Starting phenix.real_space_refine (version: dev) on Thu Feb 23 02:46:55 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2z_23146/02_2023/7l2z_23146.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2z_23146/02_2023/7l2z_23146.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2z_23146/02_2023/7l2z_23146.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2z_23146/02_2023/7l2z_23146.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2z_23146/02_2023/7l2z_23146.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2z_23146/02_2023/7l2z_23146.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.057 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 Process input model Symmetric amino acids flipped Residue "B GLU 99": "OE1" <-> "OE2" Residue "B GLU 106": "OE1" <-> "OE2" Residue "B TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 137": "OE1" <-> "OE2" Residue "B PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 180": "OD1" <-> "OD2" Residue "B ASP 193": "OD1" <-> "OD2" Residue "B ARG 196": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 201": "OD1" <-> "OD2" Residue "B TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 288": "OD1" <-> "OD2" Residue "B ASP 292": "OD1" <-> "OD2" Residue "B GLU 302": "OE1" <-> "OE2" Residue "B ASP 324": "OD1" <-> "OD2" Residue "B GLU 342": "OE1" <-> "OE2" Residue "B ARG 355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 367": "OD1" <-> "OD2" Residue "B GLU 380": "OE1" <-> "OE2" Residue "B TYR 416": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 430": "OD1" <-> "OD2" Residue "B PHE 437": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 468": "OD1" <-> "OD2" Residue "B PHE 484": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 485": "OD1" <-> "OD2" Residue "B PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 488": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 515": "OD1" <-> "OD2" Residue "B PHE 542": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 547": "OD1" <-> "OD2" Residue "B GLU 561": "OE1" <-> "OE2" Residue "B PHE 580": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 589": "OD1" <-> "OD2" Residue "B PHE 637": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 643": "OD1" <-> "OD2" Residue "B GLU 644": "OE1" <-> "OE2" Residue "B ASP 646": "OD1" <-> "OD2" Residue "B PHE 667": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 671": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 689": "OE1" <-> "OE2" Residue "B ASP 697": "OD1" <-> "OD2" Residue "B ARG 701": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 705": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 712": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 713": "OE1" <-> "OE2" Residue "B ASP 723": "OD1" <-> "OD2" Residue "A ASP 105": "OD1" <-> "OD2" Residue "A PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 183": "OE1" <-> "OE2" Residue "A ASP 193": "OD1" <-> "OD2" Residue "A ARG 196": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 284": "OD1" <-> "OD2" Residue "A ASP 292": "OD1" <-> "OD2" Residue "A PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 339": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 342": "OE1" <-> "OE2" Residue "A ARG 355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 358": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 359": "OD1" <-> "OD2" Residue "A GLU 374": "OE1" <-> "OE2" Residue "A GLU 379": "OE1" <-> "OE2" Residue "A ASP 401": "OD1" <-> "OD2" Residue "A ASP 411": "OD1" <-> "OD2" Residue "A TYR 416": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 437": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 485": "OD1" <-> "OD2" Residue "A PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 515": "OD1" <-> "OD2" Residue "A PHE 520": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 523": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 524": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 526": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 540": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 565": "OE1" <-> "OE2" Residue "A ASP 609": "OD1" <-> "OD2" Residue "A ASP 613": "OD1" <-> "OD2" Residue "A PHE 667": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 673": "OD1" <-> "OD2" Residue "A TYR 688": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 693": "OD1" <-> "OD2" Residue "A ASP 697": "OD1" <-> "OD2" Residue "A ARG 701": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 712": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 713": "OE1" <-> "OE2" Residue "A TYR 725": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 726": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 105": "OD1" <-> "OD2" Residue "C TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 136": "OD1" <-> "OD2" Residue "C GLU 137": "OE1" <-> "OE2" Residue "C PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 196": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 212": "OD1" <-> "OD2" Residue "C PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 225": "OD1" <-> "OD2" Residue "C PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 292": "OD1" <-> "OD2" Residue "C TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 321": "OD1" <-> "OD2" Residue "C PHE 339": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 348": "OE1" <-> "OE2" Residue "C ARG 355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 358": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 359": "OD1" <-> "OD2" Residue "C GLU 374": "OE1" <-> "OE2" Residue "C GLU 388": "OE1" <-> "OE2" Residue "C ASP 413": "OD1" <-> "OD2" Residue "C ASP 464": "OD1" <-> "OD2" Residue "C PHE 484": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 485": "OD1" <-> "OD2" Residue "C PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 487": "OE1" <-> "OE2" Residue "C TYR 488": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 515": "OD1" <-> "OD2" Residue "C TYR 524": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 535": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 540": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 565": "OE1" <-> "OE2" Residue "C PHE 580": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 589": "OD1" <-> "OD2" Residue "C ASP 600": "OD1" <-> "OD2" Residue "C ASP 609": "OD1" <-> "OD2" Residue "C GLU 625": "OE1" <-> "OE2" Residue "C PHE 637": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 650": "OE1" <-> "OE2" Residue "C TYR 671": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 673": "OD1" <-> "OD2" Residue "C ASP 693": "OD1" <-> "OD2" Residue "C ASP 697": "OD1" <-> "OD2" Residue "C ARG 701": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 712": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 713": "OE1" <-> "OE2" Residue "C TYR 726": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 99": "OE1" <-> "OE2" Residue "D GLU 116": "OE1" <-> "OE2" Residue "D GLU 147": "OE1" <-> "OE2" Residue "D ARG 196": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ASP 201": "OD1" <-> "OD2" Residue "D TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 288": "OD1" <-> "OD2" Residue "D ASP 322": "OD1" <-> "OD2" Residue "D GLU 342": "OE1" <-> "OE2" Residue "D GLU 348": "OE1" <-> "OE2" Residue "D ARG 355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 358": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 372": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 411": "OD1" <-> "OD2" Residue "D ASP 413": "OD1" <-> "OD2" Residue "D TYR 416": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 425": "OD1" <-> "OD2" Residue "D PHE 437": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 464": "OD1" <-> "OD2" Residue "D PHE 484": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 485": "OD1" <-> "OD2" Residue "D PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 488": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 515": "OD1" <-> "OD2" Residue "D ASP 531": "OD1" <-> "OD2" Residue "D GLU 561": "OE1" <-> "OE2" Residue "D GLU 565": "OE1" <-> "OE2" Residue "D PHE 580": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 609": "OD1" <-> "OD2" Residue "D GLU 650": "OE1" <-> "OE2" Residue "D PHE 667": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 688": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 689": "OE1" <-> "OE2" Residue "D ASP 693": "OD1" <-> "OD2" Residue "D ASP 697": "OD1" <-> "OD2" Residue "D ARG 701": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 712": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 725": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 137": "OE1" <-> "OE2" Residue "E GLU 147": "OE1" <-> "OE2" Residue "E TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 183": "OE1" <-> "OE2" Residue "E ARG 196": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 222": "OD1" <-> "OD2" Residue "E PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 240": "OD1" <-> "OD2" Residue "E ASP 274": "OD1" <-> "OD2" Residue "E ASP 284": "OD1" <-> "OD2" Residue "E PHE 289": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 292": "OD1" <-> "OD2" Residue "E ASP 321": "OD1" <-> "OD2" Residue "E PHE 339": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E TYR 358": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 372": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 380": "OE1" <-> "OE2" Residue "E TYR 403": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 413": "OD1" <-> "OD2" Residue "E PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 468": "OD1" <-> "OD2" Residue "E PHE 484": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 488": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 514": "OD1" <-> "OD2" Residue "E TYR 524": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 526": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 531": "OD1" <-> "OD2" Residue "E PHE 535": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 540": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 542": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 547": "OD1" <-> "OD2" Residue "E GLU 561": "OE1" <-> "OE2" Residue "E PHE 580": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 598": "OD1" <-> "OD2" Residue "E ASP 614": "OD1" <-> "OD2" Residue "E GLU 625": "OE1" <-> "OE2" Residue "E PHE 637": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 643": "OD1" <-> "OD2" Residue "E ASP 646": "OD1" <-> "OD2" Residue "E GLU 650": "OE1" <-> "OE2" Residue "E TYR 688": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 697": "OD1" <-> "OD2" Residue "E ARG 701": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E PHE 705": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 712": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 713": "OE1" <-> "OE2" Residue "E ASP 723": "OD1" <-> "OD2" Residue "E TYR 725": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 106": "OE1" <-> "OE2" Residue "F ASP 136": "OD1" <-> "OD2" Residue "F GLU 137": "OE1" <-> "OE2" Residue "F GLU 147": "OE1" <-> "OE2" Residue "F ARG 196": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 222": "OD1" <-> "OD2" Residue "F PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 289": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 302": "OE1" <-> "OE2" Residue "F PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 342": "OE1" <-> "OE2" Residue "F ARG 355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ASP 359": "OD1" <-> "OD2" Residue "F ASP 367": "OD1" <-> "OD2" Residue "F GLU 388": "OE1" <-> "OE2" Residue "F ASP 401": "OD1" <-> "OD2" Residue "F ASP 411": "OD1" <-> "OD2" Residue "F ASP 413": "OD1" <-> "OD2" Residue "F TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 425": "OD1" <-> "OD2" Residue "F PHE 437": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 464": "OD1" <-> "OD2" Residue "F ASP 485": "OD1" <-> "OD2" Residue "F TYR 488": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 498": "OD1" <-> "OD2" Residue "F PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 515": "OD1" <-> "OD2" Residue "F PHE 520": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 526": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 531": "OD1" <-> "OD2" Residue "F PHE 535": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 540": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 542": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 565": "OE1" <-> "OE2" Residue "F PHE 573": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 580": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 590": "OD1" <-> "OD2" Residue "F ASP 598": "OD1" <-> "OD2" Residue "F ASP 600": "OD1" <-> "OD2" Residue "F ASP 613": "OD1" <-> "OD2" Residue "F ASP 614": "OD1" <-> "OD2" Residue "F ASP 618": "OD1" <-> "OD2" Residue "F GLU 625": "OE1" <-> "OE2" Residue "F PHE 637": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 644": "OE1" <-> "OE2" Residue "F ASP 646": "OD1" <-> "OD2" Residue "F ASP 673": "OD1" <-> "OD2" Residue "F TYR 688": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 693": "OD1" <-> "OD2" Residue "F ARG 701": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F PHE 705": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 712": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F GLU 713": "OE1" <-> "OE2" Residue "F TYR 725": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 59631 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 9952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 645, 9952 Classifications: {'peptide': 645} Link IDs: {'PCIS': 1, 'PTRANS': 50, 'TRANS': 593} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 9550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 619, 9550 Classifications: {'peptide': 619} Link IDs: {'PCIS': 1, 'PTRANS': 46, 'TRANS': 571} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 9971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 647, 9971 Classifications: {'peptide': 647} Link IDs: {'PCIS': 1, 'PTRANS': 50, 'TRANS': 595} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 9938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 645, 9938 Classifications: {'peptide': 645} Link IDs: {'PCIS': 1, 'PTRANS': 50, 'TRANS': 593} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 9957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 646, 9957 Classifications: {'peptide': 646} Link IDs: {'PCIS': 1, 'PTRANS': 50, 'TRANS': 594} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 10263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 664, 10263 Classifications: {'peptide': 664} Link IDs: {'PCIS': 1, 'PTRANS': 51, 'TRANS': 611} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 20.83, per 1000 atoms: 0.35 Number of scatterers: 59631 At special positions: 0 Unit cell: (137.16, 184.68, 187.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 143 16.00 O 5710 8.00 N 5098 7.00 C 19004 6.00 H 29676 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS B 182 " - pdb=" SG CYS B 500 " distance=2.03 Simple disulfide: pdb=" SG CYS A 182 " - pdb=" SG CYS A 500 " distance=2.03 Simple disulfide: pdb=" SG CYS C 182 " - pdb=" SG CYS C 500 " distance=2.03 Simple disulfide: pdb=" SG CYS D 182 " - pdb=" SG CYS D 500 " distance=2.03 Simple disulfide: pdb=" SG CYS E 182 " - pdb=" SG CYS E 500 " distance=2.03 Simple disulfide: pdb=" SG CYS F 182 " - pdb=" SG CYS F 500 " distance=2.03 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: 38.45 Conformation dependent library (CDL) restraints added in 4.1 seconds 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7206 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 68 sheets defined 15.0% alpha, 27.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.83 Creating SS restraints... Processing helix chain 'B' and resid 76 through 81 removed outlier: 4.114A pdb=" N ILE B 80 " --> pdb=" O THR B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 149 removed outlier: 3.570A pdb=" N LEU B 149 " --> pdb=" O LYS B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 216 removed outlier: 3.672A pdb=" N HIS B 215 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 259 Processing helix chain 'B' and resid 321 through 334 Processing helix chain 'B' and resid 532 through 538 Processing helix chain 'B' and resid 560 through 578 Processing helix chain 'B' and resid 684 through 697 Processing helix chain 'B' and resid 698 through 703 removed outlier: 3.980A pdb=" N THR B 703 " --> pdb=" O GLY B 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 164 removed outlier: 3.975A pdb=" N PHE A 163 " --> pdb=" O ASN A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 259 Processing helix chain 'A' and resid 321 through 335 removed outlier: 3.567A pdb=" N LEU A 325 " --> pdb=" O ASP A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 381 removed outlier: 3.590A pdb=" N GLN A 381 " --> pdb=" O TYR A 378 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 378 through 381' Processing helix chain 'A' and resid 531 through 539 removed outlier: 4.101A pdb=" N PHE A 535 " --> pdb=" O ASP A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 578 Processing helix chain 'A' and resid 617 through 630 removed outlier: 3.841A pdb=" N VAL A 621 " --> pdb=" O ILE A 617 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR A 630 " --> pdb=" O SER A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 684 through 697 Processing helix chain 'A' and resid 697 through 703 removed outlier: 3.511A pdb=" N THR A 703 " --> pdb=" O GLY A 699 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 149 removed outlier: 3.665A pdb=" N LEU C 149 " --> pdb=" O LYS C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 164 removed outlier: 3.702A pdb=" N PHE C 163 " --> pdb=" O ASN C 160 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE C 164 " --> pdb=" O PRO C 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 160 through 164' Processing helix chain 'C' and resid 212 through 216 removed outlier: 3.862A pdb=" N HIS C 215 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 259 Processing helix chain 'C' and resid 321 through 335 Processing helix chain 'C' and resid 373 through 375 No H-bonds generated for 'chain 'C' and resid 373 through 375' Processing helix chain 'C' and resid 532 through 537 Processing helix chain 'C' and resid 541 through 545 removed outlier: 3.917A pdb=" N ARG C 544 " --> pdb=" O PRO C 541 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N MET C 545 " --> pdb=" O PHE C 542 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 541 through 545' Processing helix chain 'C' and resid 560 through 578 Processing helix chain 'C' and resid 684 through 697 removed outlier: 3.862A pdb=" N ASP C 697 " --> pdb=" O ASP C 693 " (cutoff:3.500A) Processing helix chain 'C' and resid 697 through 702 removed outlier: 3.633A pdb=" N ARG C 701 " --> pdb=" O ASP C 697 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 164 removed outlier: 3.652A pdb=" N PHE D 163 " --> pdb=" O ASN D 160 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE D 164 " --> pdb=" O PRO D 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 160 through 164' Processing helix chain 'D' and resid 240 through 259 Processing helix chain 'D' and resid 321 through 334 Processing helix chain 'D' and resid 373 through 376 removed outlier: 3.979A pdb=" N LYS D 376 " --> pdb=" O GLY D 373 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 373 through 376' Processing helix chain 'D' and resid 532 through 538 Processing helix chain 'D' and resid 560 through 578 Processing helix chain 'D' and resid 590 through 594 removed outlier: 3.702A pdb=" N THR D 593 " --> pdb=" O ASP D 590 " (cutoff:3.500A) Processing helix chain 'D' and resid 684 through 697 Processing helix chain 'E' and resid 240 through 259 Processing helix chain 'E' and resid 321 through 335 Processing helix chain 'E' and resid 373 through 376 removed outlier: 3.924A pdb=" N LYS E 376 " --> pdb=" O GLY E 373 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 373 through 376' Processing helix chain 'E' and resid 532 through 538 Processing helix chain 'E' and resid 560 through 578 Processing helix chain 'E' and resid 611 through 615 removed outlier: 3.761A pdb=" N LYS E 615 " --> pdb=" O LYS E 612 " (cutoff:3.500A) Processing helix chain 'E' and resid 684 through 697 Processing helix chain 'E' and resid 697 through 702 Processing helix chain 'F' and resid 145 through 149 removed outlier: 3.519A pdb=" N LEU F 149 " --> pdb=" O LYS F 146 " (cutoff:3.500A) Processing helix chain 'F' and resid 241 through 259 Processing helix chain 'F' and resid 321 through 334 Processing helix chain 'F' and resid 532 through 538 Processing helix chain 'F' and resid 539 through 544 Processing helix chain 'F' and resid 560 through 578 Processing helix chain 'F' and resid 590 through 594 Processing helix chain 'F' and resid 684 through 697 Processing helix chain 'F' and resid 697 through 704 removed outlier: 4.244A pdb=" N THR F 703 " --> pdb=" O GLY F 699 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N MET F 704 " --> pdb=" O LYS F 700 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 72 through 74 Processing sheet with id=AA2, first strand: chain 'B' and resid 72 through 74 Processing sheet with id=AA3, first strand: chain 'B' and resid 88 through 90 Processing sheet with id=AA4, first strand: chain 'B' and resid 97 through 101 removed outlier: 3.686A pdb=" N GLY B 140 " --> pdb=" O VAL B 132 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 229 through 230 removed outlier: 6.072A pdb=" N ASN B 229 " --> pdb=" O ASN B 264 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 267 through 269 removed outlier: 4.171A pdb=" N LEU B 268 " --> pdb=" O MET B 233 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE B 280 " --> pdb=" O VAL B 234 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ASN B 347 " --> pdb=" O THR C 654 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N THR C 654 " --> pdb=" O ASN B 347 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N VAL B 349 " --> pdb=" O ARG C 652 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ARG C 652 " --> pdb=" O VAL B 349 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N THR C 651 " --> pdb=" O THR C 630 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N THR C 630 " --> pdb=" O THR C 651 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TRP C 627 " --> pdb=" O LEU C 620 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 305 through 306 removed outlier: 6.298A pdb=" N VAL B 312 " --> pdb=" O HIS B 306 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 370 through 371 Processing sheet with id=AA9, first strand: chain 'B' and resid 383 through 386 Processing sheet with id=AB1, first strand: chain 'B' and resid 392 through 395 removed outlier: 6.445A pdb=" N MET B 429 " --> pdb=" O SER B 440 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N SER B 440 " --> pdb=" O MET B 429 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ILE B 431 " --> pdb=" O LEU B 438 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 410 through 414 Processing sheet with id=AB3, first strand: chain 'B' and resid 492 through 493 Processing sheet with id=AB4, first strand: chain 'B' and resid 501 through 502 Processing sheet with id=AB5, first strand: chain 'B' and resid 526 through 528 removed outlier: 3.770A pdb=" N ILE B 527 " --> pdb=" O VAL B 727 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL B 727 " --> pdb=" O ILE B 527 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'B' and resid 586 through 588 removed outlier: 6.254A pdb=" N THR B 551 " --> pdb=" O THR B 586 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N THR B 588 " --> pdb=" O THR B 551 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N THR B 553 " --> pdb=" O THR B 588 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 626 through 628 removed outlier: 3.832A pdb=" N LYS A 350 " --> pdb=" O ARG B 652 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLU A 348 " --> pdb=" O THR B 654 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N THR B 656 " --> pdb=" O VAL A 346 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N VAL A 346 " --> pdb=" O THR B 656 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ALA A 277 " --> pdb=" O LEU A 315 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N VAL A 317 " --> pdb=" O ALA A 277 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL A 279 " --> pdb=" O VAL A 317 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N VAL A 234 " --> pdb=" O PHE A 280 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU A 268 " --> pdb=" O MET A 233 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 676 through 682 Processing sheet with id=AB9, first strand: chain 'A' and resid 70 through 75 removed outlier: 4.086A pdb=" N LYS A 110 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLN A 205 " --> pdb=" O VAL A 108 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N VAL A 108 " --> pdb=" O GLN A 205 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 70 through 75 removed outlier: 4.086A pdb=" N LYS A 110 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLN A 205 " --> pdb=" O VAL A 108 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N VAL A 108 " --> pdb=" O GLN A 205 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 98 through 101 removed outlier: 3.978A pdb=" N GLY A 140 " --> pdb=" O VAL A 132 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 383 through 386 removed outlier: 4.192A pdb=" N VAL A 469 " --> pdb=" O MET A 412 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 392 through 396 removed outlier: 6.375A pdb=" N MET A 429 " --> pdb=" O SER A 440 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N SER A 440 " --> pdb=" O MET A 429 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE A 431 " --> pdb=" O LEU A 438 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 527 through 528 removed outlier: 4.010A pdb=" N ILE A 527 " --> pdb=" O VAL A 727 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL A 727 " --> pdb=" O ILE A 527 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'A' and resid 586 through 588 removed outlier: 6.163A pdb=" N THR A 551 " --> pdb=" O THR A 586 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N THR A 588 " --> pdb=" O THR A 551 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N THR A 553 " --> pdb=" O THR A 588 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ILE A 552 " --> pdb=" O MET A 602 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'A' and resid 676 through 681 removed outlier: 4.207A pdb=" N ALA A 662 " --> pdb=" O ILE A 711 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE A 711 " --> pdb=" O ALA A 662 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL A 710 " --> pdb=" O ASN A 717 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLY A 715 " --> pdb=" O ARG A 712 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 70 through 73 Processing sheet with id=AC9, first strand: chain 'C' and resid 87 through 90 removed outlier: 3.562A pdb=" N MET C 87 " --> pdb=" O VAL C 194 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 95 through 101 removed outlier: 3.602A pdb=" N GLN C 129 " --> pdb=" O VAL C 175 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLY C 140 " --> pdb=" O VAL C 132 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 229 through 230 removed outlier: 3.876A pdb=" N ASN C 264 " --> pdb=" O ASN C 229 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'C' and resid 267 through 269 removed outlier: 3.584A pdb=" N PHE C 280 " --> pdb=" O VAL C 234 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ALA C 277 " --> pdb=" O LEU C 315 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N VAL C 317 " --> pdb=" O ALA C 277 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL C 279 " --> pdb=" O VAL C 317 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N VAL C 346 " --> pdb=" O THR D 656 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N THR D 656 " --> pdb=" O VAL C 346 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU C 348 " --> pdb=" O THR D 654 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 370 through 371 Processing sheet with id=AD5, first strand: chain 'C' and resid 383 through 384 Processing sheet with id=AD6, first strand: chain 'C' and resid 392 through 395 removed outlier: 3.724A pdb=" N GLN C 439 " --> pdb=" O ILE C 431 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 402 through 403 removed outlier: 4.769A pdb=" N TYR C 524 " --> pdb=" O TYR C 403 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 501 through 502 removed outlier: 3.522A pdb=" N MET D 492 " --> pdb=" O THR C 502 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 586 through 588 removed outlier: 6.223A pdb=" N THR C 551 " --> pdb=" O THR C 586 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N THR C 588 " --> pdb=" O THR C 551 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N THR C 553 " --> pdb=" O THR C 588 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ILE C 601 " --> pdb=" O ILE C 678 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N LEU C 680 " --> pdb=" O ILE C 601 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ILE C 603 " --> pdb=" O LEU C 680 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N ALA C 682 " --> pdb=" O ILE C 603 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 70 through 76 removed outlier: 7.242A pdb=" N GLY D 199 " --> pdb=" O LEU D 113 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N LEU D 113 " --> pdb=" O GLY D 199 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ASP D 201 " --> pdb=" O ALA D 111 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ALA D 111 " --> pdb=" O ASP D 201 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N MET D 87 " --> pdb=" O VAL D 194 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 70 through 76 removed outlier: 7.242A pdb=" N GLY D 199 " --> pdb=" O LEU D 113 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N LEU D 113 " --> pdb=" O GLY D 199 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ASP D 201 " --> pdb=" O ALA D 111 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ALA D 111 " --> pdb=" O ASP D 201 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ALA D 111 " --> pdb=" O ILE D 159 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 95 through 101 removed outlier: 3.633A pdb=" N GLU D 173 " --> pdb=" O LYS D 131 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLY D 140 " --> pdb=" O VAL D 132 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LEU D 134 " --> pdb=" O LEU D 138 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N LEU D 138 " --> pdb=" O LEU D 134 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 229 through 230 removed outlier: 6.226A pdb=" N ASN D 229 " --> pdb=" O ASN D 264 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'D' and resid 267 through 269 removed outlier: 5.079A pdb=" N VAL D 346 " --> pdb=" O THR E 656 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N THR E 656 " --> pdb=" O VAL D 346 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU D 348 " --> pdb=" O THR E 654 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N THR E 630 " --> pdb=" O GLU E 650 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ARG E 652 " --> pdb=" O VAL E 628 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL E 628 " --> pdb=" O ARG E 652 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N THR E 654 " --> pdb=" O SER E 626 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N SER E 626 " --> pdb=" O THR E 654 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N TRP E 627 " --> pdb=" O LEU E 620 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU E 620 " --> pdb=" O TRP E 627 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 370 through 371 Processing sheet with id=AE7, first strand: chain 'D' and resid 383 through 384 Processing sheet with id=AE8, first strand: chain 'D' and resid 392 through 396 removed outlier: 3.702A pdb=" N LEU D 396 " --> pdb=" O ASN D 480 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N MET D 429 " --> pdb=" O SER D 440 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N SER D 440 " --> pdb=" O MET D 429 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ILE D 431 " --> pdb=" O LEU D 438 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 410 through 414 Processing sheet with id=AF1, first strand: chain 'D' and resid 500 through 502 removed outlier: 6.023A pdb=" N CYS D 500 " --> pdb=" O GLY E 494 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 526 through 528 Processing sheet with id=AF3, first strand: chain 'D' and resid 586 through 588 removed outlier: 6.187A pdb=" N THR D 551 " --> pdb=" O THR D 586 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N THR D 588 " --> pdb=" O THR D 551 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N THR D 553 " --> pdb=" O THR D 588 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ILE D 601 " --> pdb=" O ILE D 678 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N LEU D 680 " --> pdb=" O ILE D 601 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE D 603 " --> pdb=" O LEU D 680 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N ALA D 682 " --> pdb=" O ILE D 603 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 70 through 76 removed outlier: 3.504A pdb=" N VAL E 73 " --> pdb=" O LEU E 202 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU E 75 " --> pdb=" O LEU E 200 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N GLY E 199 " --> pdb=" O LEU E 113 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N LEU E 113 " --> pdb=" O GLY E 199 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ASP E 201 " --> pdb=" O ALA E 111 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ALA E 111 " --> pdb=" O ASP E 201 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR E 118 " --> pdb=" O ASP E 193 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ASP E 193 " --> pdb=" O THR E 118 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 70 through 76 removed outlier: 3.504A pdb=" N VAL E 73 " --> pdb=" O LEU E 202 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU E 75 " --> pdb=" O LEU E 200 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N GLY E 199 " --> pdb=" O LEU E 113 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N LEU E 113 " --> pdb=" O GLY E 199 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ASP E 201 " --> pdb=" O ALA E 111 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ALA E 111 " --> pdb=" O ASP E 201 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ALA E 111 " --> pdb=" O ILE E 159 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR E 117 " --> pdb=" O THR E 153 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 95 through 101 removed outlier: 3.691A pdb=" N GLY E 140 " --> pdb=" O VAL E 132 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 229 through 230 removed outlier: 6.213A pdb=" N ASN E 229 " --> pdb=" O ASN E 264 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'E' and resid 268 through 269 removed outlier: 6.402A pdb=" N MET E 233 " --> pdb=" O LEU E 268 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N VAL E 279 " --> pdb=" O VAL E 317 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLU E 348 " --> pdb=" O THR F 654 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N SER F 653 " --> pdb=" O VAL F 628 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N VAL F 628 " --> pdb=" O SER F 653 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TRP F 627 " --> pdb=" O LEU F 620 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU F 620 " --> pdb=" O TRP F 627 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'E' and resid 370 through 371 removed outlier: 3.632A pdb=" N THR E 517 " --> pdb=" O ASP E 413 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP E 413 " --> pdb=" O THR E 517 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE E 410 " --> pdb=" O ILE E 471 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE E 414 " --> pdb=" O THR E 467 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N THR E 467 " --> pdb=" O ILE E 414 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N TYR E 416 " --> pdb=" O GLY E 465 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY E 465 " --> pdb=" O TYR E 416 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'E' and resid 383 through 384 Processing sheet with id=AG2, first strand: chain 'E' and resid 392 through 395 removed outlier: 6.387A pdb=" N MET E 429 " --> pdb=" O SER E 440 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N SER E 440 " --> pdb=" O MET E 429 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ILE E 431 " --> pdb=" O LEU E 438 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'E' and resid 402 through 403 removed outlier: 3.623A pdb=" N TYR E 524 " --> pdb=" O TYR E 403 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'E' and resid 586 through 588 removed outlier: 3.692A pdb=" N THR E 586 " --> pdb=" O THR E 551 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ILE E 601 " --> pdb=" O ILE E 678 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N LEU E 680 " --> pdb=" O ILE E 601 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ILE E 603 " --> pdb=" O LEU E 680 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'F' and resid 70 through 76 removed outlier: 3.639A pdb=" N THR F 203 " --> pdb=" O LYS F 110 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N LYS F 110 " --> pdb=" O THR F 203 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N GLN F 205 " --> pdb=" O VAL F 108 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N VAL F 108 " --> pdb=" O GLN F 205 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'F' and resid 70 through 76 removed outlier: 3.639A pdb=" N THR F 203 " --> pdb=" O LYS F 110 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N LYS F 110 " --> pdb=" O THR F 203 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N GLN F 205 " --> pdb=" O VAL F 108 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N VAL F 108 " --> pdb=" O GLN F 205 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'F' and resid 95 through 101 removed outlier: 4.088A pdb=" N GLY F 140 " --> pdb=" O VAL F 132 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'F' and resid 229 through 230 removed outlier: 3.827A pdb=" N ASN F 264 " --> pdb=" O ASN F 229 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG8 Processing sheet with id=AG9, first strand: chain 'F' and resid 267 through 269 removed outlier: 7.099A pdb=" N VAL F 234 " --> pdb=" O PHE F 280 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'F' and resid 370 through 371 removed outlier: 3.722A pdb=" N ASP F 411 " --> pdb=" O ASP F 519 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'F' and resid 370 through 371 removed outlier: 3.722A pdb=" N ASP F 411 " --> pdb=" O ASP F 519 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'F' and resid 392 through 397 removed outlier: 3.570A pdb=" N ASN F 480 " --> pdb=" O LEU F 396 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N SER F 427 " --> pdb=" O LEU F 443 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLN F 439 " --> pdb=" O ILE F 431 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'F' and resid 402 through 403 removed outlier: 3.702A pdb=" N TYR F 524 " --> pdb=" O TYR F 403 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ILE F 527 " --> pdb=" O VAL F 727 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL F 727 " --> pdb=" O ILE F 527 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'F' and resid 586 through 588 removed outlier: 6.862A pdb=" N THR F 551 " --> pdb=" O THR F 586 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N THR F 588 " --> pdb=" O THR F 551 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N THR F 553 " --> pdb=" O THR F 588 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE F 604 " --> pdb=" O VAL F 554 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE F 601 " --> pdb=" O SER F 676 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE F 678 " --> pdb=" O ILE F 601 " (cutoff:3.500A) 943 hydrogen bonds defined for protein. 2541 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: 25.51 Time building geometry restraints manager: 40.44 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: 29676 1.03 - 1.23: 0 1.23 - 1.42: 12525 1.42 - 1.62: 17836 1.62 - 1.81: 274 Bond restraints: 60311 Sorted by residual: bond pdb=" N LYS B 110 " pdb=" CA LYS B 110 " ideal model delta sigma weight residual 1.457 1.473 -0.015 1.29e-02 6.01e+03 1.38e+00 bond pdb=" CA ILE C 617 " pdb=" CB ILE C 617 " ideal model delta sigma weight residual 1.527 1.541 -0.014 1.31e-02 5.83e+03 1.15e+00 bond pdb=" C MET E 529 " pdb=" N PRO E 530 " ideal model delta sigma weight residual 1.336 1.346 -0.011 1.08e-02 8.57e+03 9.81e-01 bond pdb=" C THR D 118 " pdb=" N PRO D 119 " ideal model delta sigma weight residual 1.326 1.340 -0.014 1.44e-02 4.82e+03 9.62e-01 bond pdb=" N PRO E 472 " pdb=" CA PRO E 472 " ideal model delta sigma weight residual 1.469 1.480 -0.012 1.28e-02 6.10e+03 8.49e-01 ... (remaining 60306 not shown) Histogram of bond angle deviations from ideal: 79.64 - 90.51: 3 90.51 - 101.38: 123 101.38 - 112.24: 70568 112.24 - 123.11: 32596 123.11 - 133.98: 6031 Bond angle restraints: 109321 Sorted by residual: angle pdb=" CB THR B 570 " pdb=" CA THR B 570 " pdb=" HA THR B 570 " ideal model delta sigma weight residual 109.00 79.64 29.36 3.00e+00 1.11e-01 9.58e+01 angle pdb=" C THR B 570 " pdb=" CA THR B 570 " pdb=" HA THR B 570 " ideal model delta sigma weight residual 109.00 80.77 28.23 3.00e+00 1.11e-01 8.86e+01 angle pdb=" N THR B 570 " pdb=" CA THR B 570 " pdb=" HA THR B 570 " ideal model delta sigma weight residual 110.00 82.42 27.58 3.00e+00 1.11e-01 8.45e+01 angle pdb=" C THR B 570 " pdb=" CA THR B 570 " pdb=" CB THR B 570 " ideal model delta sigma weight residual 110.79 119.57 -8.78 1.66e+00 3.63e-01 2.79e+01 angle pdb=" N THR B 570 " pdb=" CA THR B 570 " pdb=" CB THR B 570 " ideal model delta sigma weight residual 110.12 117.66 -7.54 1.47e+00 4.63e-01 2.63e+01 ... (remaining 109316 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 22706 17.95 - 35.90: 1176 35.90 - 53.86: 254 53.86 - 71.81: 36 71.81 - 89.76: 17 Dihedral angle restraints: 24189 sinusoidal: 11376 harmonic: 12813 Sorted by residual: dihedral pdb=" C THR B 570 " pdb=" N THR B 570 " pdb=" CA THR B 570 " pdb=" CB THR B 570 " ideal model delta harmonic sigma weight residual -122.00 -150.03 28.03 0 2.50e+00 1.60e-01 1.26e+02 dihedral pdb=" N THR B 570 " pdb=" C THR B 570 " pdb=" CA THR B 570 " pdb=" CB THR B 570 " ideal model delta harmonic sigma weight residual 123.40 149.42 -26.02 0 2.50e+00 1.60e-01 1.08e+02 dihedral pdb=" CA PRO D 83 " pdb=" C PRO D 83 " pdb=" N PRO D 84 " pdb=" CA PRO D 84 " ideal model delta harmonic sigma weight residual 180.00 151.56 28.44 0 5.00e+00 4.00e-02 3.24e+01 ... (remaining 24186 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.231: 4679 0.231 - 0.462: 0 0.462 - 0.694: 0 0.694 - 0.925: 0 0.925 - 1.156: 1 Chirality restraints: 4680 Sorted by residual: chirality pdb=" CA THR B 570 " pdb=" N THR B 570 " pdb=" C THR B 570 " pdb=" CB THR B 570 " both_signs ideal model delta sigma weight residual False 2.53 1.37 1.16 2.00e-01 2.50e+01 3.34e+01 chirality pdb=" CA ILE E 471 " pdb=" N ILE E 471 " pdb=" C ILE E 471 " pdb=" CB ILE E 471 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.93e-01 chirality pdb=" CA ILE B 471 " pdb=" N ILE B 471 " pdb=" C ILE B 471 " pdb=" CB ILE B 471 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.89e-01 ... (remaining 4677 not shown) Planarity restraints: 9084 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO D 83 " -0.059 5.00e-02 4.00e+02 8.98e-02 1.29e+01 pdb=" N PRO D 84 " 0.155 5.00e-02 4.00e+02 pdb=" CA PRO D 84 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO D 84 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 216 " 0.025 5.00e-02 4.00e+02 3.76e-02 2.26e+00 pdb=" N PRO B 217 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO B 217 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 217 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS F 356 " 0.024 5.00e-02 4.00e+02 3.57e-02 2.04e+00 pdb=" N PRO F 357 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO F 357 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO F 357 " 0.020 5.00e-02 4.00e+02 ... (remaining 9081 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.19: 2739 2.19 - 2.79: 119352 2.79 - 3.39: 156777 3.39 - 4.00: 212050 4.00 - 4.60: 324947 Nonbonded interactions: 815865 Sorted by model distance: nonbonded pdb=" OD1 ASP E 590 " pdb=" H SER E 592 " model vdw 1.582 1.850 nonbonded pdb=" H LEU C 352 " pdb=" O GLU D 650 " model vdw 1.596 1.850 nonbonded pdb=" O CYS E 500 " pdb=" H GLY F 495 " model vdw 1.614 1.850 nonbonded pdb=" OD1 ASP A 547 " pdb=" HG SER A 549 " model vdw 1.616 1.850 nonbonded pdb=" H SER F 165 " pdb=" OD1 ASN F 168 " model vdw 1.625 1.850 ... (remaining 815860 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 67 through 444 or (resid 466 and (name N or name CA or nam \ e 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 467 through 730)) \ selection = (chain 'B' and (resid 67 through 444 or resid 466 through 630 or (resid 659 and \ (name N or name CA or name C or name O or name HA2 or name HA3)) or resid 660 th \ rough 730)) selection = (chain 'C' and (resid 67 through 444 or (resid 466 and (name N or name CA or nam \ e 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 467 through 630 o \ r (resid 659 and (name N or name CA or name C or name O or name HA2 or name HA3) \ ) or resid 660 through 730)) selection = (chain 'D' and (resid 67 through 444 or (resid 466 and (name N or name CA or nam \ e 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 467 through 630 o \ r (resid 659 and (name N or name CA or name C or name O or name HA2 or name HA3) \ ) or resid 660 through 730)) selection = (chain 'E' and (resid 67 through 444 or (resid 466 and (name N or name CA or nam \ e 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 467 through 630 o \ r (resid 659 and (name N or name CA or name C or name O or name HA2 or name HA3) \ ) or resid 660 through 730)) selection = (chain 'F' and (resid 67 through 444 or (resid 466 and (name N or name CA or nam \ e 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 467 through 630 o \ r (resid 659 and (name N or name CA or name C or name O or name HA2 or name HA3) \ ) or resid 660 through 730)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 143 5.16 5 C 19004 2.51 5 N 5098 2.21 5 O 5710 1.98 5 H 29676 0.53 5 sf(0) = scattering factor at diffraction angle 0. 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: 1.760 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: 0.670 Extract box with map and model: 13.140 Check model and map are aligned: 0.650 Process input model: 152.090 Find NCS groups from input model: 2.760 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Set scattering table: 0.430 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 173.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 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 : 0.002 0.037 30635 Z= 0.140 Angle : 0.500 8.775 41696 Z= 0.274 Chirality : 0.046 1.156 4680 Planarity : 0.003 0.090 5533 Dihedral : 12.487 89.759 11461 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer Outliers : 0.63 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.98 % 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: -2.91 (0.12), residues: 3842 helix: 0.50 (0.22), residues: 515 sheet: -1.37 (0.15), residues: 1067 loop : -2.97 (0.11), residues: 2260 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 684 is missing expected H atoms. Skipping. Residue SER 684 is missing expected H atoms. Skipping. Residue SER 684 is missing expected H atoms. Skipping. Residue SER 684 is missing expected H atoms. Skipping. Residue SER 684 is missing expected H atoms. Skipping. Residue SER 684 is missing expected H atoms. Skipping. Evaluate side-chains 640 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 619 time to evaluate : 3.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 7 residues processed: 638 average time/residue: 0.7981 time to fit residues: 800.5997 Evaluate side-chains 387 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 380 time to evaluate : 3.687 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.4997 time to fit residues: 11.2544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 323 optimal weight: 3.9990 chunk 290 optimal weight: 4.9990 chunk 161 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 195 optimal weight: 2.9990 chunk 155 optimal weight: 0.2980 chunk 300 optimal weight: 0.7980 chunk 116 optimal weight: 7.9990 chunk 182 optimal weight: 5.9990 chunk 223 optimal weight: 2.9990 chunk 347 optimal weight: 10.0000 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 577 GLN ** B 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 127 GLN C 179 GLN C 211 ASN C 293 HIS C 334 GLN C 490 ASN D 179 GLN D 334 GLN E 668 GLN F 508 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.072 30635 Z= 0.340 Angle : 0.599 8.025 41696 Z= 0.305 Chirality : 0.047 0.438 4680 Planarity : 0.004 0.081 5533 Dihedral : 3.956 32.651 4147 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer Outliers : 1.53 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.00 % Twisted Proline : 0.33 % 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: -2.22 (0.13), residues: 3842 helix: 1.60 (0.24), residues: 526 sheet: -1.23 (0.15), residues: 1104 loop : -2.50 (0.12), residues: 2212 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 684 is missing expected H atoms. Skipping. Residue SER 684 is missing expected H atoms. Skipping. Residue SER 684 is missing expected H atoms. Skipping. Residue SER 684 is missing expected H atoms. Skipping. Residue SER 684 is missing expected H atoms. Skipping. Residue SER 684 is missing expected H atoms. Skipping. Evaluate side-chains 420 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 369 time to evaluate : 4.415 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 outliers start: 51 outliers final: 31 residues processed: 409 average time/residue: 0.7366 time to fit residues: 494.6949 Evaluate side-chains 348 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 317 time to evaluate : 3.679 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.5371 time to fit residues: 35.1317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 193 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 289 optimal weight: 2.9990 chunk 236 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 348 optimal weight: 7.9990 chunk 376 optimal weight: 2.9990 chunk 310 optimal weight: 2.9990 chunk 345 optimal weight: 30.0000 chunk 118 optimal weight: 6.9990 chunk 279 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 550 GLN F 95 ASN ** F 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 622 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.064 30635 Z= 0.371 Angle : 0.598 6.509 41696 Z= 0.306 Chirality : 0.047 0.406 4680 Planarity : 0.004 0.063 5533 Dihedral : 4.375 33.304 4147 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer Outliers : 1.98 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.00 % Twisted Proline : 0.33 % 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: -1.96 (0.13), residues: 3842 helix: 2.00 (0.24), residues: 514 sheet: -1.09 (0.15), residues: 1078 loop : -2.32 (0.12), residues: 2250 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 684 is missing expected H atoms. Skipping. Residue SER 684 is missing expected H atoms. Skipping. Residue SER 684 is missing expected H atoms. Skipping. Residue SER 684 is missing expected H atoms. Skipping. Residue SER 684 is missing expected H atoms. Skipping. Residue SER 684 is missing expected H atoms. Skipping. Evaluate side-chains 368 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 302 time to evaluate : 3.708 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 outliers start: 66 outliers final: 30 residues processed: 356 average time/residue: 0.7772 time to fit residues: 457.6394 Evaluate side-chains 303 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 273 time to evaluate : 3.711 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.6098 time to fit residues: 38.4222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 344 optimal weight: 7.9990 chunk 261 optimal weight: 2.9990 chunk 180 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 166 optimal weight: 0.9980 chunk 233 optimal weight: 1.9990 chunk 349 optimal weight: 8.9990 chunk 370 optimal weight: 6.9990 chunk 182 optimal weight: 6.9990 chunk 331 optimal weight: 8.9990 chunk 99 optimal weight: 0.6980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 ASN ** B 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 95 ASN ** F 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.3788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 30635 Z= 0.214 Angle : 0.536 6.447 41696 Z= 0.269 Chirality : 0.045 0.362 4680 Planarity : 0.004 0.077 5533 Dihedral : 4.216 32.765 4147 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer Outliers : 1.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.00 % Twisted Proline : 0.66 % 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: -1.71 (0.13), residues: 3842 helix: 2.30 (0.24), residues: 526 sheet: -1.03 (0.15), residues: 1090 loop : -2.15 (0.12), residues: 2226 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 684 is missing expected H atoms. Skipping. Residue SER 684 is missing expected H atoms. Skipping. Residue SER 684 is missing expected H atoms. Skipping. Residue SER 684 is missing expected H atoms. Skipping. Residue SER 684 is missing expected H atoms. Skipping. Residue SER 684 is missing expected H atoms. Skipping. Evaluate side-chains 324 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 284 time to evaluate : 3.747 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 outliers start: 40 outliers final: 16 residues processed: 315 average time/residue: 0.7394 time to fit residues: 392.8486 Evaluate side-chains 280 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 264 time to evaluate : 3.712 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.5667 time to fit residues: 21.5227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 308 optimal weight: 4.9990 chunk 210 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 275 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 chunk 315 optimal weight: 2.9990 chunk 255 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 189 optimal weight: 3.9990 chunk 332 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 569 ASN B 696 ASN ** A 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 569 ASN E 383 GLN F 327 GLN ** F 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.4280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.069 30635 Z= 0.316 Angle : 0.578 7.989 41696 Z= 0.293 Chirality : 0.046 0.382 4680 Planarity : 0.004 0.068 5533 Dihedral : 4.440 31.102 4147 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer Outliers : 1.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.00 % Twisted Proline : 0.33 % 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: -1.72 (0.13), residues: 3842 helix: 2.29 (0.24), residues: 520 sheet: -1.06 (0.15), residues: 1104 loop : -2.14 (0.13), residues: 2218 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 684 is missing expected H atoms. Skipping. Residue SER 684 is missing expected H atoms. Skipping. Residue SER 684 is missing expected H atoms. Skipping. Residue SER 684 is missing expected H atoms. Skipping. Residue SER 684 is missing expected H atoms. Skipping. Residue SER 684 is missing expected H atoms. Skipping. Evaluate side-chains 313 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 268 time to evaluate : 3.748 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 outliers start: 45 outliers final: 23 residues processed: 303 average time/residue: 0.7277 time to fit residues: 368.7218 Evaluate side-chains 275 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 252 time to evaluate : 3.664 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.5883 time to fit residues: 29.6219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 124 optimal weight: 0.7980 chunk 333 optimal weight: 6.9990 chunk 73 optimal weight: 0.8980 chunk 217 optimal weight: 2.9990 chunk 91 optimal weight: 0.3980 chunk 370 optimal weight: 3.9990 chunk 307 optimal weight: 2.9990 chunk 171 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 194 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 293 HIS ** F 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.4311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.043 30635 Z= 0.163 Angle : 0.522 6.642 41696 Z= 0.260 Chirality : 0.045 0.360 4680 Planarity : 0.004 0.082 5533 Dihedral : 4.216 32.215 4147 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer Outliers : 0.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.00 % Twisted Proline : 0.33 % 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: -1.50 (0.14), residues: 3842 helix: 2.43 (0.24), residues: 532 sheet: -0.94 (0.15), residues: 1084 loop : -1.98 (0.13), residues: 2226 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 684 is missing expected H atoms. Skipping. Residue SER 684 is missing expected H atoms. Skipping. Residue SER 684 is missing expected H atoms. Skipping. Residue SER 684 is missing expected H atoms. Skipping. Residue SER 684 is missing expected H atoms. Skipping. Residue SER 684 is missing expected H atoms. Skipping. Evaluate side-chains 297 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 277 time to evaluate : 3.716 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 outliers start: 20 outliers final: 11 residues processed: 289 average time/residue: 0.7386 time to fit residues: 356.1883 Evaluate side-chains 269 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 258 time to evaluate : 3.711 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.5828 time to fit residues: 16.1397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 357 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 211 optimal weight: 0.7980 chunk 270 optimal weight: 4.9990 chunk 209 optimal weight: 0.9980 chunk 311 optimal weight: 2.9990 chunk 206 optimal weight: 2.9990 chunk 369 optimal weight: 8.9990 chunk 231 optimal weight: 2.9990 chunk 225 optimal weight: 4.9990 chunk 170 optimal weight: 0.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 293 HIS ** F 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.4518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 30635 Z= 0.264 Angle : 0.544 7.045 41696 Z= 0.273 Chirality : 0.045 0.369 4680 Planarity : 0.004 0.082 5533 Dihedral : 4.303 31.271 4147 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer Outliers : 0.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.00 % Twisted Proline : 0.66 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.14), residues: 3842 helix: 2.44 (0.24), residues: 526 sheet: -0.96 (0.15), residues: 1109 loop : -1.95 (0.13), residues: 2207 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 684 is missing expected H atoms. Skipping. Residue SER 684 is missing expected H atoms. Skipping. Residue SER 684 is missing expected H atoms. Skipping. Residue SER 684 is missing expected H atoms. Skipping. Residue SER 684 is missing expected H atoms. Skipping. Residue SER 684 is missing expected H atoms. Skipping. Evaluate side-chains 286 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 261 time to evaluate : 3.717 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 outliers start: 25 outliers final: 11 residues processed: 279 average time/residue: 0.7925 time to fit residues: 372.0525 Evaluate side-chains 263 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 252 time to evaluate : 3.679 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.6014 time to fit residues: 16.9534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 228 optimal weight: 3.9990 chunk 147 optimal weight: 0.8980 chunk 220 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 234 optimal weight: 2.9990 chunk 251 optimal weight: 2.9990 chunk 182 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 chunk 290 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 293 HIS ** F 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.4620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 30635 Z= 0.212 Angle : 0.531 7.162 41696 Z= 0.265 Chirality : 0.045 0.363 4680 Planarity : 0.004 0.086 5533 Dihedral : 4.264 33.692 4147 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer Outliers : 0.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.00 % Twisted Proline : 0.66 % 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: -1.37 (0.14), residues: 3842 helix: 2.49 (0.24), residues: 532 sheet: -0.90 (0.15), residues: 1079 loop : -1.85 (0.13), residues: 2231 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 684 is missing expected H atoms. Skipping. Residue SER 684 is missing expected H atoms. Skipping. Residue SER 684 is missing expected H atoms. Skipping. Residue SER 684 is missing expected H atoms. Skipping. Residue SER 684 is missing expected H atoms. Skipping. Residue SER 684 is missing expected H atoms. Skipping. Evaluate side-chains 269 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 257 time to evaluate : 3.735 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 outliers start: 12 outliers final: 3 residues processed: 265 average time/residue: 0.7360 time to fit residues: 325.5338 Evaluate side-chains 255 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 252 time to evaluate : 3.721 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.6304 time to fit residues: 7.9762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 335 optimal weight: 9.9990 chunk 353 optimal weight: 3.9990 chunk 322 optimal weight: 0.5980 chunk 344 optimal weight: 7.9990 chunk 207 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 270 optimal weight: 1.9990 chunk 105 optimal weight: 7.9990 chunk 310 optimal weight: 3.9990 chunk 325 optimal weight: 0.0870 chunk 342 optimal weight: 8.9990 overall best weight: 1.5364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 293 HIS ** F 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.4764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.061 30635 Z= 0.243 Angle : 0.541 7.098 41696 Z= 0.270 Chirality : 0.045 0.365 4680 Planarity : 0.004 0.104 5533 Dihedral : 4.287 31.526 4147 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer Outliers : 0.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.00 % Twisted Proline : 0.66 % 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: -1.36 (0.14), residues: 3842 helix: 2.50 (0.24), residues: 528 sheet: -0.90 (0.15), residues: 1117 loop : -1.84 (0.13), residues: 2197 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 684 is missing expected H atoms. Skipping. Residue SER 684 is missing expected H atoms. Skipping. Residue SER 684 is missing expected H atoms. Skipping. Residue SER 684 is missing expected H atoms. Skipping. Residue SER 684 is missing expected H atoms. Skipping. Residue SER 684 is missing expected H atoms. Skipping. Evaluate side-chains 267 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 253 time to evaluate : 3.765 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 outliers start: 14 outliers final: 8 residues processed: 261 average time/residue: 0.7430 time to fit residues: 323.7452 Evaluate side-chains 259 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 251 time to evaluate : 3.773 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 8 outliers final: 1 residues processed: 8 average time/residue: 0.6276 time to fit residues: 13.5085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 225 optimal weight: 4.9990 chunk 363 optimal weight: 3.9990 chunk 222 optimal weight: 0.9980 chunk 172 optimal weight: 0.8980 chunk 252 optimal weight: 2.9990 chunk 381 optimal weight: 5.9990 chunk 351 optimal weight: 2.9990 chunk 303 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 234 optimal weight: 2.9990 chunk 186 optimal weight: 3.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 293 HIS ** F 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.4890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 30635 Z= 0.255 Angle : 0.547 7.821 41696 Z= 0.273 Chirality : 0.045 0.365 4680 Planarity : 0.004 0.105 5533 Dihedral : 4.338 33.467 4147 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer Outliers : 0.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.00 % Twisted Proline : 0.66 % 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: -1.34 (0.14), residues: 3842 helix: 2.49 (0.24), residues: 527 sheet: -0.89 (0.15), residues: 1105 loop : -1.81 (0.13), residues: 2210 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 684 is missing expected H atoms. Skipping. Residue SER 684 is missing expected H atoms. Skipping. Residue SER 684 is missing expected H atoms. Skipping. Residue SER 684 is missing expected H atoms. Skipping. Residue SER 684 is missing expected H atoms. Skipping. Residue SER 684 is missing expected H atoms. Skipping. Evaluate side-chains 266 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 261 time to evaluate : 3.741 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 outliers start: 5 outliers final: 1 residues processed: 265 average time/residue: 0.7538 time to fit residues: 332.1346 Evaluate side-chains 255 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 254 time to evaluate : 3.708 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.7681 time to fit residues: 5.9491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 241 optimal weight: 2.9990 chunk 323 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 280 optimal weight: 0.1980 chunk 44 optimal weight: 0.9980 chunk 84 optimal weight: 0.6980 chunk 304 optimal weight: 3.9990 chunk 127 optimal weight: 0.5980 chunk 312 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 56 optimal weight: 8.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 ASN F 293 HIS ** F 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.103908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.079988 restraints weight = 178151.338| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 2.80 r_work: 0.3015 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.4888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.048 30635 Z= 0.158 Angle : 0.525 8.147 41696 Z= 0.259 Chirality : 0.045 0.357 4680 Planarity : 0.004 0.099 5533 Dihedral : 4.191 32.091 4147 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.00 % Twisted Proline : 0.66 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.14), residues: 3842 helix: 2.63 (0.24), residues: 527 sheet: -0.83 (0.15), residues: 1120 loop : -1.73 (0.13), residues: 2195 =============================================================================== Job complete usr+sys time: 9999.32 seconds wall clock time: 174 minutes 8.20 seconds (10448.20 seconds total)