Starting phenix.real_space_refine on Mon Mar 25 08:12:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kf8_22846/03_2024/7kf8_22846_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kf8_22846/03_2024/7kf8_22846.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kf8_22846/03_2024/7kf8_22846.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kf8_22846/03_2024/7kf8_22846.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kf8_22846/03_2024/7kf8_22846_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kf8_22846/03_2024/7kf8_22846_updated.pdb" } resolution = 3.0 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= 0.110 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Cu 2 5.60 5 S 108 5.16 5 C 15194 2.51 5 N 3929 2.21 5 O 4258 1.98 5 H 24247 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 ASP 37": "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 TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 98": "OE1" <-> "OE2" Residue "A ASP 99": "OD1" <-> "OD2" Residue "A ASP 102": "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 GLU 128": "OE1" <-> "OE2" 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 155": "OD1" <-> "OD2" Residue "A ARG 157": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" 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 GLU 186": "OE1" <-> "OE2" Residue "A TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 226": "OE1" <-> "OE2" Residue "A ARG 232": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 242": "OD1" <-> "OD2" 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 281": "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 TYR 325": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 327": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 361": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 417": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 441": "OD1" <-> "OD2" Residue "A GLU 445": "OE1" <-> "OE2" Residue "A PHE 461": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 TYR 525": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 560": "OE1" <-> "OE2" Residue "A PHE 561": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 GLU 613": "OE1" <-> "OE2" Residue "A GLU 625": "OE1" <-> "OE2" Residue "A ASP 643": "OD1" <-> "OD2" Residue "A ASP 650": "OD1" <-> "OD2" Residue "A ARG 654": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 692": "OD1" <-> "OD2" Residue "A ASP 694": "OD1" <-> "OD2" Residue "A ARG 705": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 717": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" 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 GLU 731": "OE1" <-> "OE2" Residue "A ARG 735": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 736": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 742": "OD1" <-> "OD2" 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 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 TYR 825": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 827": "OD1" <-> "OD2" Residue "A ARG 829": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 830": "OD1" <-> "OD2" Residue "A ARG 831": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 832": "OD1" <-> "OD2" Residue "A PHE 858": "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 TYR 888": "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 PHE 930": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 947": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 949": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 953": "OE1" <-> "OE2" Residue "A GLU 966": "OE1" <-> "OE2" Residue "A GLU 971": "OE1" <-> "OE2" Residue "A ARG 982": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1011": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 1035": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 7": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 13": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 41": "OD1" <-> "OD2" Residue "B ASP 44": "OD1" <-> "OD2" Residue "B GLU 62": "OE1" <-> "OE2" Residue "B TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 107": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 109": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 128": "OE1" <-> "OE2" Residue "B ASP 132": "OD1" <-> "OD2" Residue "B TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 152": "OD1" <-> "OD2" Residue "B ASP 155": "OD1" <-> "OD2" Residue "B ARG 157": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 161": "OD1" <-> "OD2" Residue "B PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 167": "OE1" <-> "OE2" Residue "B TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 216": "OE1" <-> "OE2" Residue "B GLU 228": "OE1" <-> "OE2" 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 241": "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 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 ARG 327": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 336": "OD1" <-> "OD2" Residue "B ARG 361": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 417": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 445": "OE1" <-> "OE2" Residue "B PHE 451": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 465": "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 PHE 561": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 584": "OE1" <-> "OE2" Residue "B ARG 604": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 634": "OE1" <-> "OE2" Residue "B ARG 654": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 692": "OD1" <-> "OD2" Residue "B GLU 701": "OE1" <-> "OE2" Residue "B ARG 717": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 722": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" 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 ASP 742": "OD1" <-> "OD2" Residue "B GLU 758": "OE1" <-> "OE2" Residue "B ARG 765": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 766": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 771": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 777": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 778": "OD1" <-> "OD2" Residue "B ARG 784": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 819": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 825": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 829": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 830": "OD1" <-> "OD2" Residue "B ARG 831": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 832": "OD1" <-> "OD2" Residue "B ASP 839": "OD1" <-> "OD2" Residue "B GLU 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 PHE 920": "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 GLU 953": "OE1" <-> "OE2" Residue "B GLU 966": "OE1" <-> "OE2" 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 "C ARG 7": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 13": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 41": "OD1" <-> "OD2" Residue "C TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 62": "OE1" <-> "OE2" Residue "C PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 90": "OD1" <-> "OD2" Residue "C TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 102": "OD1" <-> "OD2" Residue "C ARG 107": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 109": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ASP 132": "OD1" <-> "OD2" Residue "C TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 167": "OE1" <-> "OE2" Residue "C GLU 176": "OE1" <-> "OE2" Residue "C TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 216": "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 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 ASP 261": "OD1" <-> "OD2" 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 283": "OE1" <-> "OE2" Residue "C ARG 292": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 298": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 299": "OE1" <-> "OE2" Residue "C GLU 309": "OE1" <-> "OE2" Residue "C GLU 317": "OE1" <-> "OE2" Residue "C GLU 320": "OE1" <-> "OE2" Residue "C TYR 325": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 327": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ASP 336": "OD1" <-> "OD2" Residue "C ARG 361": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 417": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ASP 441": "OD1" <-> "OD2" Residue "C TYR 484": "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 GLU 567": "OE1" <-> "OE2" Residue "C ASP 569": "OD1" <-> "OD2" Residue "C GLU 584": "OE1" <-> "OE2" Residue "C ASP 593": "OD1" <-> "OD2" Residue "C GLU 601": "OE1" <-> "OE2" Residue "C ARG 604": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 606": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 643": "OD1" <-> "OD2" Residue "C GLU 647": "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 694": "OD1" <-> "OD2" Residue "C ARG 717": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 722": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 723": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 GLU 758": "OE1" <-> "OE2" Residue "C ARG 765": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 766": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 771": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 777": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ASP 778": "OD1" <-> "OD2" Residue "C ARG 784": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ASP 800": "OD1" <-> "OD2" Residue "C ARG 819": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 825": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 829": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 831": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 846": "OE1" <-> "OE2" Residue "C PHE 858": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 867": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 884": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C 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 GLU 896": "OE1" <-> "OE2" Residue "C PHE 930": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 949": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 964": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 966": "OE1" <-> "OE2" Residue "C ASP 970": "OD1" <-> "OD2" Residue "C TYR 974": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 982": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 1007": "OE1" <-> "OE2" Residue "C ARG 1011": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 1035": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 47738 Number of models: 1 Model: "" Number of chains: 5 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: 1 Conformer: "" Number of residues, atoms: 1015, 15860 Classifications: {'peptide': 1015} Link IDs: {'PTRANS': 52, 'TRANS': 962} Chain breaks: 2 Chain: "C" Number of atoms: 15853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1015, 15853 Classifications: {'peptide': 1015} Link IDs: {'PTRANS': 52, 'TRANS': 962} Chain breaks: 2 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'CU1': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'CU1': 1} Classifications: {'undetermined': 1} Time building chain proxies: 17.94, per 1000 atoms: 0.38 Number of scatterers: 47738 At special positions: 0 Unit cell: (124.2, 124.2, 151.2, 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 2 28.99 S 108 16.00 O 4258 8.00 N 3929 7.00 C 15194 6.00 H 24247 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 39.10 Conformation dependent library (CDL) restraints added in 4.8 seconds 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5648 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 111 helices and 22 sheets defined 52.9% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.44 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: 3.584A pdb=" N LEU A 74 " --> pdb=" O THR A 70 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N SER A 75 " --> pdb=" O THR A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 120 removed outlier: 3.976A pdb=" N ARG A 107 " --> pdb=" O PRO A 103 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU A 112 " --> pdb=" O SER A 108 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYR A 113 " --> pdb=" O ARG A 109 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLY A 119 " --> pdb=" O ASN A 115 " (cutoff:3.500A) removed outlier: 5.100A 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: 3.791A pdb=" N ARG A 157 " --> pdb=" O LEU A 153 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER A 158 " --> pdb=" O ALA A 154 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LYS A 165 " --> pdb=" O ASP A 161 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N TYR A 166 " --> pdb=" O TRP A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 199 removed outlier: 3.605A pdb=" N TYR A 199 " --> pdb=" O ARG A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 212 removed outlier: 3.580A 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 298 through 310 Processing helix chain 'A' and resid 328 through 357 Processing helix chain 'A' and resid 360 through 384 removed outlier: 4.599A pdb=" N SER A 369 " --> pdb=" O VAL A 365 " (cutoff:3.500A) removed outlier: 4.981A 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: 4.672A pdb=" N GLY A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ALA A 402 " --> pdb=" O ILE A 398 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N ALA A 406 " --> pdb=" O ALA A 402 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ALA A 407 " --> pdb=" O MET A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 466 removed outlier: 3.673A 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: 5.367A 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 551 removed outlier: 4.590A pdb=" N VAL A 550 " --> pdb=" O SER A 546 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N LEU A 551 " --> pdb=" O VAL A 547 " (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: 3.644A 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: 4.584A 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: 4.387A pdb=" N PHE A 746 " --> pdb=" O ASP A 742 " (cutoff:3.500A) removed outlier: 4.545A 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 873 Processing helix chain 'A' and resid 876 through 891 Processing helix chain 'A' and resid 894 through 918 removed outlier: 4.434A pdb=" N SER A 903 " --> pdb=" O LEU A 899 " (cutoff:3.500A) removed outlier: 4.823A 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: 4.048A pdb=" N GLY A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 977 Processing helix chain 'A' and resid 981 through 999 removed outlier: 3.717A 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 1019 Proline residue: A1015 - end of helix Processing helix chain 'A' and resid 1023 through 1039 removed outlier: 4.205A 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: 4.566A pdb=" N SER B 75 " --> pdb=" O THR B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 113 removed outlier: 3.934A 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 213 removed outlier: 3.803A pdb=" N SER B 213 " --> pdb=" O ALA B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 244 Processing helix chain 'B' and resid 297 through 314 removed outlier: 4.623A pdb=" N SER B 313 " --> pdb=" O GLU B 309 " (cutoff:3.500A) removed outlier: 5.329A 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 384 removed outlier: 4.060A pdb=" N ILE B 368 " --> pdb=" O VAL B 365 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N LEU B 370 " --> pdb=" O ILE B 367 " (cutoff:3.500A) Proline residue: B 371 - end of helix Processing helix chain 'B' and resid 390 through 394 Processing helix chain 'B' and resid 396 through 423 removed outlier: 3.734A pdb=" N GLY B 401 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ASP B 405 " --> pdb=" O GLY B 401 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N ALA B 406 " --> pdb=" O ALA B 402 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA B 407 " --> pdb=" O MET B 403 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN B 422 " --> pdb=" O LEU B 418 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N HIS B 423 " --> pdb=" O GLU B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 465 removed outlier: 4.175A pdb=" N VAL B 446 " --> pdb=" O ALA B 442 " (cutoff:3.500A) Proline residue: B 448 - end of helix removed outlier: 4.593A pdb=" N PHE B 461 " --> pdb=" O ILE B 457 " (cutoff:3.500A) removed outlier: 5.076A 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: 3.571A pdb=" N HIS B 534 " --> pdb=" O LEU B 530 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N TRP B 535 " --> pdb=" O LYS B 531 " (cutoff:3.500A) Proline residue: B 536 - end of helix removed outlier: 4.640A pdb=" N LEU B 551 " --> pdb=" O VAL B 547 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N TRP B 552 " --> pdb=" O LEU B 548 " (cutoff:3.500A) Proline residue: B 553 - end of helix removed outlier: 3.541A pdb=" N LYS B 556 " --> pdb=" O TRP B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 598 removed outlier: 3.536A pdb=" N ALA B 586 " --> pdb=" O ALA B 582 " (cutoff:3.500A) removed outlier: 3.607A 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 704 removed outlier: 3.546A pdb=" N GLN B 699 " --> pdb=" O ALA B 695 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLU B 702 " --> pdb=" O GLU B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 730 through 734 Processing helix chain 'B' and resid 740 through 749 removed outlier: 3.916A 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: 3.765A pdb=" N GLN B 785 " --> pdb=" O GLN B 781 " (cutoff:3.500A) Processing helix chain 'B' and resid 836 through 847 Processing helix chain 'B' and resid 861 through 891 removed outlier: 4.264A pdb=" N GLU B 866 " --> pdb=" O GLU B 863 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ASN B 869 " --> pdb=" O GLU B 866 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N VAL B 876 " --> pdb=" O LYS B 873 " (cutoff:3.500A) Proline residue: B 877 - end of helix removed outlier: 4.315A pdb=" N VAL B 885 " --> pdb=" O ILE B 882 " (cutoff:3.500A) removed outlier: 4.071A 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: 4.249A pdb=" N LEU B 914 " --> pdb=" O GLY B 910 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LEU B 915 " --> pdb=" O GLY B 911 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N TRP B 916 " --> pdb=" O ILE B 912 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N TRP B 917 " --> pdb=" O TRP B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 924 through 952 removed outlier: 3.520A pdb=" N TYR B 947 " --> pdb=" O VAL B 943 " (cutoff:3.500A) Processing helix chain 'B' and resid 955 through 960 removed outlier: 4.249A pdb=" N ASN B 960 " --> pdb=" O SER B 957 " (cutoff:3.500A) Processing helix chain 'B' and resid 967 through 980 removed outlier: 4.486A pdb=" N VAL B 978 " --> pdb=" O HIS B 975 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N LEU B 979 " --> pdb=" O GLY B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 982 through 999 Proline residue: B 997 - end of helix Processing helix chain 'B' and resid 1006 through 1019 Proline residue: B1015 - end of helix Processing helix chain 'B' and resid 1023 through 1036 removed outlier: 4.836A 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 66 through 75 removed outlier: 4.685A pdb=" N SER C 75 " --> pdb=" O THR C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 113 removed outlier: 4.067A pdb=" N TYR C 113 " --> pdb=" O ARG C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 162 Processing helix chain 'C' and resid 164 through 168 Processing helix chain 'C' and resid 193 through 199 Processing helix chain 'C' and resid 203 through 211 Processing helix chain 'C' and resid 240 through 244 Processing helix chain 'C' and resid 297 through 314 removed outlier: 4.662A pdb=" N SER C 313 " --> pdb=" O GLU C 309 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N SER C 314 " --> pdb=" O THR C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 356 Processing helix chain 'C' and resid 361 through 367 Processing helix chain 'C' and resid 370 through 384 Processing helix chain 'C' and resid 390 through 394 Processing helix chain 'C' and resid 396 through 423 removed outlier: 3.730A pdb=" N GLY C 401 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ASP C 405 " --> pdb=" O GLY C 401 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N ALA C 406 " --> pdb=" O ALA C 402 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ALA C 407 " --> pdb=" O MET C 403 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN C 422 " --> pdb=" O LEU C 418 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N HIS C 423 " --> pdb=" O GLU C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 434 through 466 removed outlier: 4.290A pdb=" N VAL C 446 " --> pdb=" O ALA C 442 " (cutoff:3.500A) Proline residue: C 448 - end of helix removed outlier: 4.614A pdb=" N PHE C 461 " --> pdb=" O ILE C 457 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N ILE C 462 " --> pdb=" O THR C 458 " (cutoff:3.500A) Proline residue: C 463 - end of helix Processing helix chain 'C' and resid 470 through 495 Proline residue: C 477 - end of helix Processing helix chain 'C' and resid 497 through 502 Processing helix chain 'C' and resid 518 through 556 Proline residue: C 527 - end of helix removed outlier: 3.543A pdb=" N HIS C 534 " --> pdb=" O LEU C 530 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N TRP C 535 " --> pdb=" O LYS C 531 " (cutoff:3.500A) Proline residue: C 536 - end of helix removed outlier: 4.630A pdb=" N LEU C 551 " --> pdb=" O VAL C 547 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N TRP C 552 " --> pdb=" O LEU C 548 " (cutoff:3.500A) Proline residue: C 553 - end of helix removed outlier: 3.952A pdb=" N LYS C 556 " --> pdb=" O TRP C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 582 through 598 removed outlier: 3.556A pdb=" N ALA C 586 " --> pdb=" O ALA C 582 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER C 598 " --> pdb=" O LYS C 594 " (cutoff:3.500A) Processing helix chain 'C' and resid 642 through 652 Processing helix chain 'C' and resid 665 through 673 Processing helix chain 'C' and resid 690 through 705 removed outlier: 3.503A pdb=" N GLN C 699 " --> pdb=" O ALA C 695 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLU C 702 " --> pdb=" O GLU C 698 " (cutoff:3.500A) Processing helix chain 'C' and resid 730 through 736 removed outlier: 4.228A pdb=" N TYR C 736 " --> pdb=" O LYS C 732 " (cutoff:3.500A) Processing helix chain 'C' and resid 740 through 749 removed outlier: 3.882A pdb=" N PHE C 746 " --> pdb=" O ASP C 742 " (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 785 removed outlier: 3.738A pdb=" N GLN C 785 " --> pdb=" O GLN C 781 " (cutoff:3.500A) Processing helix chain 'C' and resid 836 through 847 Processing helix chain 'C' and resid 862 through 891 removed outlier: 4.115A pdb=" N ARG C 867 " --> pdb=" O GLU C 863 " (cutoff:3.500A) Proline residue: C 877 - end of helix removed outlier: 3.872A pdb=" N LEU C 886 " --> pdb=" O ILE C 882 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 918 Proline residue: C 905 - end of helix removed outlier: 4.275A pdb=" N LEU C 914 " --> pdb=" O GLY C 910 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LEU C 915 " --> pdb=" O GLY C 911 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N TRP C 916 " --> pdb=" O ILE C 912 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N TRP C 917 " --> pdb=" O TRP C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 924 through 952 removed outlier: 3.503A pdb=" N TYR C 947 " --> pdb=" O VAL C 943 " (cutoff:3.500A) Processing helix chain 'C' and resid 955 through 960 removed outlier: 4.301A pdb=" N ASN C 960 " --> pdb=" O SER C 957 " (cutoff:3.500A) Processing helix chain 'C' and resid 967 through 980 removed outlier: 4.459A pdb=" N VAL C 978 " --> pdb=" O HIS C 975 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N LEU C 979 " --> pdb=" O GLY C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 982 through 999 Proline residue: C 997 - end of helix Processing helix chain 'C' and resid 1006 through 1021 Proline residue: C1015 - end of helix removed outlier: 4.437A pdb=" N ILE C1021 " --> pdb=" O ILE C1017 " (cutoff:3.500A) Processing helix chain 'C' and resid 1023 through 1036 removed outlier: 4.758A pdb=" N ILE C1031 " --> pdb=" O SER C1027 " (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: 8.601A pdb=" N ARG A 765 " --> pdb=" O LYS A 185 " (cutoff:3.500A) removed outlier: 9.321A pdb=" N TYR A 187 " --> pdb=" O ARG A 765 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N VAL A 189 " --> pdb=" O PRO A 767 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ASN A 769 " --> pdb=" O VAL A 189 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ILE A 191 " --> pdb=" O ASN A 769 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N ARG A 771 " --> pdb=" O ILE A 191 " (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 Processing sheet with id= F, first strand: chain 'A' and resid 854 through 860 removed outlier: 3.578A pdb=" N GLY A 682 " --> pdb=" O SER A 859 " (cutoff:3.500A) removed outlier: 4.161A 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 319 through 325 removed outlier: 6.714A pdb=" N GLU A 141 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL A 289 " --> pdb=" O ILE A 139 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLU A 141 " --> pdb=" O GLY A 287 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N GLY A 287 " --> pdb=" O GLU A 141 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N ALA A 143 " --> pdb=" O ALA A 285 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ALA A 285 " --> pdb=" O ALA A 143 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 46 through 52 Processing sheet with id= J, first strand: chain 'B' and resid 263 through 269 Processing sheet with id= K, first strand: chain 'B' and resid 274 through 277 removed outlier: 6.904A pdb=" N GLN B 629 " --> pdb=" O ALA B 603 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N VAL B 605 " --> pdb=" O THR B 627 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N THR B 627 " --> pdb=" O VAL B 605 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N GLY B 607 " --> pdb=" O GLU B 625 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N GLU B 625 " --> pdb=" O GLY B 607 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 821 through 826 Processing sheet with id= M, first strand: chain 'B' and resid 758 through 760 Processing sheet with id= N, first strand: chain 'B' and resid 319 through 325 removed outlier: 6.457A pdb=" N GLU B 141 " --> pdb=" O THR B 324 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL B 289 " --> pdb=" O ILE B 139 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N GLU B 141 " --> pdb=" O GLY B 287 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N GLY B 287 " --> pdb=" O GLU B 141 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N ALA B 143 " --> pdb=" O ALA B 285 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ALA B 285 " --> pdb=" O ALA B 143 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU B 176 " --> pdb=" O ILE B 290 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 719 through 728 removed outlier: 5.999A pdb=" N GLY B 809 " --> pdb=" O GLY B 720 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N ARG B 722 " --> pdb=" O SER B 807 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N SER B 807 " --> pdb=" O ARG B 722 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ILE B 724 " --> pdb=" O LYS B 805 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N LYS B 805 " --> pdb=" O ILE B 724 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N VAL B 726 " --> pdb=" O ASP B 803 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N ASP B 803 " --> pdb=" O VAL B 726 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 46 through 52 Processing sheet with id= Q, first strand: chain 'C' and resid 263 through 269 Processing sheet with id= R, first strand: chain 'C' and resid 274 through 277 removed outlier: 6.890A pdb=" N GLN C 629 " --> pdb=" O ALA C 603 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N VAL C 605 " --> pdb=" O THR C 627 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N THR C 627 " --> pdb=" O VAL C 605 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N GLY C 607 " --> pdb=" O GLU C 625 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLU C 625 " --> pdb=" O GLY C 607 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 821 through 826 Processing sheet with id= T, first strand: chain 'C' and resid 758 through 760 Processing sheet with id= U, first strand: chain 'C' and resid 319 through 326 removed outlier: 6.469A pdb=" N GLU C 141 " --> pdb=" O THR C 324 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ASP C 326 " --> pdb=" O ILE C 139 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N ILE C 139 " --> pdb=" O ASP C 326 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL C 289 " --> pdb=" O ILE C 139 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLU C 141 " --> pdb=" O GLY C 287 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N GLY C 287 " --> pdb=" O GLU C 141 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N ALA C 143 " --> pdb=" O ALA C 285 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ALA C 285 " --> pdb=" O ALA C 143 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU C 176 " --> pdb=" O ILE C 290 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'C' and resid 719 through 728 removed outlier: 5.981A pdb=" N GLY C 809 " --> pdb=" O GLY C 720 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N ARG C 722 " --> pdb=" O SER C 807 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N SER C 807 " --> pdb=" O ARG C 722 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ILE C 724 " --> pdb=" O LYS C 805 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N LYS C 805 " --> pdb=" O ILE C 724 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N VAL C 726 " --> pdb=" O ASP C 803 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N ASP C 803 " --> pdb=" O VAL C 726 " (cutoff:3.500A) 1177 hydrogen bonds defined for protein. 3309 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: 18.90 Time building geometry restraints manager: 40.60 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: 24241 1.03 - 1.23: 21 1.23 - 1.42: 9509 1.42 - 1.62: 14234 1.62 - 1.81: 210 Bond restraints: 48215 Sorted by residual: bond pdb=" N ILE B 464 " pdb=" CA ILE B 464 " ideal model delta sigma weight residual 1.460 1.497 -0.037 1.09e-02 8.42e+03 1.18e+01 bond pdb=" N GLU B 468 " pdb=" CA GLU B 468 " ideal model delta sigma weight residual 1.454 1.489 -0.036 1.18e-02 7.18e+03 9.15e+00 bond pdb=" N GLU B 560 " pdb=" CA GLU B 560 " ideal model delta sigma weight residual 1.454 1.492 -0.038 1.29e-02 6.01e+03 8.78e+00 bond pdb=" N ILE C 246 " pdb=" CA ILE C 246 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.17e-02 7.31e+03 8.42e+00 bond pdb=" N ILE C 222 " pdb=" CA ILE C 222 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.35e-02 5.49e+03 8.31e+00 ... (remaining 48210 not shown) Histogram of bond angle deviations from ideal: 100.14 - 106.95: 968 106.95 - 113.76: 59457 113.76 - 120.57: 15295 120.57 - 127.38: 11696 127.38 - 134.18: 327 Bond angle restraints: 87743 Sorted by residual: angle pdb=" C ARG A 637 " pdb=" CA ARG A 637 " pdb=" CB ARG A 637 " ideal model delta sigma weight residual 109.27 116.28 -7.01 1.61e+00 3.86e-01 1.90e+01 angle pdb=" CA GLY C 472 " pdb=" C GLY C 472 " pdb=" O GLY C 472 " ideal model delta sigma weight residual 120.66 116.42 4.24 1.06e+00 8.90e-01 1.60e+01 angle pdb=" CA TYR A 229 " pdb=" C TYR A 229 " pdb=" N MET A 230 " ideal model delta sigma weight residual 116.05 120.75 -4.70 1.19e+00 7.06e-01 1.56e+01 angle pdb=" N ARG A 735 " pdb=" CA ARG A 735 " pdb=" C ARG A 735 " ideal model delta sigma weight residual 111.71 107.27 4.44 1.15e+00 7.56e-01 1.49e+01 angle pdb=" C PRO A 632 " pdb=" N GLN A 633 " pdb=" CA GLN A 633 " ideal model delta sigma weight residual 120.60 126.55 -5.95 1.60e+00 3.91e-01 1.38e+01 ... (remaining 87738 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 20104 17.98 - 35.95: 1634 35.95 - 53.93: 582 53.93 - 71.90: 133 71.90 - 89.88: 17 Dihedral angle restraints: 22470 sinusoidal: 12436 harmonic: 10034 Sorted by residual: 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 -157.71 -22.29 0 5.00e+00 4.00e-02 1.99e+01 dihedral pdb=" CA PRO B 54 " pdb=" C PRO B 54 " pdb=" N GLY B 55 " pdb=" CA GLY B 55 " ideal model delta harmonic sigma weight residual -180.00 -160.95 -19.05 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA PRO C 54 " pdb=" C PRO C 54 " pdb=" N GLY C 55 " pdb=" CA GLY C 55 " ideal model delta harmonic sigma weight residual -180.00 -163.15 -16.85 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 22467 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 3100 0.047 - 0.094: 539 0.094 - 0.141: 220 0.141 - 0.188: 15 0.188 - 0.234: 3 Chirality restraints: 3877 Sorted by residual: chirality pdb=" CA ILE C 246 " pdb=" N ILE C 246 " pdb=" C ILE C 246 " pdb=" CB ILE C 246 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CA TYR C 53 " pdb=" N TYR C 53 " pdb=" C TYR C 53 " pdb=" CB TYR C 53 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA ILE B 565 " pdb=" N ILE B 565 " pdb=" C ILE B 565 " pdb=" CB ILE B 565 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.58e-01 ... (remaining 3874 not shown) Planarity restraints: 6996 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A 633 " -0.227 2.00e-02 2.50e+03 2.66e-01 1.06e+03 pdb=" CD GLN A 633 " 0.017 2.00e-02 2.50e+03 pdb=" OE1 GLN A 633 " 0.218 2.00e-02 2.50e+03 pdb=" NE2 GLN A 633 " 0.002 2.00e-02 2.50e+03 pdb="HE21 GLN A 633 " -0.408 2.00e-02 2.50e+03 pdb="HE22 GLN A 633 " 0.398 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 635 " 0.162 2.00e-02 2.50e+03 1.77e-01 4.72e+02 pdb=" CD GLN A 635 " -0.010 2.00e-02 2.50e+03 pdb=" OE1 GLN A 635 " -0.156 2.00e-02 2.50e+03 pdb=" NE2 GLN A 635 " 0.001 2.00e-02 2.50e+03 pdb="HE21 GLN A 635 " -0.261 2.00e-02 2.50e+03 pdb="HE22 GLN A 635 " 0.264 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 223 " 0.026 2.00e-02 2.50e+03 5.27e-02 2.78e+01 pdb=" C GLU C 223 " -0.091 2.00e-02 2.50e+03 pdb=" O GLU C 223 " 0.035 2.00e-02 2.50e+03 pdb=" N LEU C 224 " 0.030 2.00e-02 2.50e+03 ... (remaining 6993 not shown) Histogram of nonbonded interaction distances: 1.02 - 1.74: 53 1.74 - 2.45: 28059 2.45 - 3.17: 146010 3.17 - 3.88: 185586 3.88 - 4.60: 298611 Nonbonded interactions: 658319 Sorted by model distance: nonbonded pdb=" CE2 TRP C 552 " pdb=" HZ3 LYS C 556 " model vdw 1.019 2.800 nonbonded pdb=" CD2 TRP C 552 " pdb=" HZ3 LYS C 556 " model vdw 1.192 2.800 nonbonded pdb=" O PRO B 553 " pdb="HG23 VAL B 557 " model vdw 1.207 2.620 nonbonded pdb=" CD1 TRP C 552 " pdb=" HZ1 LYS C 556 " model vdw 1.229 2.800 nonbonded pdb=" HG2 PRO A 600 " pdb="HH11 ARG A 637 " model vdw 1.266 2.270 ... (remaining 658314 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 559 or (resid 5 \ 60 and (name N or name CA or name C or name O or name CB or name CG or name CD o \ r name OE1 or name OE2 or name H or name HA )) or resid 561 through 922 or (resi \ d 923 and (name N or name CA or name C or name O or name CB or name OG or name H \ or name HA )) or resid 924 through 1039)) selection = (chain 'B' and (resid 5 through 559 or (resid 560 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name OE1 or name OE2 or name H \ or name HA )) or resid 561 through 922 or (resid 923 and (name N or name CA or n \ ame C or name O or name CB or name OG or name H or name HA )) or resid 924 throu \ gh 1039)) selection = (chain 'C' and resid 5 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.710 Extract box with map and model: 3.680 Check model and map are aligned: 0.700 Set scattering table: 0.460 Process input model: 146.690 Find NCS groups from input model: 2.620 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: 0.010 Load rotamer database and sin/cos tables:12.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 168.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 23968 Z= 0.205 Angle : 0.573 7.475 32627 Z= 0.351 Chirality : 0.042 0.234 3877 Planarity : 0.003 0.053 4103 Dihedral : 15.435 89.881 8744 Min Nonbonded Distance : 1.527 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 0.04 % Allowed : 5.65 % Favored : 94.31 % 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: -2.34 (0.14), residues: 3039 helix: -0.50 (0.13), residues: 1631 sheet: -1.93 (0.21), residues: 401 loop : -3.03 (0.16), residues: 1007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 105 HIS 0.002 0.001 HIS B 526 PHE 0.017 0.001 PHE B 561 TYR 0.026 0.001 TYR A 229 ARG 0.011 0.001 ARG A 272 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 923 is missing expected H atoms. Skipping. Evaluate side-chains 769 residues out of total 2514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 768 time to evaluate : 3.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 LYS cc_start: 0.8449 (ttpt) cc_final: 0.8216 (ttmm) REVERT: A 190 VAL cc_start: 0.7940 (m) cc_final: 0.7618 (p) REVERT: A 416 LYS cc_start: 0.8964 (tppt) cc_final: 0.8701 (tppp) REVERT: A 494 ILE cc_start: 0.8819 (tp) cc_final: 0.8577 (tp) REVERT: A 671 ASP cc_start: 0.8113 (m-30) cc_final: 0.7867 (m-30) REVERT: A 805 LYS cc_start: 0.8456 (ptmm) cc_final: 0.8036 (ptmm) REVERT: A 874 LEU cc_start: 0.9045 (tp) cc_final: 0.8801 (tp) REVERT: A 883 ILE cc_start: 0.9019 (mt) cc_final: 0.8727 (mt) REVERT: A 939 GLU cc_start: 0.8318 (tm-30) cc_final: 0.8014 (tm-30) REVERT: A 1009 MET cc_start: 0.8895 (mmm) cc_final: 0.8627 (mpp) REVERT: B 73 MET cc_start: 0.8697 (mmt) cc_final: 0.8462 (mmt) REVERT: B 132 ASP cc_start: 0.7728 (t0) cc_final: 0.7290 (t0) REVERT: B 258 TYR cc_start: 0.7407 (m-10) cc_final: 0.6960 (m-10) REVERT: B 293 SER cc_start: 0.8811 (t) cc_final: 0.8560 (m) REVERT: B 422 GLN cc_start: 0.7984 (tt0) cc_final: 0.7739 (tm-30) REVERT: B 584 GLU cc_start: 0.7819 (tp30) cc_final: 0.7603 (tp30) REVERT: B 633 GLN cc_start: 0.7564 (tm-30) cc_final: 0.7253 (tp-100) REVERT: B 842 LYS cc_start: 0.8533 (mttp) cc_final: 0.7988 (mttt) REVERT: B 949 ARG cc_start: 0.8145 (mtp180) cc_final: 0.7937 (mtm110) REVERT: C 165 LYS cc_start: 0.8660 (ttmm) cc_final: 0.8455 (ttmm) REVERT: C 462 ILE cc_start: 0.9053 (mt) cc_final: 0.8821 (mm) REVERT: C 532 VAL cc_start: 0.9067 (t) cc_final: 0.8855 (t) REVERT: C 875 MET cc_start: 0.8263 (mmt) cc_final: 0.7730 (mmt) outliers start: 1 outliers final: 1 residues processed: 769 average time/residue: 2.2493 time to fit residues: 2065.2800 Evaluate side-chains 607 residues out of total 2514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 606 time to evaluate : 3.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 562 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 256 optimal weight: 0.8980 chunk 230 optimal weight: 10.0000 chunk 127 optimal weight: 10.0000 chunk 78 optimal weight: 9.9990 chunk 155 optimal weight: 10.0000 chunk 123 optimal weight: 8.9990 chunk 238 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 144 optimal weight: 4.9990 chunk 177 optimal weight: 7.9990 chunk 276 optimal weight: 7.9990 overall best weight: 3.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN A 526 HIS A 635 GLN A 774 GLN B 33 ASN B 279 ASN C 160 GLN C 296 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 23968 Z= 0.244 Angle : 0.561 6.496 32627 Z= 0.280 Chirality : 0.041 0.144 3877 Planarity : 0.004 0.080 4103 Dihedral : 3.363 32.555 3274 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 2.15 % Allowed : 19.73 % Favored : 78.12 % 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: -1.13 (0.15), residues: 3039 helix: 0.53 (0.13), residues: 1635 sheet: -1.37 (0.22), residues: 430 loop : -2.62 (0.18), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 552 HIS 0.009 0.001 HIS C 526 PHE 0.017 0.001 PHE B 862 TYR 0.022 0.001 TYR B 974 ARG 0.006 0.000 ARG B 195 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 923 is missing expected H atoms. Skipping. Evaluate side-chains 683 residues out of total 2514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 629 time to evaluate : 3.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 LYS cc_start: 0.8646 (ttpt) cc_final: 0.8362 (ttmm) REVERT: A 190 VAL cc_start: 0.8131 (m) cc_final: 0.7840 (p) REVERT: A 416 LYS cc_start: 0.9035 (tppt) cc_final: 0.8735 (tppp) REVERT: A 494 ILE cc_start: 0.8927 (tp) cc_final: 0.8675 (tp) REVERT: A 530 LEU cc_start: 0.8832 (mm) cc_final: 0.8593 (mp) REVERT: A 805 LYS cc_start: 0.8520 (ptmm) cc_final: 0.8110 (ptmm) REVERT: A 874 LEU cc_start: 0.9069 (tp) cc_final: 0.8821 (tt) REVERT: A 939 GLU cc_start: 0.8391 (tm-30) cc_final: 0.8159 (tm-30) REVERT: A 1009 MET cc_start: 0.8948 (mmm) cc_final: 0.8624 (mpp) REVERT: B 73 MET cc_start: 0.8725 (mmt) cc_final: 0.8446 (mmp) REVERT: B 132 ASP cc_start: 0.8014 (t0) cc_final: 0.7312 (t0) REVERT: B 231 VAL cc_start: 0.6986 (OUTLIER) cc_final: 0.6781 (t) REVERT: B 293 SER cc_start: 0.9045 (t) cc_final: 0.8684 (m) REVERT: B 422 GLN cc_start: 0.8117 (tt0) cc_final: 0.7795 (tm-30) REVERT: C 132 ASP cc_start: 0.7280 (t0) cc_final: 0.6939 (t0) REVERT: C 165 LYS cc_start: 0.8813 (ttmm) cc_final: 0.8558 (ttmm) REVERT: C 501 MET cc_start: 0.6566 (ptm) cc_final: 0.6183 (ptm) REVERT: C 524 VAL cc_start: 0.9386 (t) cc_final: 0.9136 (t) REVERT: C 661 LEU cc_start: 0.8480 (mt) cc_final: 0.8234 (mp) REVERT: C 671 ASP cc_start: 0.7614 (m-30) cc_final: 0.7351 (m-30) REVERT: C 672 MET cc_start: 0.8393 (mmm) cc_final: 0.8167 (mmm) REVERT: C 875 MET cc_start: 0.8372 (mmt) cc_final: 0.8085 (tpp) REVERT: C 984 LYS cc_start: 0.8427 (tppt) cc_final: 0.8179 (tppt) outliers start: 54 outliers final: 23 residues processed: 657 average time/residue: 2.2281 time to fit residues: 1757.0523 Evaluate side-chains 606 residues out of total 2514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 582 time to evaluate : 4.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 581 SER Chi-restraints excluded: chain A residue 775 SER Chi-restraints excluded: chain A residue 796 ILE Chi-restraints excluded: chain A residue 855 SER Chi-restraints excluded: chain A residue 873 LYS Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 353 CYS Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 815 THR Chi-restraints excluded: chain B residue 833 MET Chi-restraints excluded: chain B residue 950 HIS Chi-restraints excluded: chain B residue 969 LEU Chi-restraints excluded: chain B residue 973 LEU Chi-restraints excluded: chain C residue 358 TRP Chi-restraints excluded: chain C residue 462 ILE Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 646 ILE Chi-restraints excluded: chain C residue 859 SER Chi-restraints excluded: chain C residue 880 LEU Chi-restraints excluded: chain C residue 959 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 153 optimal weight: 4.9990 chunk 85 optimal weight: 9.9990 chunk 229 optimal weight: 8.9990 chunk 187 optimal weight: 2.9990 chunk 76 optimal weight: 0.3980 chunk 276 optimal weight: 0.0670 chunk 298 optimal weight: 4.9990 chunk 246 optimal weight: 6.9990 chunk 274 optimal weight: 8.9990 chunk 94 optimal weight: 10.0000 chunk 221 optimal weight: 1.9990 overall best weight: 2.0924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN A 87 GLN A 526 HIS B 253 ASN B 384 GLN B 387 ASN B 635 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 23968 Z= 0.174 Angle : 0.531 5.778 32627 Z= 0.259 Chirality : 0.041 0.156 3877 Planarity : 0.004 0.060 4103 Dihedral : 3.281 22.427 3272 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 1.71 % Allowed : 22.91 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.16), residues: 3039 helix: 1.03 (0.14), residues: 1634 sheet: -0.99 (0.23), residues: 431 loop : -2.29 (0.19), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 552 HIS 0.006 0.001 HIS C 526 PHE 0.014 0.001 PHE B 465 TYR 0.018 0.001 TYR B 974 ARG 0.006 0.000 ARG B 195 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 923 is missing expected H atoms. Skipping. Evaluate side-chains 635 residues out of total 2514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 592 time to evaluate : 4.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 LYS cc_start: 0.8682 (ttpt) cc_final: 0.8433 (ttmm) REVERT: A 190 VAL cc_start: 0.8213 (m) cc_final: 0.7850 (p) REVERT: A 416 LYS cc_start: 0.9060 (tppt) cc_final: 0.8759 (tppp) REVERT: A 437 GLN cc_start: 0.7277 (tm-30) cc_final: 0.7074 (tm-30) REVERT: A 494 ILE cc_start: 0.8901 (tp) cc_final: 0.8641 (tp) REVERT: A 530 LEU cc_start: 0.8715 (mm) cc_final: 0.8456 (mp) REVERT: A 535 TRP cc_start: 0.7569 (m-10) cc_final: 0.7238 (m-10) REVERT: A 805 LYS cc_start: 0.8504 (ptmm) cc_final: 0.8166 (ptmm) REVERT: A 939 GLU cc_start: 0.8407 (tm-30) cc_final: 0.8135 (tm-30) REVERT: B 73 MET cc_start: 0.8710 (mmt) cc_final: 0.8437 (mmp) REVERT: B 132 ASP cc_start: 0.8063 (t0) cc_final: 0.7356 (t0) REVERT: B 293 SER cc_start: 0.9076 (t) cc_final: 0.8699 (m) REVERT: B 422 GLN cc_start: 0.8112 (tt0) cc_final: 0.7798 (tm-30) REVERT: B 441 ASP cc_start: 0.8092 (p0) cc_final: 0.7876 (p0) REVERT: B 519 ARG cc_start: 0.5608 (mtt-85) cc_final: 0.5404 (mmt180) REVERT: B 949 ARG cc_start: 0.8376 (OUTLIER) cc_final: 0.7727 (mtm180) REVERT: C 132 ASP cc_start: 0.7283 (t0) cc_final: 0.6950 (t0) REVERT: C 165 LYS cc_start: 0.8825 (ttmm) cc_final: 0.8539 (ttmm) REVERT: C 524 VAL cc_start: 0.9408 (t) cc_final: 0.9166 (t) REVERT: C 593 ASP cc_start: 0.8561 (m-30) cc_final: 0.8219 (m-30) REVERT: C 661 LEU cc_start: 0.8531 (mt) cc_final: 0.8261 (mp) outliers start: 43 outliers final: 21 residues processed: 615 average time/residue: 2.3008 time to fit residues: 1694.9662 Evaluate side-chains 587 residues out of total 2514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 565 time to evaluate : 3.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 873 LYS Chi-restraints excluded: chain A residue 889 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 353 CYS Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 833 MET Chi-restraints excluded: chain B residue 949 ARG Chi-restraints excluded: chain B residue 969 LEU Chi-restraints excluded: chain B residue 973 LEU Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 358 TRP Chi-restraints excluded: chain C residue 439 ILE Chi-restraints excluded: chain C residue 445 GLU Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 844 ILE Chi-restraints excluded: chain C residue 959 ASN Chi-restraints excluded: chain C residue 969 LEU Chi-restraints excluded: chain C residue 998 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 273 optimal weight: 0.8980 chunk 207 optimal weight: 10.0000 chunk 143 optimal weight: 10.0000 chunk 30 optimal weight: 7.9990 chunk 131 optimal weight: 7.9990 chunk 185 optimal weight: 9.9990 chunk 277 optimal weight: 7.9990 chunk 293 optimal weight: 6.9990 chunk 145 optimal weight: 4.9990 chunk 263 optimal weight: 1.9990 chunk 79 optimal weight: 10.0000 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN ** A 959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 384 GLN B 729 ASN C 424 GLN C 795 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.3835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.129 23968 Z= 0.290 Angle : 0.576 5.966 32627 Z= 0.293 Chirality : 0.042 0.184 3877 Planarity : 0.004 0.078 4103 Dihedral : 3.643 23.372 3272 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 3.02 % Allowed : 22.16 % Favored : 74.82 % 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: -0.19 (0.16), residues: 3039 helix: 1.15 (0.13), residues: 1640 sheet: -0.73 (0.23), residues: 429 loop : -2.04 (0.19), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 552 HIS 0.006 0.001 HIS C 526 PHE 0.021 0.001 PHE B 862 TYR 0.025 0.001 TYR B 974 ARG 0.008 0.001 ARG A 819 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 923 is missing expected H atoms. Skipping. Evaluate side-chains 659 residues out of total 2514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 583 time to evaluate : 3.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 LYS cc_start: 0.8824 (ttpt) cc_final: 0.8566 (ttmm) REVERT: A 85 PHE cc_start: 0.8386 (OUTLIER) cc_final: 0.7401 (p90) REVERT: A 416 LYS cc_start: 0.9136 (tppt) cc_final: 0.8850 (tppp) REVERT: A 494 ILE cc_start: 0.8978 (tp) cc_final: 0.8659 (tp) REVERT: A 597 MET cc_start: 0.9039 (mmm) cc_final: 0.8652 (mmm) REVERT: A 756 VAL cc_start: 0.9081 (p) cc_final: 0.8798 (m) REVERT: A 805 LYS cc_start: 0.8538 (ptmm) cc_final: 0.8185 (ptmm) REVERT: A 939 GLU cc_start: 0.8419 (tm-30) cc_final: 0.8202 (tm-30) REVERT: B 441 ASP cc_start: 0.8125 (p0) cc_final: 0.7851 (p0) REVERT: B 526 HIS cc_start: 0.6593 (m-70) cc_final: 0.6091 (m170) REVERT: B 567 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7917 (mt-10) REVERT: B 729 ASN cc_start: 0.8545 (OUTLIER) cc_final: 0.8343 (t0) REVERT: B 949 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.7719 (mtm110) REVERT: C 132 ASP cc_start: 0.7585 (t0) cc_final: 0.7355 (t0) REVERT: C 165 LYS cc_start: 0.8831 (ttmm) cc_final: 0.8572 (ttmm) REVERT: C 230 MET cc_start: 0.8596 (ptm) cc_final: 0.8342 (ptm) REVERT: C 258 TYR cc_start: 0.8815 (m-80) cc_final: 0.8601 (m-80) REVERT: C 327 ARG cc_start: 0.8732 (OUTLIER) cc_final: 0.8054 (mtt-85) REVERT: C 671 ASP cc_start: 0.7655 (m-30) cc_final: 0.7300 (m-30) REVERT: C 875 MET cc_start: 0.8562 (tpp) cc_final: 0.8177 (tpp) outliers start: 76 outliers final: 34 residues processed: 626 average time/residue: 2.3662 time to fit residues: 1756.9132 Evaluate side-chains 585 residues out of total 2514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 547 time to evaluate : 3.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 PHE Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 796 ILE Chi-restraints excluded: chain A residue 873 LYS Chi-restraints excluded: chain B residue 33 ASN Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 353 CYS Chi-restraints excluded: chain B residue 358 TRP Chi-restraints excluded: chain B residue 384 GLN Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 588 MET Chi-restraints excluded: chain B residue 729 ASN Chi-restraints excluded: chain B residue 815 THR Chi-restraints excluded: chain B residue 859 SER Chi-restraints excluded: chain B residue 949 ARG Chi-restraints excluded: chain B residue 969 LEU Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 272 ARG Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain C residue 358 TRP Chi-restraints excluded: chain C residue 439 ILE Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 647 GLU Chi-restraints excluded: chain C residue 760 VAL Chi-restraints excluded: chain C residue 844 ILE Chi-restraints excluded: chain C residue 859 SER Chi-restraints excluded: chain C residue 959 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 244 optimal weight: 9.9990 chunk 166 optimal weight: 0.0770 chunk 4 optimal weight: 8.9990 chunk 218 optimal weight: 7.9990 chunk 121 optimal weight: 7.9990 chunk 250 optimal weight: 10.0000 chunk 203 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 chunk 150 optimal weight: 7.9990 chunk 263 optimal weight: 7.9990 chunk 74 optimal weight: 6.9990 overall best weight: 6.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 962 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.4319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 23968 Z= 0.348 Angle : 0.598 6.215 32627 Z= 0.305 Chirality : 0.043 0.161 3877 Planarity : 0.005 0.080 4103 Dihedral : 3.838 24.099 3272 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 3.46 % Allowed : 23.95 % Favored : 72.59 % 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: -0.17 (0.16), residues: 3039 helix: 1.12 (0.13), residues: 1642 sheet: -0.66 (0.23), residues: 435 loop : -1.99 (0.20), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 162 HIS 0.006 0.001 HIS A 526 PHE 0.017 0.001 PHE A 85 TYR 0.027 0.001 TYR B 974 ARG 0.008 0.001 ARG B 195 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 923 is missing expected H atoms. Skipping. Evaluate side-chains 642 residues out of total 2514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 555 time to evaluate : 3.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 LYS cc_start: 0.8836 (ttpt) cc_final: 0.8612 (ttmm) REVERT: A 85 PHE cc_start: 0.8373 (OUTLIER) cc_final: 0.7416 (p90) REVERT: A 416 LYS cc_start: 0.9146 (tppt) cc_final: 0.8872 (tppp) REVERT: A 528 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8511 (mm) REVERT: A 597 MET cc_start: 0.9030 (mmm) cc_final: 0.8575 (mmm) REVERT: A 939 GLU cc_start: 0.8424 (tm-30) cc_final: 0.8218 (tm-30) REVERT: B 271 MET cc_start: 0.7729 (OUTLIER) cc_final: 0.7322 (mpp) REVERT: B 441 ASP cc_start: 0.7788 (p0) cc_final: 0.7487 (p0) REVERT: B 526 HIS cc_start: 0.6850 (OUTLIER) cc_final: 0.6092 (m170) REVERT: B 949 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.7754 (mtm110) REVERT: C 327 ARG cc_start: 0.8764 (OUTLIER) cc_final: 0.8100 (mtt-85) REVERT: C 370 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8579 (mt) REVERT: C 462 ILE cc_start: 0.9153 (OUTLIER) cc_final: 0.8889 (mm) REVERT: C 565 ILE cc_start: 0.8967 (pt) cc_final: 0.8582 (mt) REVERT: C 588 MET cc_start: 0.7944 (mmm) cc_final: 0.7737 (tpt) REVERT: C 671 ASP cc_start: 0.7591 (m-30) cc_final: 0.7267 (m-30) REVERT: C 875 MET cc_start: 0.8542 (tpp) cc_final: 0.7801 (tpp) outliers start: 87 outliers final: 47 residues processed: 596 average time/residue: 2.3985 time to fit residues: 1706.1864 Evaluate side-chains 580 residues out of total 2514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 525 time to evaluate : 3.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 PHE Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 581 SER Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 796 ILE Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 855 SER Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 33 ASN Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 271 MET Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 353 CYS Chi-restraints excluded: chain B residue 358 TRP Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 526 HIS Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 566 ASN Chi-restraints excluded: chain B residue 588 MET Chi-restraints excluded: chain B residue 815 THR Chi-restraints excluded: chain B residue 949 ARG Chi-restraints excluded: chain B residue 969 LEU Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 272 ARG Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain C residue 358 TRP Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 462 ILE Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 643 ASP Chi-restraints excluded: chain C residue 718 LEU Chi-restraints excluded: chain C residue 760 VAL Chi-restraints excluded: chain C residue 844 ILE Chi-restraints excluded: chain C residue 859 SER Chi-restraints excluded: chain C residue 946 MET Chi-restraints excluded: chain C residue 959 ASN Chi-restraints excluded: chain C residue 969 LEU Chi-restraints excluded: chain C residue 998 ILE Chi-restraints excluded: chain C residue 1002 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 98 optimal weight: 6.9990 chunk 264 optimal weight: 9.9990 chunk 58 optimal weight: 4.9990 chunk 172 optimal weight: 8.9990 chunk 72 optimal weight: 9.9990 chunk 294 optimal weight: 3.9990 chunk 244 optimal weight: 10.0000 chunk 136 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 97 optimal weight: 3.9990 chunk 154 optimal weight: 0.9990 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 781 GLN ** A 959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 962 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 590 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.4496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 23968 Z= 0.252 Angle : 0.576 6.429 32627 Z= 0.289 Chirality : 0.042 0.184 3877 Planarity : 0.004 0.080 4103 Dihedral : 3.791 24.791 3272 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 3.38 % Allowed : 24.98 % Favored : 71.64 % 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: 0.04 (0.16), residues: 3039 helix: 1.29 (0.13), residues: 1640 sheet: -0.55 (0.23), residues: 430 loop : -1.90 (0.20), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 436 HIS 0.005 0.001 HIS A 526 PHE 0.020 0.001 PHE C 465 TYR 0.024 0.001 TYR B 974 ARG 0.010 0.000 ARG B 195 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 923 is missing expected H atoms. Skipping. Evaluate side-chains 631 residues out of total 2514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 546 time to evaluate : 3.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 LYS cc_start: 0.8829 (ttpt) cc_final: 0.8567 (ttmm) REVERT: A 416 LYS cc_start: 0.9139 (tppt) cc_final: 0.8876 (tppp) REVERT: A 528 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8476 (mm) REVERT: A 597 MET cc_start: 0.9002 (mmm) cc_final: 0.8439 (mmm) REVERT: A 756 VAL cc_start: 0.9297 (p) cc_final: 0.9046 (m) REVERT: A 939 GLU cc_start: 0.8405 (tm-30) cc_final: 0.8186 (tm-30) REVERT: B 132 ASP cc_start: 0.8099 (t0) cc_final: 0.7551 (t0) REVERT: B 271 MET cc_start: 0.7725 (OUTLIER) cc_final: 0.7323 (mpp) REVERT: B 441 ASP cc_start: 0.7723 (p0) cc_final: 0.7457 (p0) REVERT: C 5 ILE cc_start: 0.3607 (OUTLIER) cc_final: 0.3261 (pt) REVERT: C 327 ARG cc_start: 0.8715 (OUTLIER) cc_final: 0.8065 (mtt-85) REVERT: C 370 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8555 (mt) REVERT: C 462 ILE cc_start: 0.9154 (OUTLIER) cc_final: 0.8900 (mm) REVERT: C 671 ASP cc_start: 0.7574 (m-30) cc_final: 0.7243 (m-30) outliers start: 85 outliers final: 50 residues processed: 589 average time/residue: 2.4642 time to fit residues: 1746.7083 Evaluate side-chains 583 residues out of total 2514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 527 time to evaluate : 3.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 581 SER Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 796 ILE Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 33 ASN Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 271 MET Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 353 CYS Chi-restraints excluded: chain B residue 358 TRP Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 435 ARG Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 497 ILE Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 566 ASN Chi-restraints excluded: chain B residue 588 MET Chi-restraints excluded: chain B residue 815 THR Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 969 LEU Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 6 ILE Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 272 ARG Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain C residue 358 TRP Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 462 ILE Chi-restraints excluded: chain C residue 465 PHE Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 643 ASP Chi-restraints excluded: chain C residue 647 GLU Chi-restraints excluded: chain C residue 718 LEU Chi-restraints excluded: chain C residue 760 VAL Chi-restraints excluded: chain C residue 844 ILE Chi-restraints excluded: chain C residue 859 SER Chi-restraints excluded: chain C residue 946 MET Chi-restraints excluded: chain C residue 959 ASN Chi-restraints excluded: chain C residue 998 ILE Chi-restraints excluded: chain C residue 1002 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 283 optimal weight: 7.9990 chunk 33 optimal weight: 8.9990 chunk 167 optimal weight: 5.9990 chunk 214 optimal weight: 9.9990 chunk 166 optimal weight: 7.9990 chunk 247 optimal weight: 8.9990 chunk 164 optimal weight: 0.3980 chunk 293 optimal weight: 10.0000 chunk 183 optimal weight: 10.0000 chunk 178 optimal weight: 7.9990 chunk 135 optimal weight: 7.9990 overall best weight: 6.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 962 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.4843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 23968 Z= 0.345 Angle : 0.609 6.198 32627 Z= 0.312 Chirality : 0.043 0.172 3877 Planarity : 0.005 0.073 4103 Dihedral : 3.990 26.820 3272 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.78 % Favored : 93.19 % Rotamer: Outliers : 3.86 % Allowed : 24.98 % Favored : 71.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.15), residues: 3039 helix: 1.15 (0.13), residues: 1641 sheet: -0.57 (0.23), residues: 435 loop : -1.88 (0.20), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 535 HIS 0.007 0.001 HIS A 526 PHE 0.017 0.001 PHE A 22 TYR 0.029 0.002 TYR B 974 ARG 0.008 0.000 ARG C 7 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 923 is missing expected H atoms. Skipping. Evaluate side-chains 643 residues out of total 2514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 546 time to evaluate : 3.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 LYS cc_start: 0.8822 (ttpt) cc_final: 0.8593 (ttmm) REVERT: A 85 PHE cc_start: 0.8342 (OUTLIER) cc_final: 0.7411 (p90) REVERT: A 320 GLU cc_start: 0.7149 (mp0) cc_final: 0.6913 (mp0) REVERT: A 416 LYS cc_start: 0.9148 (tppt) cc_final: 0.8892 (tppp) REVERT: A 528 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8472 (mm) REVERT: A 597 MET cc_start: 0.8985 (mmm) cc_final: 0.8468 (mmm) REVERT: A 756 VAL cc_start: 0.9342 (p) cc_final: 0.9132 (m) REVERT: A 898 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8550 (mm) REVERT: A 939 GLU cc_start: 0.8421 (tm-30) cc_final: 0.8201 (tm-30) REVERT: B 271 MET cc_start: 0.7678 (OUTLIER) cc_final: 0.7269 (mpp) REVERT: B 438 VAL cc_start: 0.6987 (t) cc_final: 0.6556 (t) REVERT: B 441 ASP cc_start: 0.7699 (p0) cc_final: 0.7496 (p0) REVERT: B 526 HIS cc_start: 0.6759 (OUTLIER) cc_final: 0.5883 (m170) REVERT: B 623 MET cc_start: 0.9172 (ttt) cc_final: 0.8753 (ttt) REVERT: B 842 LYS cc_start: 0.8307 (mttt) cc_final: 0.7736 (mttt) REVERT: C 5 ILE cc_start: 0.3511 (OUTLIER) cc_final: 0.3213 (pt) REVERT: C 211 ASP cc_start: 0.8047 (p0) cc_final: 0.7795 (p0) REVERT: C 327 ARG cc_start: 0.8737 (OUTLIER) cc_final: 0.8089 (mtt-85) REVERT: C 462 ILE cc_start: 0.9157 (mt) cc_final: 0.8940 (mm) REVERT: C 565 ILE cc_start: 0.8832 (pt) cc_final: 0.8546 (mt) REVERT: C 588 MET cc_start: 0.8213 (OUTLIER) cc_final: 0.7980 (mmm) REVERT: C 643 ASP cc_start: 0.8052 (OUTLIER) cc_final: 0.7823 (m-30) REVERT: C 671 ASP cc_start: 0.7571 (m-30) cc_final: 0.7243 (m-30) REVERT: C 875 MET cc_start: 0.8350 (tpp) cc_final: 0.8110 (tpt) outliers start: 97 outliers final: 54 residues processed: 600 average time/residue: 2.3571 time to fit residues: 1687.1694 Evaluate side-chains 592 residues out of total 2514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 529 time to evaluate : 3.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 PHE Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 581 SER Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 796 ILE Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 855 SER Chi-restraints excluded: chain A residue 873 LYS Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 33 ASN Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 271 MET Chi-restraints excluded: chain B residue 353 CYS Chi-restraints excluded: chain B residue 358 TRP Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 435 ARG Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 445 GLU Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 526 HIS Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 566 ASN Chi-restraints excluded: chain B residue 588 MET Chi-restraints excluded: chain B residue 815 THR Chi-restraints excluded: chain B residue 859 SER Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 918 MET Chi-restraints excluded: chain B residue 959 ASN Chi-restraints excluded: chain B residue 969 LEU Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 6 ILE Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 272 ARG Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain C residue 358 TRP Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 445 GLU Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain C residue 465 PHE Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 588 MET Chi-restraints excluded: chain C residue 643 ASP Chi-restraints excluded: chain C residue 647 GLU Chi-restraints excluded: chain C residue 760 VAL Chi-restraints excluded: chain C residue 859 SER Chi-restraints excluded: chain C residue 946 MET Chi-restraints excluded: chain C residue 959 ASN Chi-restraints excluded: chain C residue 1002 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 181 optimal weight: 4.9990 chunk 117 optimal weight: 5.9990 chunk 174 optimal weight: 9.9990 chunk 88 optimal weight: 0.9990 chunk 57 optimal weight: 8.9990 chunk 56 optimal weight: 7.9990 chunk 186 optimal weight: 7.9990 chunk 199 optimal weight: 3.9990 chunk 144 optimal weight: 7.9990 chunk 27 optimal weight: 6.9990 chunk 230 optimal weight: 8.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 781 GLN ** A 959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 384 GLN B 635 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.5021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 23968 Z= 0.275 Angle : 0.599 7.240 32627 Z= 0.303 Chirality : 0.042 0.158 3877 Planarity : 0.005 0.076 4103 Dihedral : 3.960 27.932 3272 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 3.10 % Allowed : 26.81 % Favored : 70.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.16), residues: 3039 helix: 1.27 (0.13), residues: 1642 sheet: -0.50 (0.23), residues: 433 loop : -1.81 (0.20), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 636 HIS 0.007 0.001 HIS A 526 PHE 0.020 0.001 PHE A 22 TYR 0.026 0.001 TYR B 974 ARG 0.010 0.000 ARG B 195 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 923 is missing expected H atoms. Skipping. Evaluate side-chains 619 residues out of total 2514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 541 time to evaluate : 3.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 LYS cc_start: 0.8794 (ttpt) cc_final: 0.8573 (ttmm) REVERT: A 85 PHE cc_start: 0.8344 (OUTLIER) cc_final: 0.7390 (p90) REVERT: A 320 GLU cc_start: 0.7159 (mp0) cc_final: 0.6929 (mp0) REVERT: A 416 LYS cc_start: 0.9151 (tppt) cc_final: 0.8889 (tppp) REVERT: A 528 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8451 (mm) REVERT: A 597 MET cc_start: 0.8981 (mmm) cc_final: 0.8423 (mmm) REVERT: A 781 GLN cc_start: 0.7422 (mm-40) cc_final: 0.7198 (mp-120) REVERT: A 898 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8533 (mm) REVERT: A 939 GLU cc_start: 0.8406 (tm-30) cc_final: 0.8151 (tm-30) REVERT: B 271 MET cc_start: 0.7718 (OUTLIER) cc_final: 0.7291 (mpp) REVERT: B 438 VAL cc_start: 0.7083 (t) cc_final: 0.6755 (t) REVERT: B 526 HIS cc_start: 0.6659 (OUTLIER) cc_final: 0.5854 (m170) REVERT: B 528 LEU cc_start: 0.9393 (mm) cc_final: 0.9131 (mm) REVERT: B 842 LYS cc_start: 0.8362 (mttt) cc_final: 0.7708 (mttt) REVERT: C 5 ILE cc_start: 0.3606 (OUTLIER) cc_final: 0.3251 (pt) REVERT: C 211 ASP cc_start: 0.7986 (p0) cc_final: 0.7741 (p0) REVERT: C 327 ARG cc_start: 0.8685 (OUTLIER) cc_final: 0.8054 (mtt-85) REVERT: C 370 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8594 (mp) REVERT: C 565 ILE cc_start: 0.8851 (pt) cc_final: 0.8588 (mt) REVERT: C 588 MET cc_start: 0.8175 (OUTLIER) cc_final: 0.7778 (mmm) REVERT: C 593 ASP cc_start: 0.8512 (m-30) cc_final: 0.8269 (m-30) REVERT: C 643 ASP cc_start: 0.8058 (OUTLIER) cc_final: 0.7818 (m-30) REVERT: C 671 ASP cc_start: 0.7553 (m-30) cc_final: 0.7235 (m-30) REVERT: C 875 MET cc_start: 0.8500 (tpp) cc_final: 0.8082 (tpp) outliers start: 78 outliers final: 51 residues processed: 585 average time/residue: 2.3811 time to fit residues: 1663.3089 Evaluate side-chains 583 residues out of total 2514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 522 time to evaluate : 3.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 PHE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 581 SER Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 855 SER Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 33 ASN Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 271 MET Chi-restraints excluded: chain B residue 353 CYS Chi-restraints excluded: chain B residue 358 TRP Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain B residue 384 GLN Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 435 ARG Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 445 GLU Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 526 HIS Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 566 ASN Chi-restraints excluded: chain B residue 588 MET Chi-restraints excluded: chain B residue 815 THR Chi-restraints excluded: chain B residue 859 SER Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 918 MET Chi-restraints excluded: chain B residue 959 ASN Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 6 ILE Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 272 ARG Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain C residue 358 TRP Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 445 GLU Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain C residue 465 PHE Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 588 MET Chi-restraints excluded: chain C residue 643 ASP Chi-restraints excluded: chain C residue 760 VAL Chi-restraints excluded: chain C residue 859 SER Chi-restraints excluded: chain C residue 946 MET Chi-restraints excluded: chain C residue 959 ASN Chi-restraints excluded: chain C residue 1002 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 266 optimal weight: 3.9990 chunk 280 optimal weight: 0.9990 chunk 256 optimal weight: 5.9990 chunk 273 optimal weight: 2.9990 chunk 164 optimal weight: 1.9990 chunk 118 optimal weight: 8.9990 chunk 214 optimal weight: 0.6980 chunk 83 optimal weight: 9.9990 chunk 246 optimal weight: 3.9990 chunk 258 optimal weight: 1.9990 chunk 272 optimal weight: 10.0000 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 635 GLN C 870 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.4990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 23968 Z= 0.178 Angle : 0.581 6.678 32627 Z= 0.288 Chirality : 0.041 0.172 3877 Planarity : 0.004 0.078 4103 Dihedral : 3.794 26.364 3272 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 1.99 % Allowed : 28.04 % Favored : 69.97 % 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: 0.38 (0.16), residues: 3039 helix: 1.53 (0.13), residues: 1633 sheet: -0.37 (0.23), residues: 430 loop : -1.67 (0.20), residues: 976 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 0.020 0.001 PHE A 22 TYR 0.021 0.001 TYR B 974 ARG 0.010 0.000 ARG B 195 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 923 is missing expected H atoms. Skipping. Evaluate side-chains 591 residues out of total 2514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 541 time to evaluate : 4.019 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 80 LYS cc_start: 0.8777 (ttpt) cc_final: 0.8553 (ttmm) REVERT: A 320 GLU cc_start: 0.7154 (mp0) cc_final: 0.6925 (mp0) REVERT: A 416 LYS cc_start: 0.9138 (tppt) cc_final: 0.8878 (tppp) REVERT: A 528 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8459 (mm) REVERT: A 597 MET cc_start: 0.8984 (mmm) cc_final: 0.8545 (mmm) REVERT: A 898 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8469 (mm) REVERT: A 939 GLU cc_start: 0.8328 (tm-30) cc_final: 0.8120 (tm-30) REVERT: B 132 ASP cc_start: 0.8095 (t0) cc_final: 0.7454 (t0) REVERT: C 211 ASP cc_start: 0.7992 (p0) cc_final: 0.7714 (p0) REVERT: C 435 ARG cc_start: 0.3632 (ptt180) cc_final: 0.3250 (ptt180) REVERT: C 565 ILE cc_start: 0.8845 (pt) cc_final: 0.8595 (mt) REVERT: C 593 ASP cc_start: 0.8455 (m-30) cc_final: 0.8193 (m-30) REVERT: C 671 ASP cc_start: 0.7518 (m-30) cc_final: 0.7211 (m-30) REVERT: C 696 MET cc_start: 0.8507 (mtm) cc_final: 0.8114 (mtp) REVERT: C 875 MET cc_start: 0.8481 (tpp) cc_final: 0.8072 (tpp) outliers start: 50 outliers final: 33 residues processed: 568 average time/residue: 2.2771 time to fit residues: 1542.4597 Evaluate side-chains 563 residues out of total 2514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 528 time to evaluate : 3.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 581 SER Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 855 SER Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 353 CYS Chi-restraints excluded: chain B residue 358 TRP Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 435 ARG Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 588 MET Chi-restraints excluded: chain B residue 859 SER Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 918 MET Chi-restraints excluded: chain C residue 6 ILE Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 358 TRP Chi-restraints excluded: chain C residue 445 GLU Chi-restraints excluded: chain C residue 465 PHE Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 760 VAL Chi-restraints excluded: chain C residue 859 SER Chi-restraints excluded: chain C residue 959 ASN Chi-restraints excluded: chain C residue 1002 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 179 optimal weight: 0.9980 chunk 288 optimal weight: 1.9990 chunk 176 optimal weight: 0.6980 chunk 136 optimal weight: 7.9990 chunk 200 optimal weight: 5.9990 chunk 302 optimal weight: 7.9990 chunk 278 optimal weight: 5.9990 chunk 241 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 186 optimal weight: 4.9990 chunk 147 optimal weight: 5.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 781 GLN ** A 959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 384 GLN C 870 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.5076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23968 Z= 0.212 Angle : 0.587 6.664 32627 Z= 0.293 Chirality : 0.042 0.163 3877 Planarity : 0.005 0.080 4103 Dihedral : 3.780 25.867 3272 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 1.79 % Allowed : 28.36 % Favored : 69.85 % 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: 0.43 (0.16), residues: 3039 helix: 1.59 (0.13), residues: 1629 sheet: -0.37 (0.23), residues: 431 loop : -1.64 (0.20), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 552 HIS 0.005 0.001 HIS A 526 PHE 0.022 0.001 PHE A 22 TYR 0.023 0.001 TYR B 974 ARG 0.010 0.000 ARG B 195 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 923 is missing expected H atoms. Skipping. Evaluate side-chains 574 residues out of total 2514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 529 time to evaluate : 3.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 LYS cc_start: 0.8788 (ttpt) cc_final: 0.8572 (ttmm) REVERT: A 416 LYS cc_start: 0.9135 (tppt) cc_final: 0.8878 (tppp) REVERT: A 528 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8448 (mm) REVERT: A 597 MET cc_start: 0.8979 (mmm) cc_final: 0.8534 (mmm) REVERT: A 898 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8513 (mm) REVERT: A 939 GLU cc_start: 0.8340 (tm-30) cc_final: 0.8129 (tm-30) REVERT: B 132 ASP cc_start: 0.8083 (t0) cc_final: 0.7488 (t0) REVERT: B 528 LEU cc_start: 0.9388 (mm) cc_final: 0.9114 (mm) REVERT: B 623 MET cc_start: 0.8957 (ttt) cc_final: 0.8585 (ttt) REVERT: C 211 ASP cc_start: 0.7995 (p0) cc_final: 0.7712 (p0) REVERT: C 327 ARG cc_start: 0.8605 (OUTLIER) cc_final: 0.7945 (mtt-85) REVERT: C 435 ARG cc_start: 0.3846 (ptt180) cc_final: 0.2749 (pmt170) REVERT: C 565 ILE cc_start: 0.8869 (pt) cc_final: 0.8611 (mt) REVERT: C 593 ASP cc_start: 0.8469 (m-30) cc_final: 0.8156 (m-30) REVERT: C 671 ASP cc_start: 0.7506 (m-30) cc_final: 0.7208 (m-30) REVERT: C 875 MET cc_start: 0.8445 (tpp) cc_final: 0.8039 (tpp) outliers start: 45 outliers final: 37 residues processed: 557 average time/residue: 2.3928 time to fit residues: 1602.0292 Evaluate side-chains 564 residues out of total 2514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 524 time to evaluate : 3.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 855 SER Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 353 CYS Chi-restraints excluded: chain B residue 358 TRP Chi-restraints excluded: chain B residue 384 GLN Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 435 ARG Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 445 GLU Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 588 MET Chi-restraints excluded: chain B residue 859 SER Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 918 MET Chi-restraints excluded: chain B residue 959 ASN Chi-restraints excluded: chain C residue 6 ILE Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 327 ARG Chi-restraints excluded: chain C residue 358 TRP Chi-restraints excluded: chain C residue 445 GLU Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain C residue 465 PHE Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 760 VAL Chi-restraints excluded: chain C residue 840 LEU Chi-restraints excluded: chain C residue 859 SER Chi-restraints excluded: chain C residue 959 ASN Chi-restraints excluded: chain C residue 1002 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 191 optimal weight: 7.9990 chunk 256 optimal weight: 7.9990 chunk 73 optimal weight: 8.9990 chunk 222 optimal weight: 5.9990 chunk 35 optimal weight: 0.3980 chunk 67 optimal weight: 4.9990 chunk 241 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 chunk 248 optimal weight: 7.9990 chunk 30 optimal weight: 8.9990 chunk 44 optimal weight: 2.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 781 GLN ** A 959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 384 GLN C 870 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.109984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.092310 restraints weight = 116355.527| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 2.41 r_work: 0.3029 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.5109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.164 23968 Z= 0.226 Angle : 0.710 59.200 32627 Z= 0.392 Chirality : 0.042 0.388 3877 Planarity : 0.005 0.081 4103 Dihedral : 3.779 25.821 3272 Min Nonbonded Distance : 1.698 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 1.63 % Allowed : 28.88 % Favored : 69.49 % 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: 0.44 (0.16), residues: 3039 helix: 1.59 (0.13), residues: 1629 sheet: -0.37 (0.23), residues: 431 loop : -1.64 (0.20), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 552 HIS 0.005 0.001 HIS A 526 PHE 0.021 0.001 PHE A 22 TYR 0.029 0.001 TYR B 974 ARG 0.007 0.000 ARG B 195 =============================================================================== Job complete usr+sys time: 22967.92 seconds wall clock time: 399 minutes 19.70 seconds (23959.70 seconds total)