resid 153 through 167 removed outlier: 4.054A pdb=" N LYS C 165 " --> pdb=" O ASP C 161 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N TYR C 166 " --> pdb=" O TRP C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 199 Processing helix chain 'C' and resid 203 through 210 Processing helix chain 'C' and resid 240 through 245 removed outlier: 3.823A pdb=" N HIS C 245 " --> pdb=" O ASP C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 310 Processing helix chain 'C' and resid 328 through 357 Processing helix chain 'C' and resid 360 through 384 removed outlier: 4.638A pdb=" N SER C 369 " --> pdb=" O VAL C 365 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N LEU C 370 " --> pdb=" O ALA C 366 " (cutoff:3.500A) Proline residue: C 371 - end of helix Processing helix chain 'C' and resid 390 through 424 removed outlier: 5.059A pdb=" N GLY C 401 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ALA C 402 " --> pdb=" O ILE C 398 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N ALA C 406 " --> pdb=" O ALA C 402 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ALA C 407 " --> pdb=" O MET C 403 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N MET C 410 " --> pdb=" O ALA C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 466 removed outlier: 3.823A pdb=" N VAL C 446 " --> pdb=" O ALA C 442 " (cutoff:3.500A) Proline residue: C 448 - end of helix Proline residue: C 463 - end of helix removed outlier: 5.535A pdb=" N THR C 466 " --> pdb=" O ILE C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 495 Proline residue: C 477 - end of helix Processing helix chain 'C' and resid 497 through 503 Processing helix chain 'C' and resid 518 through 534 Proline residue: C 527 - end of helix Processing helix chain 'C' and resid 536 through 551 removed outlier: 4.440A pdb=" N VAL C 550 " --> pdb=" O SER C 546 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N LEU C 551 " --> pdb=" O VAL C 547 " (cutoff:3.500A) Processing helix chain 'C' and resid 553 through 556 No H-bonds generated for 'chain 'C' and resid 553 through 556' Processing helix chain 'C' and resid 582 through 598 removed outlier: 3.941A pdb=" N SER C 598 " --> pdb=" O LYS C 594 " (cutoff:3.500A) Processing helix chain 'C' and resid 633 through 635 No H-bonds generated for 'chain 'C' and resid 633 through 635' Processing helix chain 'C' and resid 642 through 652 Processing helix chain 'C' and resid 665 through 674 Processing helix chain 'C' and resid 690 through 706 removed outlier: 3.667A pdb=" N ARG C 705 " --> pdb=" O GLU C 701 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N THR C 706 " --> pdb=" O GLU C 702 " (cutoff:3.500A) Processing helix chain 'C' and resid 730 through 735 Processing helix chain 'C' and resid 740 through 748 removed outlier: 4.676A pdb=" N PHE C 746 " --> pdb=" O ASP C 742 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N VAL C 747 " --> pdb=" O VAL C 743 " (cutoff:3.500A) Processing helix chain 'C' and resid 774 through 776 No H-bonds generated for 'chain 'C' and resid 774 through 776' Processing helix chain 'C' and resid 780 through 783 No H-bonds generated for 'chain 'C' and resid 780 through 783' Processing helix chain 'C' and resid 834 through 846 Processing helix chain 'C' and resid 862 through 874 Processing helix chain 'C' and resid 876 through 891 Processing helix chain 'C' and resid 894 through 918 removed outlier: 4.334A pdb=" N SER C 903 " --> pdb=" O LEU C 899 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N VAL C 904 " --> pdb=" O ILE C 900 " (cutoff:3.500A) Proline residue: C 905 - end of helix Processing helix chain 'C' and resid 924 through 954 removed outlier: 4.210A pdb=" N GLY C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL C 936 " --> pdb=" O ALA C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 967 through 977 Processing helix chain 'C' and resid 982 through 1000 Proline residue: C 997 - end of helix Processing helix chain 'C' and resid 1006 through 1019 Proline residue: C1015 - end of helix Processing helix chain 'C' and resid 1023 through 1039 removed outlier: 4.410A pdb=" N PHE C1029 " --> pdb=" O LEU C1025 " (cutoff:3.500A) Proline residue: C1032 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 46 through 52 Processing sheet with id= B, first strand: chain 'A' and resid 263 through 269 removed outlier: 3.656A pdb=" N ARG A 771 " --> pdb=" O VAL A 189 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE A 191 " --> pdb=" O ARG A 771 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 221 through 223 Processing sheet with id= D, first strand: chain 'A' and resid 274 through 277 Processing sheet with id= E, first strand: chain 'A' and resid 569 through 572 removed outlier: 3.521A pdb=" N PHE A 606 " --> pdb=" O THR A 627 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG A 604 " --> pdb=" O GLN A 629 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 855 through 860 removed outlier: 3.626A pdb=" N GLY A 682 " --> pdb=" O SER A 859 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ILE A 681 " --> pdb=" O ILE A 826 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 721 through 728 Processing sheet with id= H, first strand: chain 'A' and resid 758 through 761 Processing sheet with id= I, first strand: chain 'A' and resid 319 through 326 removed outlier: 6.614A pdb=" N GLU A 141 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ASP A 326 " --> pdb=" O ILE A 139 " (cutoff:3.500A) removed outlier: 8.747A pdb=" N ILE A 139 " --> pdb=" O ASP A 326 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL A 289 " --> pdb=" O ILE A 139 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N GLU A 141 " --> pdb=" O GLY A 287 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N GLY A 287 " --> pdb=" O GLU A 141 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ALA A 143 " --> pdb=" O ALA A 285 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ALA A 285 " --> pdb=" O ALA A 143 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 46 through 52 Processing sheet with id= K, first strand: chain 'B' and resid 263 through 269 Processing sheet with id= L, first strand: chain 'B' and resid 274 through 277 removed outlier: 6.706A pdb=" N GLN B 629 " --> pdb=" O ALA B 603 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N VAL B 605 " --> pdb=" O THR B 627 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N THR B 627 " --> pdb=" O VAL B 605 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N GLY B 607 " --> pdb=" O GLU B 625 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLU B 625 " --> pdb=" O GLY B 607 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 821 through 826 Processing sheet with id= N, first strand: chain 'B' and resid 758 through 760 Processing sheet with id= O, first strand: chain 'B' and resid 319 through 325 removed outlier: 6.333A pdb=" N GLU B 141 " --> pdb=" O THR B 324 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL B 289 " --> pdb=" O ILE B 139 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLU B 141 " --> pdb=" O GLY B 287 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N GLY B 287 " --> pdb=" O GLU B 141 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ALA B 143 " --> pdb=" O ALA B 285 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ALA B 285 " --> pdb=" O ALA B 143 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU B 176 " --> pdb=" O ILE B 290 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 719 through 728 removed outlier: 5.988A pdb=" N GLY B 809 " --> pdb=" O GLY B 720 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N ARG B 722 " --> pdb=" O SER B 807 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N SER B 807 " --> pdb=" O ARG B 722 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ILE B 724 " --> pdb=" O LYS B 805 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N LYS B 805 " --> pdb=" O ILE B 724 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N VAL B 726 " --> pdb=" O ASP B 803 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N ASP B 803 " --> pdb=" O VAL B 726 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 46 through 52 Processing sheet with id= R, first strand: chain 'C' and resid 185 through 191 Processing sheet with id= S, first strand: chain 'C' and resid 220 through 223 removed outlier: 4.363A pdb=" N SER C 220 " --> pdb=" O VAL C 231 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 274 through 277 removed outlier: 6.914A pdb=" N GLN C 629 " --> pdb=" O ALA C 603 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N VAL C 605 " --> pdb=" O THR C 627 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N THR C 627 " --> pdb=" O VAL C 605 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N GLY C 607 " --> pdb=" O GLU C 625 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N GLU C 625 " --> pdb=" O GLY C 607 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 856 through 860 removed outlier: 3.884A pdb=" N GLY C 682 " --> pdb=" O SER C 859 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ILE C 681 " --> pdb=" O ILE C 826 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE C 826 " --> pdb=" O ILE C 681 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'C' and resid 721 through 728 removed outlier: 3.634A pdb=" N SER C 807 " --> pdb=" O TYR C 723 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'C' and resid 758 through 761 Processing sheet with id= X, first strand: chain 'C' and resid 319 through 326 removed outlier: 6.593A pdb=" N GLU C 141 " --> pdb=" O THR C 324 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ASP C 326 " --> pdb=" O ILE C 139 " (cutoff:3.500A) removed outlier: 8.779A pdb=" N ILE C 139 " --> pdb=" O ASP C 326 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N VAL C 289 " --> pdb=" O ILE C 139 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N GLU C 141 " --> pdb=" O GLY C 287 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N GLY C 287 " --> pdb=" O GLU C 141 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N ALA C 143 " --> pdb=" O ALA C 285 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ALA C 285 " --> pdb=" O ALA C 143 " (cutoff:3.500A) 1187 hydrogen bonds defined for protein. 3387 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: 16.20 Time building geometry restraints manager: 31.33 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: 24318 1.03 - 1.23: 37 1.23 - 1.42: 9537 1.42 - 1.62: 14288 1.62 - 1.81: 210 Bond restraints: 48390 Sorted by residual: bond pdb=" N HIS C 526 " pdb=" CA HIS C 526 " ideal model delta sigma weight residual 1.461 1.496 -0.035 9.20e-03 1.18e+04 1.42e+01 bond pdb=" N LEU B 562 " pdb=" CA LEU B 562 " ideal model delta sigma weight residual 1.453 1.482 -0.029 8.30e-03 1.45e+04 1.24e+01 bond pdb=" C GLY B 469 " pdb=" O GLY B 469 " ideal model delta sigma weight residual 1.235 1.189 0.045 1.35e-02 5.49e+03 1.13e+01 bond pdb=" N VAL A 876 " pdb=" CA VAL A 876 " ideal model delta sigma weight residual 1.461 1.502 -0.041 1.23e-02 6.61e+03 1.09e+01 bond pdb=" C GLU B 625 " pdb=" O GLU B 625 " ideal model delta sigma weight residual 1.236 1.200 0.036 1.14e-02 7.69e+03 1.02e+01 ... (remaining 48385 not shown) Histogram of bond angle deviations from ideal: 100.31 - 108.38: 13746 108.38 - 116.45: 51160 116.45 - 124.52: 20385 124.52 - 132.59: 2711 132.59 - 140.66: 62 Bond angle restraints: 88064 Sorted by residual: angle pdb=" C LEU B 562 " pdb=" N PRO B 563 " pdb=" CA PRO B 563 " ideal model delta sigma weight residual 120.52 108.23 12.29 9.90e-01 1.02e+00 1.54e+02 angle pdb=" C ARG A 637 " pdb=" N PRO A 638 " pdb=" CA PRO A 638 " ideal model delta sigma weight residual 119.76 111.09 8.67 1.00e+00 1.00e+00 7.52e+01 angle pdb=" N GLN B 437 " pdb=" CA GLN B 437 " pdb=" C GLN B 437 " ideal model delta sigma weight residual 113.18 104.30 8.88 1.21e+00 6.83e-01 5.39e+01 angle pdb=" N LEU B 718 " pdb=" CA LEU B 718 " pdb=" C LEU B 718 " ideal model delta sigma weight residual 113.02 104.98 8.04 1.20e+00 6.94e-01 4.49e+01 angle pdb=" C VAL B 707 " pdb=" N PRO B 708 " pdb=" CA PRO B 708 " ideal model delta sigma weight residual 119.84 127.94 -8.10 1.25e+00 6.40e-01 4.20e+01 ... (remaining 88059 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 20146 17.98 - 35.97: 1647 35.97 - 53.95: 615 53.95 - 71.93: 133 71.93 - 89.91: 16 Dihedral angle restraints: 22557 sinusoidal: 12479 harmonic: 10078 Sorted by residual: dihedral pdb=" CA VAL C 955 " pdb=" C VAL C 955 " pdb=" N PRO C 956 " pdb=" CA PRO C 956 " ideal model delta harmonic sigma weight residual -180.00 -154.25 -25.75 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" CA VAL A 955 " pdb=" C VAL A 955 " pdb=" N PRO A 956 " pdb=" CA PRO A 956 " ideal model delta harmonic sigma weight residual -180.00 -154.26 -25.74 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" CB GLU B 419 " pdb=" CG GLU B 419 " pdb=" CD GLU B 419 " pdb=" OE1 GLU B 419 " ideal model delta sinusoidal sigma weight residual 0.00 -89.77 89.77 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 22554 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 3301 0.059 - 0.119: 498 0.119 - 0.178: 79 0.178 - 0.238: 11 0.238 - 0.297: 2 Chirality restraints: 3891 Sorted by residual: chirality pdb=" CA VAL B 438 " pdb=" N VAL B 438 " pdb=" C VAL B 438 " pdb=" CB VAL B 438 " both_signs ideal model delta sigma weight residual False 2.44 2.74 -0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" CA ARG C 637 " pdb=" N ARG C 637 " pdb=" C ARG C 637 " pdb=" CB ARG C 637 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CA GLN B 564 " pdb=" N GLN B 564 " pdb=" C GLN B 564 " pdb=" CB GLN B 564 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 3888 not shown) Planarity restraints: 7027 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN B 470 " 0.183 2.00e-02 2.50e+03 2.02e-01 6.09e+02 pdb=" CD GLN B 470 " -0.015 2.00e-02 2.50e+03 pdb=" OE1 GLN B 470 " -0.173 2.00e-02 2.50e+03 pdb=" NE2 GLN B 470 " 0.001 2.00e-02 2.50e+03 pdb="HE21 GLN B 470 " -0.298 2.00e-02 2.50e+03 pdb="HE22 GLN B 470 " 0.302 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 633 " 0.167 2.00e-02 2.50e+03 1.85e-01 5.16e+02 pdb=" CD GLN A 633 " -0.009 2.00e-02 2.50e+03 pdb=" OE1 GLN A 633 " -0.165 2.00e-02 2.50e+03 pdb=" NE2 GLN A 633 " 0.002 2.00e-02 2.50e+03 pdb="HE21 GLN A 633 " -0.272 2.00e-02 2.50e+03 pdb="HE22 GLN A 633 " 0.277 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 437 " 0.165 2.00e-02 2.50e+03 1.80e-01 4.87e+02 pdb=" CD GLN B 437 " -0.013 2.00e-02 2.50e+03 pdb=" OE1 GLN B 437 " -0.158 2.00e-02 2.50e+03 pdb=" NE2 GLN B 437 " 0.002 2.00e-02 2.50e+03 pdb="HE21 GLN B 437 " -0.264 2.00e-02 2.50e+03 pdb="HE22 GLN B 437 " 0.270 2.00e-02 2.50e+03 ... (remaining 7024 not shown) Histogram of nonbonded interaction distances: 1.06 - 1.77: 64 1.77 - 2.48: 32343 2.48 - 3.19: 145882 3.19 - 3.89: 187033 3.89 - 4.60: 299441 Nonbonded interactions: 664763 Sorted by model distance: nonbonded pdb="HH12 ARG B 7 " pdb=" OD1 ASP B 441 " model vdw 1.065 1.850 nonbonded pdb="HD11 ILE C 952 " pdb="HD11 LEU C 969 " model vdw 1.271 2.440 nonbonded pdb=" HG2 PRO C 600 " pdb=" HE ARG C 637 " model vdw 1.330 2.270 nonbonded pdb=" O ARG B 705 " pdb="HG22 VAL B 710 " model vdw 1.352 2.620 nonbonded pdb="HD11 ILE A 900 " pdb="HD23 LEU A 945 " model vdw 1.367 2.440 ... (remaining 664758 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' and (resid 5 through 53 or (resid 54 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name HA )) or resid 55 through 42 \ 4 or (resid 433 and (name N or name CA or name C or name O or name CB or name CG \ or name CD or name CE or name NZ or name HA or name HB2 or name HB3 or name HG2 \ or name HG3 or name HD2 or name HD3 or name HE2 or name HE3 or name HZ1 or name \ HZ2 or name HZ3)) or resid 434 through 503 or resid 516 through 561 or (resid 5 \ 62 and (name N or name CA or name C or name O or name CB or name CG or name CD1 \ or name CD2 or name H or name HA )) or resid 563 or (resid 564 and (name N or na \ me CA or name C or name O or name CB or name CG or name CD or name OE1 or name N \ E2 or name H or name HA )) or resid 565 through 833 or (resid 834 and (name N or \ name CA or name C or name O or name CB or name CG1 or name CG2 or name H or nam \ e HA )) or resid 835 through 983 or resid 985 through 1039)) selection = (chain 'B' and (resid 5 through 983 or resid 985 through 1039)) selection = (chain 'C' and (resid 5 through 53 or (resid 54 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name HA )) or resid 55 through 42 \ 4 or (resid 433 and (name N or name CA or name C or name O or name CB or name CG \ or name CD or name CE or name NZ or name HA or name HB2 or name HB3 or name HG2 \ or name HG3 or name HD2 or name HD3 or name HE2 or name HE3 or name HZ1 or name \ HZ2 or name HZ3)) or resid 434 through 503 or resid 516 through 561 or (resid 5 \ 62 and (name N or name CA or name C or name O or name CB or name CG or name CD1 \ or name CD2 or name H or name HA )) or resid 563 or (resid 564 and (name N or na \ me CA or name C or name O or name CB or name CG or name CD or name OE1 or name N \ E2 or name H or name HA )) or resid 565 through 833 or (resid 834 and (name N or \ name CA or name C or name O or name CB or name CG1 or name CG2 or name H or nam \ e HA )) or resid 835 through 983 or resid 985 through 1039)) } 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=0.50 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: 0.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.320 Construct map_model_manager: 0.530 Extract box with map and model: 2.610 Check model and map are aligned: 0.520 Set scattering table: 0.320 Process input model: 122.250 Find NCS groups from input model: 1.770 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 138.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 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 : 0.004 0.045 24066 Z= 0.246 Angle : 0.672 15.658 32766 Z= 0.428 Chirality : 0.045 0.297 3891 Planarity : 0.006 0.162 4122 Dihedral : 15.432 89.913 8779 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 0.04 % Allowed : 10.90 % Favored : 89.06 % 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: -2.38 (0.14), residues: 3054 helix: -0.60 (0.12), residues: 1644 sheet: -2.12 (0.22), residues: 420 loop : -2.85 (0.17), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 436 HIS 0.004 0.000 HIS A 526 PHE 0.010 0.001 PHE B 561 TYR 0.017 0.001 TYR B 974 ARG 0.010 0.001 ARG A 819 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 562 is missing expected H atoms. Skipping. Residue VAL 834 is missing expected H atoms. Skipping. Evaluate side-chains 780 residues out of total 2522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 780 time to evaluate : 2.653 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: A 460 SER cc_start: 0.7602 (p) cc_final: 0.7258 (p) REVERT: A 504 TRP cc_start: 0.7416 (m-10) cc_final: 0.7212 (m-10) REVERT: A 738 MET cc_start: 0.7069 (ptm) cc_final: 0.6715 (ptm) REVERT: A 803 ASP cc_start: 0.6418 (m-30) cc_final: 0.6192 (m-30) REVERT: A 825 TYR cc_start: 0.8195 (m-80) cc_final: 0.7767 (m-80) REVERT: B 8 ARG cc_start: 0.6037 (mtp180) cc_final: 0.5250 (mtm-85) REVERT: B 410 MET cc_start: 0.7628 (mmt) cc_final: 0.7405 (mmt) REVERT: B 517 LEU cc_start: 0.7645 (tp) cc_final: 0.7365 (tt) REVERT: B 918 MET cc_start: 0.7863 (mmt) cc_final: 0.7452 (mmt) REVERT: C 8 ARG cc_start: 0.6657 (ttp-110) cc_final: 0.5795 (ttp-110) REVERT: C 823 TRP cc_start: 0.8158 (m-10) cc_final: 0.7953 (m-10) outliers start: 0 outliers final: 3 residues processed: 780 average time/residue: 1.9285 time to fit residues: 1786.5789 Evaluate side-chains 608 residues out of total 2522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 605 time to evaluate : 2.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 1030 ILE Chi-restraints excluded: chain B residue 696 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 257 optimal weight: 9.9990 chunk 231 optimal weight: 6.9990 chunk 128 optimal weight: 0.3980 chunk 78 optimal weight: 9.9990 chunk 155 optimal weight: 10.0000 chunk 123 optimal weight: 10.0000 chunk 239 optimal weight: 8.9990 chunk 92 optimal weight: 9.9990 chunk 145 optimal weight: 0.9990 chunk 177 optimal weight: 4.9990 chunk 276 optimal weight: 8.9990 overall best weight: 4.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN ** A 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 151 HIS A 359 HIS A 413 ASN A 651 ASN B 33 ASN B 470 GLN B 769 ASN B 794 GLN C 785 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 24066 Z= 0.242 Angle : 0.564 5.736 32766 Z= 0.284 Chirality : 0.041 0.156 3891 Planarity : 0.004 0.049 4122 Dihedral : 3.998 53.970 3293 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.11 % Favored : 94.85 % Rotamer: Outliers : 2.46 % Allowed : 22.15 % Favored : 75.40 % 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: -1.35 (0.15), residues: 3054 helix: 0.25 (0.13), residues: 1665 sheet: -1.56 (0.23), residues: 421 loop : -2.52 (0.18), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 29 HIS 0.005 0.001 HIS A 526 PHE 0.012 0.001 PHE B 383 TYR 0.039 0.001 TYR B 53 ARG 0.007 0.001 ARG B 7 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 562 is missing expected H atoms. Skipping. Residue VAL 834 is missing expected H atoms. Skipping. Evaluate side-chains 683 residues out of total 2522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 621 time to evaluate : 2.657 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: A 41 ASP cc_start: 0.5863 (p0) cc_final: 0.5593 (p0) REVERT: A 460 SER cc_start: 0.7745 (p) cc_final: 0.7412 (p) REVERT: A 580 ILE cc_start: 0.6860 (OUTLIER) cc_final: 0.6583 (pt) REVERT: A 738 MET cc_start: 0.6982 (ptm) cc_final: 0.6651 (ptm) REVERT: A 825 TYR cc_start: 0.8180 (m-80) cc_final: 0.7775 (m-80) REVERT: B 8 ARG cc_start: 0.6219 (mtp180) cc_final: 0.5443 (mtm-85) REVERT: B 358 TRP cc_start: 0.6977 (OUTLIER) cc_final: 0.6419 (m-90) REVERT: B 517 LEU cc_start: 0.7807 (tp) cc_final: 0.7483 (tt) REVERT: B 661 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7770 (mp) REVERT: B 696 MET cc_start: 0.7144 (mmm) cc_final: 0.6903 (mtm) REVERT: B 760 VAL cc_start: 0.9084 (OUTLIER) cc_final: 0.8878 (m) REVERT: B 918 MET cc_start: 0.7872 (mmt) cc_final: 0.7410 (mmt) REVERT: C 8 ARG cc_start: 0.6643 (ttp-170) cc_final: 0.4719 (tpm-80) REVERT: C 32 ILE cc_start: 0.8028 (pt) cc_final: 0.7807 (pt) REVERT: C 532 VAL cc_start: 0.7655 (OUTLIER) cc_final: 0.7362 (t) REVERT: C 774 GLN cc_start: 0.7841 (tp40) cc_final: 0.7608 (tp-100) REVERT: C 917 TRP cc_start: 0.7512 (t-100) cc_final: 0.7257 (t60) REVERT: C 1000 TRP cc_start: 0.7432 (m100) cc_final: 0.7173 (m100) outliers start: 62 outliers final: 31 residues processed: 646 average time/residue: 1.9423 time to fit residues: 1493.7509 Evaluate side-chains 621 residues out of total 2522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 585 time to evaluate : 2.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 812 MET Chi-restraints excluded: chain A residue 815 THR Chi-restraints excluded: chain A residue 859 SER Chi-restraints excluded: chain A residue 978 VAL Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 358 TRP Chi-restraints excluded: chain B residue 565 ILE Chi-restraints excluded: chain B residue 588 MET Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain B residue 674 SER Chi-restraints excluded: chain B residue 677 ILE Chi-restraints excluded: chain B residue 760 VAL Chi-restraints excluded: chain B residue 808 THR Chi-restraints excluded: chain B residue 815 THR Chi-restraints excluded: chain B residue 981 VAL Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 468 GLU Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 566 ASN Chi-restraints excluded: chain C residue 598 SER Chi-restraints excluded: chain C residue 641 THR Chi-restraints excluded: chain C residue 699 GLN Chi-restraints excluded: chain C residue 760 VAL Chi-restraints excluded: chain C residue 794 GLN Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1021 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 153 optimal weight: 0.0670 chunk 85 optimal weight: 10.0000 chunk 230 optimal weight: 7.9990 chunk 188 optimal weight: 8.9990 chunk 76 optimal weight: 20.0000 chunk 277 optimal weight: 9.9990 chunk 299 optimal weight: 5.9990 chunk 247 optimal weight: 7.9990 chunk 275 optimal weight: 20.0000 chunk 94 optimal weight: 10.0000 chunk 222 optimal weight: 8.9990 overall best weight: 6.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN A 629 GLN A 651 ASN B 33 ASN B 566 ASN B 629 GLN B 769 ASN C 389 ASN C 769 ASN C 841 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 24066 Z= 0.302 Angle : 0.587 7.388 32766 Z= 0.299 Chirality : 0.042 0.166 3891 Planarity : 0.005 0.043 4122 Dihedral : 4.067 28.431 3285 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 3.41 % Allowed : 22.54 % Favored : 74.05 % 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: -1.04 (0.15), residues: 3054 helix: 0.42 (0.13), residues: 1670 sheet: -1.22 (0.23), residues: 431 loop : -2.34 (0.19), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 552 HIS 0.010 0.001 HIS A 975 PHE 0.016 0.001 PHE C 85 TYR 0.038 0.002 TYR B 53 ARG 0.005 0.001 ARG A 157 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 562 is missing expected H atoms. Skipping. Residue VAL 834 is missing expected H atoms. Skipping. Evaluate side-chains 701 residues out of total 2522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 615 time to evaluate : 2.657 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: A 41 ASP cc_start: 0.5923 (p0) cc_final: 0.5634 (p0) REVERT: A 460 SER cc_start: 0.7875 (p) cc_final: 0.7523 (p) REVERT: A 535 TRP cc_start: 0.6481 (m-10) cc_final: 0.6025 (m-90) REVERT: A 738 MET cc_start: 0.6976 (ptm) cc_final: 0.6675 (ptm) REVERT: A 748 THR cc_start: 0.7346 (OUTLIER) cc_final: 0.7126 (t) REVERT: A 825 TYR cc_start: 0.8316 (m-80) cc_final: 0.7869 (m-80) REVERT: B 8 ARG cc_start: 0.6255 (mtp180) cc_final: 0.5744 (mtm-85) REVERT: B 410 MET cc_start: 0.8091 (mmt) cc_final: 0.7521 (mmt) REVERT: B 517 LEU cc_start: 0.7959 (tp) cc_final: 0.7633 (tt) REVERT: B 624 VAL cc_start: 0.8090 (OUTLIER) cc_final: 0.7767 (p) REVERT: B 661 LEU cc_start: 0.8117 (OUTLIER) cc_final: 0.7774 (mp) REVERT: B 696 MET cc_start: 0.7259 (mmm) cc_final: 0.6969 (mtm) REVERT: B 918 MET cc_start: 0.7918 (mmt) cc_final: 0.7430 (mmt) REVERT: C 8 ARG cc_start: 0.6584 (ttp-170) cc_final: 0.5409 (mtm-85) REVERT: C 12 ASN cc_start: 0.8046 (OUTLIER) cc_final: 0.7385 (p0) REVERT: C 32 ILE cc_start: 0.8177 (pt) cc_final: 0.7973 (pt) REVERT: C 189 VAL cc_start: 0.8641 (OUTLIER) cc_final: 0.8436 (p) REVERT: C 532 VAL cc_start: 0.7882 (OUTLIER) cc_final: 0.7554 (t) REVERT: C 705 ARG cc_start: 0.7618 (ptm-80) cc_final: 0.7401 (ptm160) REVERT: C 917 TRP cc_start: 0.7546 (t-100) cc_final: 0.7247 (t60) outliers start: 86 outliers final: 45 residues processed: 655 average time/residue: 1.9677 time to fit residues: 1547.2122 Evaluate side-chains 642 residues out of total 2522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 591 time to evaluate : 2.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 566 ASN Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 748 THR 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 830 ASP Chi-restraints excluded: chain A residue 855 SER Chi-restraints excluded: chain A residue 859 SER Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 978 VAL Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 387 ASN Chi-restraints excluded: chain B residue 452 ILE Chi-restraints excluded: chain B residue 565 ILE Chi-restraints excluded: chain B residue 588 MET Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain B residue 815 THR Chi-restraints excluded: chain B residue 981 VAL Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 139 ILE Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 293 SER Chi-restraints excluded: chain C residue 468 GLU Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 566 ASN Chi-restraints excluded: chain C residue 570 LEU Chi-restraints excluded: chain C residue 641 THR Chi-restraints excluded: chain C residue 738 MET Chi-restraints excluded: chain C residue 759 THR Chi-restraints excluded: chain C residue 760 VAL Chi-restraints excluded: chain C residue 763 ILE Chi-restraints excluded: chain C residue 794 GLN Chi-restraints excluded: chain C residue 953 GLU Chi-restraints excluded: chain C residue 996 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 274 optimal weight: 20.0000 chunk 208 optimal weight: 4.9990 chunk 144 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 132 optimal weight: 9.9990 chunk 186 optimal weight: 8.9990 chunk 278 optimal weight: 3.9990 chunk 294 optimal weight: 10.0000 chunk 145 optimal weight: 0.9980 chunk 263 optimal weight: 9.9990 chunk 79 optimal weight: 9.9990 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN ** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 33 ASN B 470 GLN ** B 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 ASN C 785 GLN C 841 GLN ** C 967 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 24066 Z= 0.285 Angle : 0.588 5.688 32766 Z= 0.299 Chirality : 0.042 0.163 3891 Planarity : 0.004 0.044 4122 Dihedral : 4.134 29.231 3285 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 3.80 % Allowed : 23.26 % Favored : 72.94 % 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: -0.80 (0.15), residues: 3054 helix: 0.58 (0.13), residues: 1663 sheet: -1.06 (0.23), residues: 437 loop : -2.18 (0.19), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 552 HIS 0.005 0.001 HIS A 526 PHE 0.017 0.001 PHE A 346 TYR 0.028 0.001 TYR B 974 ARG 0.004 0.000 ARG A 157 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 562 is missing expected H atoms. Skipping. Residue VAL 834 is missing expected H atoms. Skipping. Evaluate side-chains 700 residues out of total 2522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 604 time to evaluate : 2.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 460 SER cc_start: 0.7918 (p) cc_final: 0.7551 (p) REVERT: A 738 MET cc_start: 0.6978 (ptm) cc_final: 0.6665 (ptm) REVERT: A 825 TYR cc_start: 0.8369 (m-80) cc_final: 0.7894 (m-80) REVERT: A 986 MET cc_start: 0.7993 (mtp) cc_final: 0.7449 (mtp) REVERT: B 8 ARG cc_start: 0.6328 (mtp180) cc_final: 0.5759 (mtm-85) REVERT: B 56 GLN cc_start: 0.8418 (OUTLIER) cc_final: 0.7839 (mp10) REVERT: B 410 MET cc_start: 0.8100 (mmt) cc_final: 0.7547 (mmt) REVERT: B 517 LEU cc_start: 0.7882 (tp) cc_final: 0.7561 (tt) REVERT: B 566 ASN cc_start: 0.7812 (t0) cc_final: 0.7610 (t0) REVERT: B 624 VAL cc_start: 0.8067 (OUTLIER) cc_final: 0.7764 (p) REVERT: B 661 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7746 (mp) REVERT: B 696 MET cc_start: 0.7177 (mmm) cc_final: 0.6934 (mtm) REVERT: B 918 MET cc_start: 0.7910 (mmt) cc_final: 0.7373 (mmt) REVERT: C 8 ARG cc_start: 0.6598 (ttp-170) cc_final: 0.5311 (mtm-85) REVERT: C 189 VAL cc_start: 0.8684 (OUTLIER) cc_final: 0.8458 (p) REVERT: C 521 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8574 (mt) REVERT: C 702 GLU cc_start: 0.6432 (OUTLIER) cc_final: 0.6038 (tm-30) REVERT: C 705 ARG cc_start: 0.7631 (ptm-80) cc_final: 0.7392 (ptm160) REVERT: C 901 ILE cc_start: 0.8251 (OUTLIER) cc_final: 0.7898 (tt) REVERT: C 917 TRP cc_start: 0.7569 (t-100) cc_final: 0.7258 (t60) REVERT: C 1002 THR cc_start: 0.7891 (OUTLIER) cc_final: 0.7632 (m) outliers start: 96 outliers final: 57 residues processed: 654 average time/residue: 1.8908 time to fit residues: 1476.4361 Evaluate side-chains 661 residues out of total 2522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 596 time to evaluate : 2.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 759 THR Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 803 ASP Chi-restraints excluded: chain A residue 804 ILE Chi-restraints excluded: chain A residue 830 ASP Chi-restraints excluded: chain A residue 855 SER Chi-restraints excluded: chain A residue 859 SER Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 944 MET Chi-restraints excluded: chain A residue 978 VAL Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 358 TRP Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 415 HIS Chi-restraints excluded: chain B residue 452 ILE Chi-restraints excluded: chain B residue 465 PHE Chi-restraints excluded: chain B residue 565 ILE Chi-restraints excluded: chain B residue 588 MET Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain B residue 674 SER Chi-restraints excluded: chain B residue 684 LYS Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 815 THR Chi-restraints excluded: chain B residue 981 VAL Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 314 SER Chi-restraints excluded: chain C residue 468 GLU Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 566 ASN Chi-restraints excluded: chain C residue 570 LEU Chi-restraints excluded: chain C residue 592 THR Chi-restraints excluded: chain C residue 641 THR Chi-restraints excluded: chain C residue 702 GLU Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 759 THR Chi-restraints excluded: chain C residue 760 VAL Chi-restraints excluded: chain C residue 763 ILE Chi-restraints excluded: chain C residue 794 GLN Chi-restraints excluded: chain C residue 801 VAL Chi-restraints excluded: chain C residue 821 THR Chi-restraints excluded: chain C residue 901 ILE Chi-restraints excluded: chain C residue 953 GLU Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1002 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 245 optimal weight: 0.7980 chunk 167 optimal weight: 8.9990 chunk 4 optimal weight: 9.9990 chunk 219 optimal weight: 6.9990 chunk 121 optimal weight: 5.9990 chunk 251 optimal weight: 9.9990 chunk 203 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 150 optimal weight: 5.9990 chunk 264 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 785 GLN C 841 GLN C 967 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 24066 Z= 0.213 Angle : 0.561 5.913 32766 Z= 0.283 Chirality : 0.041 0.149 3891 Planarity : 0.004 0.046 4122 Dihedral : 4.061 29.165 3285 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 3.09 % Allowed : 24.41 % Favored : 72.50 % 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: -0.53 (0.15), residues: 3054 helix: 0.79 (0.13), residues: 1667 sheet: -0.94 (0.23), residues: 437 loop : -2.07 (0.19), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 552 HIS 0.005 0.001 HIS A 526 PHE 0.013 0.001 PHE C 85 TYR 0.027 0.001 TYR B 974 ARG 0.004 0.000 ARG A 13 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 562 is missing expected H atoms. Skipping. Residue VAL 834 is missing expected H atoms. Skipping. Evaluate side-chains 685 residues out of total 2522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 607 time to evaluate : 2.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 460 SER cc_start: 0.7849 (p) cc_final: 0.7487 (p) REVERT: A 535 TRP cc_start: 0.6661 (m-10) cc_final: 0.6443 (m-90) REVERT: A 738 MET cc_start: 0.6975 (ptm) cc_final: 0.6593 (ptm) REVERT: A 825 TYR cc_start: 0.8377 (m-80) cc_final: 0.7903 (m-80) REVERT: A 900 ILE cc_start: 0.8078 (OUTLIER) cc_final: 0.7832 (pt) REVERT: A 986 MET cc_start: 0.7960 (mtp) cc_final: 0.7438 (mtp) REVERT: B 8 ARG cc_start: 0.6350 (mtp180) cc_final: 0.5771 (mtm-85) REVERT: B 56 GLN cc_start: 0.8420 (OUTLIER) cc_final: 0.7814 (mp10) REVERT: B 624 VAL cc_start: 0.8039 (OUTLIER) cc_final: 0.7730 (p) REVERT: B 661 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7782 (mp) REVERT: B 696 MET cc_start: 0.7201 (OUTLIER) cc_final: 0.6951 (mtm) REVERT: B 918 MET cc_start: 0.7876 (mmt) cc_final: 0.7295 (mmt) REVERT: C 8 ARG cc_start: 0.6619 (ttp-170) cc_final: 0.5390 (mtm-85) REVERT: C 189 VAL cc_start: 0.8671 (OUTLIER) cc_final: 0.8457 (p) REVERT: C 384 GLN cc_start: 0.7966 (tt0) cc_final: 0.7676 (tt0) REVERT: C 597 MET cc_start: 0.8486 (tpt) cc_final: 0.7610 (tpt) REVERT: C 901 ILE cc_start: 0.8223 (OUTLIER) cc_final: 0.7869 (tt) REVERT: C 917 TRP cc_start: 0.7504 (t-100) cc_final: 0.7183 (t60) REVERT: C 967 GLN cc_start: 0.6199 (OUTLIER) cc_final: 0.5907 (pp30) REVERT: C 1002 THR cc_start: 0.7847 (OUTLIER) cc_final: 0.7625 (m) outliers start: 78 outliers final: 52 residues processed: 643 average time/residue: 1.9447 time to fit residues: 1500.6059 Evaluate side-chains 658 residues out of total 2522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 597 time to evaluate : 3.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 759 THR Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 803 ASP Chi-restraints excluded: chain A residue 804 ILE Chi-restraints excluded: chain A residue 830 ASP Chi-restraints excluded: chain A residue 855 SER Chi-restraints excluded: chain A residue 859 SER Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 912 ILE Chi-restraints excluded: chain A residue 944 MET Chi-restraints excluded: chain A residue 978 VAL Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 358 TRP Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 415 HIS Chi-restraints excluded: chain B residue 452 ILE Chi-restraints excluded: chain B residue 465 PHE Chi-restraints excluded: chain B residue 588 MET Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain B residue 684 LYS Chi-restraints excluded: chain B residue 696 MET Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 808 THR Chi-restraints excluded: chain B residue 815 THR Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 468 GLU Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 566 ASN Chi-restraints excluded: chain C residue 570 LEU Chi-restraints excluded: chain C residue 592 THR Chi-restraints excluded: chain C residue 641 THR Chi-restraints excluded: chain C residue 706 THR Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 760 VAL Chi-restraints excluded: chain C residue 794 GLN Chi-restraints excluded: chain C residue 801 VAL Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 821 THR Chi-restraints excluded: chain C residue 901 ILE Chi-restraints excluded: chain C residue 953 GLU Chi-restraints excluded: chain C residue 967 GLN Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1002 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 99 optimal weight: 9.9990 chunk 265 optimal weight: 0.8980 chunk 58 optimal weight: 8.9990 chunk 173 optimal weight: 6.9990 chunk 72 optimal weight: 10.0000 chunk 295 optimal weight: 9.9990 chunk 244 optimal weight: 9.9990 chunk 136 optimal weight: 7.9990 chunk 24 optimal weight: 20.0000 chunk 97 optimal weight: 0.9980 chunk 154 optimal weight: 10.0000 overall best weight: 5.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 785 GLN C 841 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.3404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 24066 Z= 0.264 Angle : 0.578 6.448 32766 Z= 0.293 Chirality : 0.042 0.158 3891 Planarity : 0.004 0.047 4122 Dihedral : 4.113 29.497 3285 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 3.92 % Allowed : 24.05 % Favored : 72.03 % 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: -0.48 (0.16), residues: 3054 helix: 0.81 (0.13), residues: 1671 sheet: -0.92 (0.23), residues: 441 loop : -2.00 (0.20), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 552 HIS 0.005 0.001 HIS A 526 PHE 0.018 0.001 PHE A 346 TYR 0.028 0.001 TYR B 974 ARG 0.003 0.000 ARG A 771 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 562 is missing expected H atoms. Skipping. Residue VAL 834 is missing expected H atoms. Skipping. Evaluate side-chains 694 residues out of total 2522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 595 time to evaluate : 2.939 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: A 355 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.8061 (tp) REVERT: A 460 SER cc_start: 0.7928 (p) cc_final: 0.7570 (p) REVERT: A 738 MET cc_start: 0.6931 (ptm) cc_final: 0.6494 (ptm) REVERT: A 825 TYR cc_start: 0.8393 (m-80) cc_final: 0.7924 (m-80) REVERT: A 900 ILE cc_start: 0.8075 (OUTLIER) cc_final: 0.7852 (pt) REVERT: A 986 MET cc_start: 0.7966 (mtp) cc_final: 0.7450 (mtp) REVERT: B 8 ARG cc_start: 0.6365 (mtp180) cc_final: 0.5817 (mtm-85) REVERT: B 56 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.7824 (mp10) REVERT: B 661 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7772 (mp) REVERT: B 696 MET cc_start: 0.7214 (OUTLIER) cc_final: 0.6952 (mtm) REVERT: B 918 MET cc_start: 0.7864 (mmt) cc_final: 0.7179 (mmt) REVERT: C 8 ARG cc_start: 0.6568 (ttp-170) cc_final: 0.5221 (mtm-85) REVERT: C 189 VAL cc_start: 0.8691 (OUTLIER) cc_final: 0.8476 (p) REVERT: C 384 GLN cc_start: 0.7990 (tt0) cc_final: 0.7695 (tt0) REVERT: C 462 ILE cc_start: 0.6792 (OUTLIER) cc_final: 0.6423 (tt) REVERT: C 597 MET cc_start: 0.8510 (tpt) cc_final: 0.7656 (tpt) REVERT: C 702 GLU cc_start: 0.6384 (OUTLIER) cc_final: 0.6026 (tm-30) REVERT: C 901 ILE cc_start: 0.8239 (OUTLIER) cc_final: 0.7895 (tt) REVERT: C 917 TRP cc_start: 0.7529 (t-100) cc_final: 0.7099 (t-100) REVERT: C 1002 THR cc_start: 0.7905 (OUTLIER) cc_final: 0.7628 (m) outliers start: 99 outliers final: 63 residues processed: 642 average time/residue: 1.9994 time to fit residues: 1550.8351 Evaluate side-chains 659 residues out of total 2522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 586 time to evaluate : 2.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 759 THR Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 803 ASP Chi-restraints excluded: chain A residue 804 ILE Chi-restraints excluded: chain A residue 830 ASP Chi-restraints excluded: chain A residue 855 SER Chi-restraints excluded: chain A residue 859 SER Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 912 ILE Chi-restraints excluded: chain A residue 944 MET Chi-restraints excluded: chain A residue 978 VAL Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 415 HIS Chi-restraints excluded: chain B residue 452 ILE Chi-restraints excluded: chain B residue 465 PHE Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 565 ILE Chi-restraints excluded: chain B residue 588 MET Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain B residue 674 SER Chi-restraints excluded: chain B residue 684 LYS Chi-restraints excluded: chain B residue 696 MET Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 808 THR Chi-restraints excluded: chain B residue 815 THR Chi-restraints excluded: chain B residue 902 SER Chi-restraints excluded: chain B residue 946 MET Chi-restraints excluded: chain B residue 981 VAL Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 314 SER Chi-restraints excluded: chain C residue 462 ILE Chi-restraints excluded: chain C residue 468 GLU Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 566 ASN Chi-restraints excluded: chain C residue 570 LEU Chi-restraints excluded: chain C residue 592 THR Chi-restraints excluded: chain C residue 641 THR Chi-restraints excluded: chain C residue 702 GLU Chi-restraints excluded: chain C residue 706 THR Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 759 THR Chi-restraints excluded: chain C residue 760 VAL Chi-restraints excluded: chain C residue 794 GLN Chi-restraints excluded: chain C residue 801 VAL Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 821 THR Chi-restraints excluded: chain C residue 901 ILE Chi-restraints excluded: chain C residue 953 GLU Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1002 THR Chi-restraints excluded: chain C residue 1021 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 284 optimal weight: 20.0000 chunk 33 optimal weight: 10.0000 chunk 168 optimal weight: 6.9990 chunk 215 optimal weight: 9.9990 chunk 166 optimal weight: 7.9990 chunk 248 optimal weight: 10.0000 chunk 164 optimal weight: 6.9990 chunk 293 optimal weight: 9.9990 chunk 183 optimal weight: 20.0000 chunk 179 optimal weight: 8.9990 chunk 135 optimal weight: 9.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 785 GLN C 841 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.3726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 24066 Z= 0.370 Angle : 0.632 6.604 32766 Z= 0.325 Chirality : 0.044 0.191 3891 Planarity : 0.005 0.046 4122 Dihedral : 4.384 30.677 3285 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.75 % Favored : 93.22 % Rotamer: Outliers : 4.16 % Allowed : 24.48 % Favored : 71.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % 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 (0.15), residues: 3054 helix: 0.61 (0.13), residues: 1674 sheet: -0.86 (0.23), residues: 446 loop : -2.07 (0.20), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 552 HIS 0.007 0.001 HIS A 526 PHE 0.019 0.002 PHE C 85 TYR 0.030 0.002 TYR B 974 ARG 0.007 0.001 ARG A 8 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 562 is missing expected H atoms. Skipping. Residue VAL 834 is missing expected H atoms. Skipping. Evaluate side-chains 694 residues out of total 2522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 589 time to evaluate : 2.681 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: A 41 ASP cc_start: 0.6015 (p0) cc_final: 0.5728 (p0) REVERT: A 460 SER cc_start: 0.7905 (p) cc_final: 0.7543 (p) REVERT: A 738 MET cc_start: 0.6988 (ptm) cc_final: 0.6534 (ptm) REVERT: A 825 TYR cc_start: 0.8428 (m-80) cc_final: 0.7961 (m-80) REVERT: A 986 MET cc_start: 0.7977 (mtp) cc_final: 0.7469 (mtp) REVERT: B 8 ARG cc_start: 0.6478 (mtp180) cc_final: 0.5884 (mtm-85) REVERT: B 566 ASN cc_start: 0.7808 (OUTLIER) cc_final: 0.7522 (t0) REVERT: B 661 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7736 (mp) REVERT: B 918 MET cc_start: 0.7988 (mmt) cc_final: 0.7291 (mmt) REVERT: C 8 ARG cc_start: 0.6617 (ttp-170) cc_final: 0.5599 (mtm-85) REVERT: C 85 PHE cc_start: 0.6629 (OUTLIER) cc_final: 0.6363 (p90) REVERT: C 462 ILE cc_start: 0.7280 (OUTLIER) cc_final: 0.6928 (tt) REVERT: C 532 VAL cc_start: 0.8070 (OUTLIER) cc_final: 0.7710 (t) REVERT: C 597 MET cc_start: 0.8456 (tpt) cc_final: 0.7489 (tpt) REVERT: C 702 GLU cc_start: 0.6322 (OUTLIER) cc_final: 0.5956 (tm-30) REVERT: C 738 MET cc_start: 0.7631 (OUTLIER) cc_final: 0.7302 (ptm) REVERT: C 901 ILE cc_start: 0.8268 (OUTLIER) cc_final: 0.7897 (tt) REVERT: C 917 TRP cc_start: 0.7545 (t-100) cc_final: 0.7134 (t-100) REVERT: C 1002 THR cc_start: 0.8004 (OUTLIER) cc_final: 0.7650 (m) outliers start: 105 outliers final: 70 residues processed: 642 average time/residue: 1.9156 time to fit residues: 1467.3305 Evaluate side-chains 654 residues out of total 2522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 575 time to evaluate : 2.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 358 TRP Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 566 ASN Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 592 THR 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 855 SER Chi-restraints excluded: chain A residue 859 SER Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 944 MET Chi-restraints excluded: chain A residue 978 VAL Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 33 ASN Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 415 HIS Chi-restraints excluded: chain B residue 452 ILE Chi-restraints excluded: chain B residue 465 PHE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 565 ILE Chi-restraints excluded: chain B residue 566 ASN Chi-restraints excluded: chain B residue 588 MET Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 815 THR Chi-restraints excluded: chain B residue 822 SER Chi-restraints excluded: chain B residue 889 LEU Chi-restraints excluded: chain B residue 902 SER Chi-restraints excluded: chain B residue 946 MET Chi-restraints excluded: chain B residue 959 ASN Chi-restraints excluded: chain B residue 981 VAL Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 85 PHE Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 462 ILE Chi-restraints excluded: chain C residue 468 GLU Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 566 ASN Chi-restraints excluded: chain C residue 570 LEU Chi-restraints excluded: chain C residue 592 THR Chi-restraints excluded: chain C residue 641 THR Chi-restraints excluded: chain C residue 702 GLU Chi-restraints excluded: chain C residue 706 THR Chi-restraints excluded: chain C residue 738 MET Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 759 THR Chi-restraints excluded: chain C residue 760 VAL Chi-restraints excluded: chain C residue 763 ILE Chi-restraints excluded: chain C residue 794 GLN Chi-restraints excluded: chain C residue 801 VAL Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 821 THR Chi-restraints excluded: chain C residue 901 ILE Chi-restraints excluded: chain C residue 953 GLU Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1002 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 181 optimal weight: 5.9990 chunk 117 optimal weight: 2.9990 chunk 175 optimal weight: 2.9990 chunk 88 optimal weight: 7.9990 chunk 57 optimal weight: 7.9990 chunk 56 optimal weight: 30.0000 chunk 186 optimal weight: 7.9990 chunk 200 optimal weight: 8.9990 chunk 145 optimal weight: 4.9990 chunk 27 optimal weight: 10.0000 chunk 231 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 534 HIS C 785 GLN C 841 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.3753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24066 Z= 0.222 Angle : 0.582 7.987 32766 Z= 0.293 Chirality : 0.042 0.148 3891 Planarity : 0.004 0.047 4122 Dihedral : 4.243 31.612 3285 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 3.17 % Allowed : 25.79 % Favored : 71.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % 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: -0.39 (0.16), residues: 3054 helix: 0.83 (0.13), residues: 1675 sheet: -0.73 (0.24), residues: 427 loop : -1.94 (0.20), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 552 HIS 0.006 0.001 HIS A 526 PHE 0.019 0.001 PHE C 520 TYR 0.030 0.001 TYR B 974 ARG 0.004 0.000 ARG A 980 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 562 is missing expected H atoms. Skipping. Residue VAL 834 is missing expected H atoms. Skipping. Evaluate side-chains 666 residues out of total 2522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 586 time to evaluate : 2.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 460 SER cc_start: 0.7807 (p) cc_final: 0.7454 (p) REVERT: A 738 MET cc_start: 0.6921 (ptm) cc_final: 0.6510 (ptm) REVERT: A 986 MET cc_start: 0.7957 (mtp) cc_final: 0.7420 (mtp) REVERT: B 8 ARG cc_start: 0.6469 (mtp180) cc_final: 0.5848 (mtm-85) REVERT: B 661 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7863 (tp) REVERT: B 918 MET cc_start: 0.7867 (mmt) cc_final: 0.7175 (mmt) REVERT: C 8 ARG cc_start: 0.6588 (ttp-170) cc_final: 0.5639 (mtm-85) REVERT: C 85 PHE cc_start: 0.6631 (OUTLIER) cc_final: 0.6346 (p90) REVERT: C 462 ILE cc_start: 0.6851 (OUTLIER) cc_final: 0.6479 (tt) REVERT: C 597 MET cc_start: 0.8425 (tpt) cc_final: 0.7634 (tpt) REVERT: C 738 MET cc_start: 0.7551 (OUTLIER) cc_final: 0.7237 (ptm) REVERT: C 917 TRP cc_start: 0.7503 (t-100) cc_final: 0.7095 (t-100) REVERT: C 1002 THR cc_start: 0.7982 (OUTLIER) cc_final: 0.7655 (m) outliers start: 80 outliers final: 57 residues processed: 625 average time/residue: 1.9583 time to fit residues: 1463.9019 Evaluate side-chains 639 residues out of total 2522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 577 time to evaluate : 2.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 759 THR Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 855 SER Chi-restraints excluded: chain A residue 859 SER Chi-restraints excluded: chain A residue 944 MET Chi-restraints excluded: chain A residue 978 VAL Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 33 ASN Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 415 HIS Chi-restraints excluded: chain B residue 452 ILE Chi-restraints excluded: chain B residue 465 PHE Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 565 ILE Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 778 ASP Chi-restraints excluded: chain B residue 815 THR Chi-restraints excluded: chain B residue 889 LEU Chi-restraints excluded: chain B residue 902 SER Chi-restraints excluded: chain B residue 946 MET Chi-restraints excluded: chain B residue 981 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 85 PHE Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 462 ILE Chi-restraints excluded: chain C residue 468 GLU Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 566 ASN Chi-restraints excluded: chain C residue 570 LEU Chi-restraints excluded: chain C residue 592 THR Chi-restraints excluded: chain C residue 641 THR Chi-restraints excluded: chain C residue 706 THR Chi-restraints excluded: chain C residue 738 MET Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 748 THR Chi-restraints excluded: chain C residue 759 THR Chi-restraints excluded: chain C residue 760 VAL Chi-restraints excluded: chain C residue 801 VAL Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 821 THR Chi-restraints excluded: chain C residue 953 GLU Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1002 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 267 optimal weight: 10.0000 chunk 281 optimal weight: 9.9990 chunk 256 optimal weight: 0.9980 chunk 273 optimal weight: 8.9990 chunk 164 optimal weight: 8.9990 chunk 119 optimal weight: 1.9990 chunk 215 optimal weight: 9.9990 chunk 84 optimal weight: 9.9990 chunk 247 optimal weight: 0.6980 chunk 259 optimal weight: 10.0000 chunk 272 optimal weight: 6.9990 overall best weight: 3.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 795 GLN ** B 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 534 HIS C 785 GLN C 841 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.3844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 24066 Z= 0.219 Angle : 0.578 9.518 32766 Z= 0.291 Chirality : 0.042 0.150 3891 Planarity : 0.004 0.046 4122 Dihedral : 4.174 30.800 3285 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 2.93 % Allowed : 26.39 % Favored : 70.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % 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: -0.24 (0.16), residues: 3054 helix: 0.94 (0.13), residues: 1675 sheet: -0.67 (0.24), residues: 427 loop : -1.86 (0.20), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 552 HIS 0.006 0.001 HIS A 526 PHE 0.016 0.001 PHE A 346 TYR 0.028 0.001 TYR B 974 ARG 0.003 0.000 ARG A 980 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 562 is missing expected H atoms. Skipping. Residue VAL 834 is missing expected H atoms. Skipping. Evaluate side-chains 653 residues out of total 2522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 579 time to evaluate : 2.613 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: A 460 SER cc_start: 0.7782 (p) cc_final: 0.7435 (p) REVERT: A 738 MET cc_start: 0.6896 (ptm) cc_final: 0.6502 (ptm) REVERT: A 978 VAL cc_start: 0.8152 (OUTLIER) cc_final: 0.7876 (t) REVERT: A 986 MET cc_start: 0.7948 (mtp) cc_final: 0.7418 (mtp) REVERT: B 8 ARG cc_start: 0.6637 (mtp180) cc_final: 0.6000 (mtm-85) REVERT: B 661 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7844 (tp) REVERT: B 918 MET cc_start: 0.7828 (mmt) cc_final: 0.7161 (mmt) REVERT: C 8 ARG cc_start: 0.6593 (ttp-170) cc_final: 0.5563 (mtm-85) REVERT: C 85 PHE cc_start: 0.6630 (OUTLIER) cc_final: 0.6299 (p90) REVERT: C 462 ILE cc_start: 0.6808 (OUTLIER) cc_final: 0.6430 (tt) REVERT: C 597 MET cc_start: 0.8417 (tpt) cc_final: 0.7605 (tpt) REVERT: C 738 MET cc_start: 0.7530 (OUTLIER) cc_final: 0.7230 (ptm) REVERT: C 917 TRP cc_start: 0.7498 (t-100) cc_final: 0.7086 (t-100) REVERT: C 1002 THR cc_start: 0.7982 (OUTLIER) cc_final: 0.7657 (m) outliers start: 74 outliers final: 55 residues processed: 615 average time/residue: 1.9440 time to fit residues: 1419.3153 Evaluate side-chains 634 residues out of total 2522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 573 time to evaluate : 2.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 759 THR Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 803 ASP Chi-restraints excluded: chain A residue 855 SER Chi-restraints excluded: chain A residue 944 MET Chi-restraints excluded: chain A residue 978 VAL Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 415 HIS Chi-restraints excluded: chain B residue 465 PHE Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 565 ILE Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 778 ASP Chi-restraints excluded: chain B residue 815 THR Chi-restraints excluded: chain B residue 902 SER Chi-restraints excluded: chain B residue 946 MET Chi-restraints excluded: chain B residue 959 ASN Chi-restraints excluded: chain B residue 981 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 85 PHE Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 462 ILE Chi-restraints excluded: chain C residue 468 GLU Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 566 ASN Chi-restraints excluded: chain C residue 570 LEU Chi-restraints excluded: chain C residue 592 THR Chi-restraints excluded: chain C residue 641 THR Chi-restraints excluded: chain C residue 706 THR Chi-restraints excluded: chain C residue 738 MET Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 748 THR Chi-restraints excluded: chain C residue 759 THR Chi-restraints excluded: chain C residue 760 VAL Chi-restraints excluded: chain C residue 801 VAL Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 821 THR Chi-restraints excluded: chain C residue 953 GLU Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1002 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 179 optimal weight: 0.0980 chunk 289 optimal weight: 9.9990 chunk 176 optimal weight: 0.7980 chunk 137 optimal weight: 0.6980 chunk 201 optimal weight: 0.9980 chunk 303 optimal weight: 6.9990 chunk 279 optimal weight: 0.5980 chunk 241 optimal weight: 9.9990 chunk 25 optimal weight: 20.0000 chunk 186 optimal weight: 5.9990 chunk 148 optimal weight: 8.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 729 ASN B 238 GLN ** B 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 534 HIS C 785 GLN C 841 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.3791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 24066 Z= 0.150 Angle : 0.545 10.485 32766 Z= 0.270 Chirality : 0.041 0.145 3891 Planarity : 0.004 0.052 4122 Dihedral : 3.934 29.870 3285 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 1.15 % Allowed : 28.37 % Favored : 70.48 % 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: 0.16 (0.16), residues: 3054 helix: 1.29 (0.13), residues: 1676 sheet: -0.51 (0.25), residues: 426 loop : -1.72 (0.20), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 552 HIS 0.005 0.000 HIS A 526 PHE 0.018 0.001 PHE C 520 TYR 0.027 0.001 TYR B 974 ARG 0.005 0.000 ARG C 777 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 562 is missing expected H atoms. Skipping. Residue VAL 834 is missing expected H atoms. Skipping. Evaluate side-chains 612 residues out of total 2522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 583 time to evaluate : 2.762 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: A 460 SER cc_start: 0.7681 (p) cc_final: 0.7364 (p) REVERT: A 738 MET cc_start: 0.6910 (ptm) cc_final: 0.6556 (ptm) REVERT: A 978 VAL cc_start: 0.8094 (OUTLIER) cc_final: 0.7834 (t) REVERT: A 986 MET cc_start: 0.7934 (mtp) cc_final: 0.7443 (mtp) REVERT: B 8 ARG cc_start: 0.6393 (mtp180) cc_final: 0.5762 (mtm-85) REVERT: B 623 MET cc_start: 0.7810 (ttm) cc_final: 0.7116 (ttt) REVERT: B 661 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7833 (tp) REVERT: B 918 MET cc_start: 0.7799 (mmt) cc_final: 0.7158 (mmt) REVERT: C 8 ARG cc_start: 0.6544 (ttp-170) cc_final: 0.4542 (ttp-110) REVERT: C 597 MET cc_start: 0.8343 (tpt) cc_final: 0.7581 (tpt) REVERT: C 917 TRP cc_start: 0.7450 (t-100) cc_final: 0.7145 (t60) outliers start: 29 outliers final: 19 residues processed: 595 average time/residue: 1.9733 time to fit residues: 1390.5007 Evaluate side-chains 585 residues out of total 2522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 564 time to evaluate : 2.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 859 SER Chi-restraints excluded: chain A residue 978 VAL Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 588 MET Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 902 SER Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 566 ASN Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 748 THR Chi-restraints excluded: chain C residue 760 VAL Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 953 GLU Chi-restraints excluded: chain C residue 996 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 192 optimal weight: 6.9990 chunk 257 optimal weight: 10.0000 chunk 74 optimal weight: 3.9990 chunk 223 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 67 optimal weight: 9.9990 chunk 242 optimal weight: 6.9990 chunk 101 optimal weight: 6.9990 chunk 248 optimal weight: 7.9990 chunk 30 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 238 GLN ** B 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 769 ASN C 534 HIS C 785 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.163321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.140145 restraints weight = 91877.029| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 1.84 r_work: 0.3580 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3494 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3434 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3434 r_free = 0.3434 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3434 r_free = 0.3434 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3434 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.3979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 24066 Z= 0.328 Angle : 0.613 9.363 32766 Z= 0.311 Chirality : 0.043 0.180 3891 Planarity : 0.005 0.045 4122 Dihedral : 4.170 30.552 3285 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.23 % Favored : 93.74 % Rotamer: Outliers : 1.82 % Allowed : 27.93 % Favored : 70.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % 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: 3054 helix: 1.08 (0.13), residues: 1663 sheet: -0.59 (0.25), residues: 423 loop : -1.74 (0.20), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 552 HIS 0.005 0.001 HIS A 526 PHE 0.018 0.002 PHE C 520 TYR 0.027 0.002 TYR B 974 ARG 0.005 0.001 ARG C 765 =============================================================================== Job complete usr+sys time: 19781.13 seconds wall clock time: 339 minutes 17.36 seconds (20357.36 seconds total)