Starting phenix.real_space_refine on Sat Apr 6 19:34:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2z_23146/04_2024/7l2z_23146.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2z_23146/04_2024/7l2z_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_23146/04_2024/7l2z_23146.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2z_23146/04_2024/7l2z_23146.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2z_23146/04_2024/7l2z_23146.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2z_23146/04_2024/7l2z_23146.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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 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. 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: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 19.73, per 1000 atoms: 0.33 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: 39.25 Conformation dependent library (CDL) restraints added in 5.1 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: 3.81 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: 21.97 Time building geometry restraints manager: 41.56 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: 26397 17.95 - 35.90: 1633 35.90 - 53.86: 551 53.86 - 71.81: 117 71.81 - 89.76: 17 Dihedral angle restraints: 28715 sinusoidal: 15902 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 28712 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 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: 1.680 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: 11.570 Check model and map are aligned: 0.680 Set scattering table: 0.450 Process input model: 149.490 Find NCS groups from input model: 2.900 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 170.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 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 % Allowed : 10.41 % Favored : 88.96 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 627 HIS 0.003 0.001 HIS E 306 PHE 0.010 0.001 PHE D 289 TYR 0.008 0.001 TYR A 133 ARG 0.003 0.000 ARG D 368 *********************** 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 : 3.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 318 PHE cc_start: 0.7493 (OUTLIER) cc_final: 0.7144 (m-80) REVERT: B 430 ASP cc_start: 0.7784 (m-30) cc_final: 0.7504 (m-30) REVERT: B 468 ASP cc_start: 0.8097 (t0) cc_final: 0.7792 (m-30) REVERT: B 653 SER cc_start: 0.8606 (m) cc_final: 0.8342 (p) REVERT: A 112 MET cc_start: 0.6441 (tpp) cc_final: 0.6105 (mmm) REVERT: A 524 TYR cc_start: 0.7654 (m-80) cc_final: 0.7241 (m-80) REVERT: A 724 VAL cc_start: 0.8518 (t) cc_final: 0.8214 (p) REVERT: C 92 ILE cc_start: 0.8252 (pt) cc_final: 0.8039 (mm) REVERT: C 425 ASP cc_start: 0.6918 (p0) cc_final: 0.6671 (p0) REVERT: C 515 ASP cc_start: 0.6670 (p0) cc_final: 0.6305 (p0) REVERT: D 116 GLU cc_start: 0.7405 (tt0) cc_final: 0.7166 (tt0) REVERT: D 405 MET cc_start: 0.6450 (ptt) cc_final: 0.5356 (tpt) REVERT: E 110 LYS cc_start: 0.8182 (ttpt) cc_final: 0.7813 (tmtt) REVERT: E 274 ASP cc_start: 0.7694 (p0) cc_final: 0.7238 (t0) REVERT: E 412 MET cc_start: 0.8673 (ptp) cc_final: 0.8338 (ptp) REVERT: E 602 MET cc_start: 0.7438 (ttt) cc_final: 0.7220 (ttt) REVERT: F 116 GLU cc_start: 0.7094 (tt0) cc_final: 0.6887 (tm-30) REVERT: F 154 LEU cc_start: 0.6765 (mp) cc_final: 0.5961 (tt) REVERT: F 207 LEU cc_start: 0.7368 (pp) cc_final: 0.6524 (tp) REVERT: F 269 TYR cc_start: 0.6519 (m-10) cc_final: 0.6305 (m-10) REVERT: F 332 ILE cc_start: 0.8446 (mm) cc_final: 0.8050 (mm) REVERT: F 415 ASN cc_start: 0.6917 (t0) cc_final: 0.6558 (t0) REVERT: F 542 PHE cc_start: 0.6998 (m-10) cc_final: 0.6607 (m-10) REVERT: F 580 PHE cc_start: 0.7722 (t80) cc_final: 0.7158 (t80) REVERT: F 711 ILE cc_start: 0.7239 (mm) cc_final: 0.7034 (mt) REVERT: F 717 ASN cc_start: 0.7188 (t0) cc_final: 0.6704 (m110) REVERT: F 718 SER cc_start: 0.8458 (p) cc_final: 0.7946 (p) outliers start: 21 outliers final: 7 residues processed: 638 average time/residue: 0.8113 time to fit residues: 816.4752 Evaluate side-chains 397 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 389 time to evaluate : 3.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 347 ASN Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 430 ASP Chi-restraints excluded: chain E residue 710 VAL Chi-restraints excluded: chain F residue 349 VAL 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: 3.9990 chunk 161 optimal weight: 4.9990 chunk 99 optimal weight: 0.9990 chunk 195 optimal weight: 2.9990 chunk 155 optimal weight: 0.0870 chunk 300 optimal weight: 0.9980 chunk 116 optimal weight: 7.9990 chunk 182 optimal weight: 5.9990 chunk 223 optimal weight: 3.9990 chunk 347 optimal weight: 9.9990 overall best weight: 1.8164 ------------------------------------------------------------------------------- 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 415 ASN C 490 ASN D 179 GLN E 668 GLN F 508 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 30635 Z= 0.278 Angle : 0.552 6.620 41696 Z= 0.278 Chirality : 0.046 0.402 4680 Planarity : 0.004 0.082 5533 Dihedral : 4.152 55.542 4159 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 1.59 % Allowed : 13.89 % Favored : 84.52 % 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: -2.21 (0.13), residues: 3842 helix: 1.63 (0.24), residues: 529 sheet: -1.22 (0.15), residues: 1101 loop : -2.51 (0.12), residues: 2212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 191 HIS 0.005 0.001 HIS B 306 PHE 0.020 0.001 PHE F 163 TYR 0.011 0.001 TYR A 133 ARG 0.006 0.000 ARG F 71 *********************** 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 432 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 379 time to evaluate : 3.649 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: B 102 MET cc_start: 0.7237 (mmm) cc_final: 0.6526 (ttp) REVERT: B 318 PHE cc_start: 0.7797 (OUTLIER) cc_final: 0.7291 (m-80) REVERT: B 468 ASP cc_start: 0.8254 (t0) cc_final: 0.8022 (m-30) REVERT: B 512 ILE cc_start: 0.8520 (tp) cc_final: 0.8282 (tp) REVERT: A 139 MET cc_start: 0.7708 (mmt) cc_final: 0.7324 (mmt) REVERT: A 397 ASN cc_start: 0.8405 (OUTLIER) cc_final: 0.8141 (p0) REVERT: A 524 TYR cc_start: 0.7834 (m-80) cc_final: 0.7360 (m-80) REVERT: A 717 ASN cc_start: 0.7472 (m-40) cc_final: 0.6977 (t0) REVERT: A 724 VAL cc_start: 0.8747 (t) cc_final: 0.8452 (p) REVERT: C 405 MET cc_start: 0.7466 (mmp) cc_final: 0.6138 (mtt) REVERT: C 425 ASP cc_start: 0.7023 (p0) cc_final: 0.6754 (p0) REVERT: C 515 ASP cc_start: 0.6749 (p0) cc_final: 0.6507 (p0) REVERT: D 405 MET cc_start: 0.6438 (ptt) cc_final: 0.5696 (tpt) REVERT: E 110 LYS cc_start: 0.8028 (ttpt) cc_final: 0.7638 (tmtt) REVERT: E 274 ASP cc_start: 0.7698 (p0) cc_final: 0.7373 (t0) REVERT: E 412 MET cc_start: 0.8763 (ptp) cc_final: 0.8315 (ptp) REVERT: F 154 LEU cc_start: 0.7118 (mp) cc_final: 0.6242 (tt) REVERT: F 207 LEU cc_start: 0.7382 (pp) cc_final: 0.6507 (tp) REVERT: F 293 HIS cc_start: 0.6893 (t-90) cc_final: 0.6560 (t-170) REVERT: F 327 GLN cc_start: 0.7832 (tp-100) cc_final: 0.7508 (mp10) REVERT: F 332 ILE cc_start: 0.8508 (mm) cc_final: 0.8124 (mm) REVERT: F 564 MET cc_start: 0.8116 (tpp) cc_final: 0.7772 (tpp) outliers start: 53 outliers final: 36 residues processed: 420 average time/residue: 0.7520 time to fit residues: 519.9717 Evaluate side-chains 367 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 329 time to evaluate : 3.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 274 ASP Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 504 GLN Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 157 MET Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 397 ASN Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 378 TYR Chi-restraints excluded: chain C residue 490 ASN Chi-restraints excluded: chain C residue 514 ASP Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 551 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 168 ASN Chi-restraints excluded: chain E residue 398 LEU Chi-restraints excluded: chain E residue 430 ASP Chi-restraints excluded: chain E residue 480 ASN Chi-restraints excluded: chain E residue 573 PHE Chi-restraints excluded: chain E residue 617 ILE Chi-restraints excluded: chain E residue 656 THR Chi-restraints excluded: chain E residue 710 VAL Chi-restraints excluded: chain F residue 114 ASN Chi-restraints excluded: chain F residue 349 VAL Chi-restraints excluded: chain F residue 573 PHE 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: 4.9990 chunk 289 optimal weight: 3.9990 chunk 236 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 348 optimal weight: 7.9990 chunk 376 optimal weight: 3.9990 chunk 310 optimal weight: 5.9990 chunk 345 optimal weight: 5.9990 chunk 118 optimal weight: 10.0000 chunk 279 optimal weight: 4.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- 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 135 ASN ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 550 GLN ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 95 ASN ** F 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 622 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 30635 Z= 0.423 Angle : 0.639 7.137 41696 Z= 0.331 Chirality : 0.048 0.407 4680 Planarity : 0.005 0.066 5533 Dihedral : 4.934 55.899 4157 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.91 % Favored : 92.06 % Rotamer: Outliers : 3.45 % Allowed : 14.28 % Favored : 82.27 % 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: -2.06 (0.13), residues: 3842 helix: 1.75 (0.24), residues: 520 sheet: -1.19 (0.15), residues: 1102 loop : -2.34 (0.12), residues: 2220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 191 HIS 0.011 0.002 HIS B 306 PHE 0.026 0.002 PHE F 163 TYR 0.017 0.002 TYR B 378 ARG 0.005 0.001 ARG E 355 *********************** 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 421 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 306 time to evaluate : 3.725 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: B 77 PHE cc_start: 0.8674 (OUTLIER) cc_final: 0.7813 (t80) REVERT: B 201 ASP cc_start: 0.7860 (OUTLIER) cc_final: 0.7598 (p0) REVERT: B 318 PHE cc_start: 0.8255 (OUTLIER) cc_final: 0.7153 (m-80) REVERT: B 468 ASP cc_start: 0.8372 (t0) cc_final: 0.8010 (m-30) REVERT: B 721 VAL cc_start: 0.9193 (OUTLIER) cc_final: 0.8931 (p) REVERT: A 139 MET cc_start: 0.8137 (mmt) cc_final: 0.7863 (mmt) REVERT: A 222 ASP cc_start: 0.8528 (OUTLIER) cc_final: 0.8191 (p0) REVERT: A 234 VAL cc_start: 0.8099 (OUTLIER) cc_final: 0.7832 (p) REVERT: A 263 GLN cc_start: 0.7028 (mp10) cc_final: 0.6623 (mp-120) REVERT: A 397 ASN cc_start: 0.8646 (OUTLIER) cc_final: 0.8317 (p0) REVERT: A 420 MET cc_start: 0.6502 (mmt) cc_final: 0.5974 (mmt) REVERT: A 545 MET cc_start: 0.8278 (tpp) cc_final: 0.7644 (tpt) REVERT: A 717 ASN cc_start: 0.7642 (m-40) cc_final: 0.7219 (t0) REVERT: C 318 PHE cc_start: 0.8720 (OUTLIER) cc_final: 0.8424 (m-80) REVERT: C 425 ASP cc_start: 0.7208 (p0) cc_final: 0.7001 (p0) REVERT: C 489 MET cc_start: 0.8083 (ttp) cc_final: 0.7869 (ttp) REVERT: C 529 MET cc_start: 0.7264 (OUTLIER) cc_final: 0.6921 (tpt) REVERT: D 405 MET cc_start: 0.6588 (ptt) cc_final: 0.5996 (tpt) REVERT: D 529 MET cc_start: 0.7822 (tmm) cc_final: 0.7500 (tmm) REVERT: D 554 VAL cc_start: 0.8244 (OUTLIER) cc_final: 0.8031 (t) REVERT: D 690 MET cc_start: 0.8411 (OUTLIER) cc_final: 0.8183 (mtm) REVERT: E 75 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8391 (pp) REVERT: E 110 LYS cc_start: 0.7910 (ttpt) cc_final: 0.7596 (ttpp) REVERT: E 274 ASP cc_start: 0.7762 (p0) cc_final: 0.7532 (t70) REVERT: E 412 MET cc_start: 0.8821 (ptp) cc_final: 0.8573 (ptm) REVERT: F 207 LEU cc_start: 0.7390 (pp) cc_final: 0.6535 (tp) REVERT: F 332 ILE cc_start: 0.8497 (mm) cc_final: 0.8134 (mm) REVERT: F 645 SER cc_start: 0.7382 (t) cc_final: 0.7070 (p) outliers start: 115 outliers final: 68 residues processed: 394 average time/residue: 0.6805 time to fit residues: 448.7887 Evaluate side-chains 350 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 270 time to evaluate : 3.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 77 PHE Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 274 ASP Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 490 ASN Chi-restraints excluded: chain B residue 504 GLN Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 653 SER Chi-restraints excluded: chain B residue 669 SER Chi-restraints excluded: chain B residue 721 VAL Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 157 MET Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 397 ASN Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 435 ASN Chi-restraints excluded: chain A residue 519 ASP Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 723 ASP Chi-restraints excluded: chain C residue 137 GLU Chi-restraints excluded: chain C residue 201 ASP Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 347 ASN Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 378 TYR Chi-restraints excluded: chain C residue 514 ASP Chi-restraints excluded: chain C residue 517 THR Chi-restraints excluded: chain C residue 529 MET Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 189 THR Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 480 ASN Chi-restraints excluded: chain D residue 517 THR Chi-restraints excluded: chain D residue 554 VAL Chi-restraints excluded: chain D residue 573 PHE Chi-restraints excluded: chain D residue 680 LEU Chi-restraints excluded: chain D residue 690 MET Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 77 PHE Chi-restraints excluded: chain E residue 87 MET Chi-restraints excluded: chain E residue 102 MET Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 157 MET Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 168 ASN Chi-restraints excluded: chain E residue 347 ASN Chi-restraints excluded: chain E residue 398 LEU Chi-restraints excluded: chain E residue 413 ASP Chi-restraints excluded: chain E residue 430 ASP Chi-restraints excluded: chain E residue 479 THR Chi-restraints excluded: chain E residue 573 PHE Chi-restraints excluded: chain E residue 617 ILE Chi-restraints excluded: chain E residue 656 THR Chi-restraints excluded: chain E residue 680 LEU Chi-restraints excluded: chain E residue 703 THR Chi-restraints excluded: chain E residue 710 VAL Chi-restraints excluded: chain F residue 114 ASN Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 349 VAL Chi-restraints excluded: chain F residue 498 ASP Chi-restraints excluded: chain F residue 573 PHE Chi-restraints excluded: chain F residue 656 THR Chi-restraints excluded: chain F residue 718 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 344 optimal weight: 10.0000 chunk 261 optimal weight: 1.9990 chunk 180 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 166 optimal weight: 0.6980 chunk 233 optimal weight: 0.7980 chunk 349 optimal weight: 10.0000 chunk 370 optimal weight: 6.9990 chunk 182 optimal weight: 2.9990 chunk 331 optimal weight: 7.9990 chunk 99 optimal weight: 0.5980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 114 ASN ** B 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 GLN F 95 ASN ** F 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.3841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 30635 Z= 0.225 Angle : 0.540 6.444 41696 Z= 0.272 Chirality : 0.045 0.361 4680 Planarity : 0.004 0.077 5533 Dihedral : 4.684 54.677 4157 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 2.61 % Allowed : 15.30 % Favored : 82.09 % 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: -1.79 (0.13), residues: 3842 helix: 2.11 (0.24), residues: 526 sheet: -1.05 (0.15), residues: 1047 loop : -2.17 (0.12), residues: 2269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 253 HIS 0.009 0.001 HIS F 293 PHE 0.013 0.001 PHE E 220 TYR 0.011 0.001 TYR E 204 ARG 0.002 0.000 ARG C 291 *********************** 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 368 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 281 time to evaluate : 3.633 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: B 102 MET cc_start: 0.7396 (mmm) cc_final: 0.6813 (ttp) REVERT: B 318 PHE cc_start: 0.8167 (OUTLIER) cc_final: 0.7325 (m-80) REVERT: B 468 ASP cc_start: 0.8354 (t0) cc_final: 0.7961 (m-30) REVERT: B 512 ILE cc_start: 0.9020 (tp) cc_final: 0.8805 (tp) REVERT: A 222 ASP cc_start: 0.8576 (OUTLIER) cc_final: 0.8133 (p0) REVERT: A 234 VAL cc_start: 0.8145 (OUTLIER) cc_final: 0.7871 (p) REVERT: A 263 GLN cc_start: 0.6930 (mp10) cc_final: 0.6550 (mp-120) REVERT: A 397 ASN cc_start: 0.8545 (OUTLIER) cc_final: 0.8137 (p0) REVERT: A 717 ASN cc_start: 0.7605 (m-40) cc_final: 0.7180 (t0) REVERT: C 425 ASP cc_start: 0.7082 (p0) cc_final: 0.6837 (p0) REVERT: D 405 MET cc_start: 0.6532 (ptt) cc_final: 0.5878 (tpt) REVERT: E 110 LYS cc_start: 0.7842 (ttpt) cc_final: 0.7387 (tmtt) REVERT: E 412 MET cc_start: 0.8792 (ptp) cc_final: 0.8436 (ptp) REVERT: F 207 LEU cc_start: 0.7345 (pp) cc_final: 0.6510 (tp) REVERT: F 332 ILE cc_start: 0.8512 (mm) cc_final: 0.8148 (mm) REVERT: F 492 MET cc_start: 0.8333 (mtm) cc_final: 0.7666 (ptp) REVERT: F 645 SER cc_start: 0.7453 (t) cc_final: 0.7174 (p) REVERT: F 716 ILE cc_start: 0.7689 (OUTLIER) cc_final: 0.7155 (pt) REVERT: F 717 ASN cc_start: 0.7323 (t0) cc_final: 0.6652 (m110) outliers start: 87 outliers final: 56 residues processed: 347 average time/residue: 0.6838 time to fit residues: 400.7963 Evaluate side-chains 323 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 262 time to evaluate : 3.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 274 ASP Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 347 ASN Chi-restraints excluded: chain B residue 504 GLN Chi-restraints excluded: chain B residue 508 ASN Chi-restraints excluded: chain B residue 573 PHE Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 653 SER Chi-restraints excluded: chain B residue 672 ASN Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 157 MET Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 397 ASN Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 347 ASN Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 378 TYR Chi-restraints excluded: chain C residue 508 ASN Chi-restraints excluded: chain C residue 514 ASP Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 573 PHE Chi-restraints excluded: chain D residue 680 LEU Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 77 PHE Chi-restraints excluded: chain E residue 102 MET Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 157 MET Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 168 ASN Chi-restraints excluded: chain E residue 396 LEU Chi-restraints excluded: chain E residue 398 LEU Chi-restraints excluded: chain E residue 413 ASP Chi-restraints excluded: chain E residue 430 ASP Chi-restraints excluded: chain E residue 516 SER Chi-restraints excluded: chain E residue 532 LEU Chi-restraints excluded: chain E residue 573 PHE Chi-restraints excluded: chain E residue 617 ILE Chi-restraints excluded: chain E residue 680 LEU Chi-restraints excluded: chain E residue 710 VAL Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 95 ASN Chi-restraints excluded: chain F residue 114 ASN Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 349 VAL Chi-restraints excluded: chain F residue 573 PHE Chi-restraints excluded: chain F residue 593 THR Chi-restraints excluded: chain F residue 704 MET Chi-restraints excluded: chain F residue 716 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 308 optimal weight: 6.9990 chunk 210 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 275 optimal weight: 3.9990 chunk 152 optimal weight: 1.9990 chunk 315 optimal weight: 0.8980 chunk 255 optimal weight: 0.3980 chunk 0 optimal weight: 3.9990 chunk 189 optimal weight: 3.9990 chunk 332 optimal weight: 0.8980 chunk 93 optimal weight: 4.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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** ** C 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.4010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 30635 Z= 0.238 Angle : 0.529 6.277 41696 Z= 0.267 Chirality : 0.045 0.371 4680 Planarity : 0.004 0.084 5533 Dihedral : 4.630 55.935 4157 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 2.52 % Allowed : 15.33 % Favored : 82.15 % 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: -1.65 (0.13), residues: 3842 helix: 2.38 (0.24), residues: 520 sheet: -1.04 (0.15), residues: 1073 loop : -2.07 (0.13), residues: 2249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 260 HIS 0.009 0.001 HIS F 293 PHE 0.013 0.001 PHE E 220 TYR 0.011 0.001 TYR E 204 ARG 0.002 0.000 ARG F 171 *********************** 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 353 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 269 time to evaluate : 3.772 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: B 102 MET cc_start: 0.7390 (mmm) cc_final: 0.6843 (ttp) REVERT: B 318 PHE cc_start: 0.8185 (OUTLIER) cc_final: 0.7408 (m-80) REVERT: B 468 ASP cc_start: 0.8357 (t0) cc_final: 0.7936 (m-30) REVERT: A 222 ASP cc_start: 0.8585 (OUTLIER) cc_final: 0.8165 (p0) REVERT: A 234 VAL cc_start: 0.8134 (OUTLIER) cc_final: 0.7874 (p) REVERT: A 289 PHE cc_start: 0.7755 (p90) cc_final: 0.7407 (p90) REVERT: A 397 ASN cc_start: 0.8598 (OUTLIER) cc_final: 0.8194 (p0) REVERT: A 555 MET cc_start: 0.9053 (mmm) cc_final: 0.8841 (mmm) REVERT: A 717 ASN cc_start: 0.7544 (m-40) cc_final: 0.7180 (t0) REVERT: C 318 PHE cc_start: 0.8678 (OUTLIER) cc_final: 0.8372 (m-80) REVERT: C 425 ASP cc_start: 0.7162 (p0) cc_final: 0.6916 (p0) REVERT: D 405 MET cc_start: 0.6544 (ptt) cc_final: 0.5954 (tpt) REVERT: D 420 MET cc_start: 0.8229 (mmm) cc_final: 0.7633 (tpt) REVERT: E 110 LYS cc_start: 0.7806 (ttpt) cc_final: 0.7396 (ttpp) REVERT: E 181 VAL cc_start: 0.9101 (p) cc_final: 0.8873 (t) REVERT: E 325 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7652 (tt) REVERT: E 420 MET cc_start: 0.7667 (mmm) cc_final: 0.7436 (mmm) REVERT: F 207 LEU cc_start: 0.7344 (pp) cc_final: 0.6493 (tp) REVERT: F 332 ILE cc_start: 0.8525 (mm) cc_final: 0.8162 (mm) REVERT: F 645 SER cc_start: 0.7529 (t) cc_final: 0.7236 (p) REVERT: F 704 MET cc_start: 0.7854 (OUTLIER) cc_final: 0.7611 (ptp) REVERT: F 717 ASN cc_start: 0.7296 (t0) cc_final: 0.6687 (m110) outliers start: 84 outliers final: 64 residues processed: 335 average time/residue: 0.6718 time to fit residues: 380.8866 Evaluate side-chains 332 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 261 time to evaluate : 3.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 274 ASP Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 347 ASN Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 500 CYS Chi-restraints excluded: chain B residue 508 ASN Chi-restraints excluded: chain B residue 573 PHE Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 653 SER Chi-restraints excluded: chain B residue 672 ASN Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 157 MET Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 397 ASN Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 723 ASP Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 347 ASN Chi-restraints excluded: chain C residue 378 TYR Chi-restraints excluded: chain C residue 508 ASN Chi-restraints excluded: chain C residue 514 ASP Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 271 GLN Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 413 ASP Chi-restraints excluded: chain D residue 480 ASN Chi-restraints excluded: chain D residue 680 LEU Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 77 PHE Chi-restraints excluded: chain E residue 102 MET Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 157 MET Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 168 ASN Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 396 LEU Chi-restraints excluded: chain E residue 398 LEU Chi-restraints excluded: chain E residue 413 ASP Chi-restraints excluded: chain E residue 430 ASP Chi-restraints excluded: chain E residue 479 THR Chi-restraints excluded: chain E residue 516 SER Chi-restraints excluded: chain E residue 532 LEU Chi-restraints excluded: chain E residue 573 PHE Chi-restraints excluded: chain E residue 617 ILE Chi-restraints excluded: chain E residue 680 LEU Chi-restraints excluded: chain E residue 710 VAL Chi-restraints excluded: chain F residue 114 ASN Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 349 VAL Chi-restraints excluded: chain F residue 573 PHE Chi-restraints excluded: chain F residue 593 THR Chi-restraints excluded: chain F residue 704 MET Chi-restraints excluded: chain F residue 711 ILE Chi-restraints excluded: chain F residue 718 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 124 optimal weight: 7.9990 chunk 333 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 chunk 217 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 370 optimal weight: 4.9990 chunk 307 optimal weight: 3.9990 chunk 171 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 194 optimal weight: 2.9990 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 569 ASN ** C 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 383 GLN ** F 168 ASN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.4495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 30635 Z= 0.322 Angle : 0.573 6.834 41696 Z= 0.291 Chirality : 0.046 0.369 4680 Planarity : 0.004 0.071 5533 Dihedral : 4.867 59.341 4157 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 3.21 % Allowed : 15.24 % Favored : 81.55 % 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: -1.65 (0.13), residues: 3842 helix: 2.32 (0.24), residues: 520 sheet: -1.07 (0.15), residues: 1074 loop : -2.03 (0.13), residues: 2248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 260 HIS 0.011 0.002 HIS F 293 PHE 0.018 0.002 PHE A 573 TYR 0.016 0.001 TYR F 671 ARG 0.003 0.000 ARG D 340 *********************** 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 379 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 272 time to evaluate : 3.701 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: B 102 MET cc_start: 0.7441 (mmm) cc_final: 0.6932 (ttp) REVERT: B 234 VAL cc_start: 0.8965 (OUTLIER) cc_final: 0.8738 (p) REVERT: B 318 PHE cc_start: 0.8286 (OUTLIER) cc_final: 0.7361 (m-80) REVERT: B 468 ASP cc_start: 0.8431 (t0) cc_final: 0.8035 (m-30) REVERT: B 721 VAL cc_start: 0.9197 (OUTLIER) cc_final: 0.8943 (p) REVERT: A 123 LEU cc_start: 0.7963 (OUTLIER) cc_final: 0.7723 (pp) REVERT: A 222 ASP cc_start: 0.8647 (OUTLIER) cc_final: 0.8206 (p0) REVERT: A 234 VAL cc_start: 0.8266 (OUTLIER) cc_final: 0.8014 (p) REVERT: A 263 GLN cc_start: 0.7057 (mp10) cc_final: 0.6706 (mp10) REVERT: A 397 ASN cc_start: 0.8596 (OUTLIER) cc_final: 0.8222 (p0) REVERT: A 555 MET cc_start: 0.9110 (mmm) cc_final: 0.8874 (mmm) REVERT: A 717 ASN cc_start: 0.7613 (m-40) cc_final: 0.7171 (t0) REVERT: C 318 PHE cc_start: 0.8725 (OUTLIER) cc_final: 0.8389 (m-80) REVERT: C 405 MET cc_start: 0.7693 (mmp) cc_final: 0.6513 (mtt) REVERT: C 425 ASP cc_start: 0.7444 (p0) cc_final: 0.7198 (p0) REVERT: C 661 MET cc_start: 0.9037 (ttp) cc_final: 0.8393 (ttt) REVERT: C 673 ASP cc_start: 0.7998 (t70) cc_final: 0.7788 (t0) REVERT: D 405 MET cc_start: 0.6493 (ptt) cc_final: 0.5874 (tpt) REVERT: D 420 MET cc_start: 0.8351 (mmm) cc_final: 0.7833 (tpt) REVERT: D 690 MET cc_start: 0.8504 (OUTLIER) cc_final: 0.8255 (mtm) REVERT: E 110 LYS cc_start: 0.7807 (ttpt) cc_final: 0.7485 (ttpp) REVERT: E 181 VAL cc_start: 0.9112 (p) cc_final: 0.8888 (t) REVERT: E 325 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7699 (tt) REVERT: E 420 MET cc_start: 0.7739 (mmm) cc_final: 0.7507 (mmm) REVERT: E 545 MET cc_start: 0.8479 (mtm) cc_final: 0.8180 (mtm) REVERT: F 207 LEU cc_start: 0.7226 (pp) cc_final: 0.6387 (tp) REVERT: F 359 ASP cc_start: 0.6588 (m-30) cc_final: 0.6004 (m-30) REVERT: F 425 ASP cc_start: 0.8185 (p0) cc_final: 0.6629 (t0) REVERT: F 645 SER cc_start: 0.7542 (t) cc_final: 0.7335 (p) REVERT: F 717 ASN cc_start: 0.7387 (t0) cc_final: 0.6870 (m110) outliers start: 107 outliers final: 73 residues processed: 358 average time/residue: 0.6864 time to fit residues: 418.0564 Evaluate side-chains 346 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 263 time to evaluate : 3.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 274 ASP Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 347 ASN Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 490 ASN Chi-restraints excluded: chain B residue 508 ASN Chi-restraints excluded: chain B residue 573 PHE Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 653 SER Chi-restraints excluded: chain B residue 672 ASN Chi-restraints excluded: chain B residue 721 VAL Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 157 MET Chi-restraints excluded: chain A residue 179 GLN Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 397 ASN Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 519 ASP Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 723 ASP Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 201 ASP Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 347 ASN Chi-restraints excluded: chain C residue 378 TYR Chi-restraints excluded: chain C residue 508 ASN Chi-restraints excluded: chain C residue 514 ASP Chi-restraints excluded: chain C residue 517 THR Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 271 GLN Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 413 ASP Chi-restraints excluded: chain D residue 480 ASN Chi-restraints excluded: chain D residue 573 PHE Chi-restraints excluded: chain D residue 680 LEU Chi-restraints excluded: chain D residue 690 MET Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 77 PHE Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 168 ASN Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 347 ASN Chi-restraints excluded: chain E residue 396 LEU Chi-restraints excluded: chain E residue 398 LEU Chi-restraints excluded: chain E residue 413 ASP Chi-restraints excluded: chain E residue 430 ASP Chi-restraints excluded: chain E residue 479 THR Chi-restraints excluded: chain E residue 516 SER Chi-restraints excluded: chain E residue 532 LEU Chi-restraints excluded: chain E residue 573 PHE Chi-restraints excluded: chain E residue 617 ILE Chi-restraints excluded: chain E residue 680 LEU Chi-restraints excluded: chain E residue 710 VAL Chi-restraints excluded: chain F residue 114 ASN Chi-restraints excluded: chain F residue 202 LEU Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 349 VAL Chi-restraints excluded: chain F residue 498 ASP Chi-restraints excluded: chain F residue 573 PHE Chi-restraints excluded: chain F residue 593 THR Chi-restraints excluded: chain F residue 711 ILE Chi-restraints excluded: chain F residue 716 ILE Chi-restraints excluded: chain F residue 718 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 357 optimal weight: 0.4980 chunk 41 optimal weight: 0.1980 chunk 211 optimal weight: 0.9980 chunk 270 optimal weight: 3.9990 chunk 209 optimal weight: 0.9980 chunk 311 optimal weight: 2.9990 chunk 206 optimal weight: 1.9990 chunk 369 optimal weight: 6.9990 chunk 231 optimal weight: 1.9990 chunk 225 optimal weight: 4.9990 chunk 170 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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** ** C 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.4531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 30635 Z= 0.176 Angle : 0.521 7.308 41696 Z= 0.261 Chirality : 0.045 0.359 4680 Planarity : 0.004 0.088 5533 Dihedral : 4.666 57.492 4157 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 2.37 % Allowed : 16.17 % Favored : 81.46 % 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: -1.44 (0.14), residues: 3842 helix: 2.60 (0.24), residues: 520 sheet: -0.99 (0.15), residues: 1082 loop : -1.88 (0.13), residues: 2240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 260 HIS 0.010 0.001 HIS F 293 PHE 0.020 0.001 PHE A 289 TYR 0.019 0.001 TYR A 671 ARG 0.003 0.000 ARG C 633 *********************** 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 350 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 271 time to evaluate : 3.652 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: B 102 MET cc_start: 0.7339 (mmm) cc_final: 0.6905 (ttp) REVERT: B 318 PHE cc_start: 0.8248 (OUTLIER) cc_final: 0.7295 (m-80) REVERT: B 468 ASP cc_start: 0.8428 (t0) cc_final: 0.7954 (m-30) REVERT: A 123 LEU cc_start: 0.7944 (OUTLIER) cc_final: 0.7690 (pp) REVERT: A 222 ASP cc_start: 0.8519 (OUTLIER) cc_final: 0.8152 (p0) REVERT: A 234 VAL cc_start: 0.8258 (OUTLIER) cc_final: 0.8006 (p) REVERT: A 263 GLN cc_start: 0.6999 (mp10) cc_final: 0.6667 (mp10) REVERT: A 397 ASN cc_start: 0.8537 (OUTLIER) cc_final: 0.8126 (p0) REVERT: A 481 GLN cc_start: 0.7966 (pt0) cc_final: 0.7674 (pt0) REVERT: A 717 ASN cc_start: 0.7578 (m-40) cc_final: 0.7143 (t0) REVERT: C 318 PHE cc_start: 0.8680 (OUTLIER) cc_final: 0.8399 (m-80) REVERT: C 425 ASP cc_start: 0.7258 (p0) cc_final: 0.7023 (p0) REVERT: C 529 MET cc_start: 0.7122 (ttm) cc_final: 0.6880 (tpt) REVERT: C 661 MET cc_start: 0.8930 (ttp) cc_final: 0.8340 (ttt) REVERT: C 673 ASP cc_start: 0.7900 (t70) cc_final: 0.7695 (t0) REVERT: D 405 MET cc_start: 0.6432 (ptt) cc_final: 0.5917 (tpt) REVERT: D 420 MET cc_start: 0.8334 (mmm) cc_final: 0.7901 (tpt) REVERT: E 110 LYS cc_start: 0.7754 (ttpt) cc_final: 0.7452 (ttpp) REVERT: E 181 VAL cc_start: 0.9135 (p) cc_final: 0.8921 (t) REVERT: E 325 LEU cc_start: 0.7964 (OUTLIER) cc_final: 0.7674 (tt) REVERT: E 420 MET cc_start: 0.7694 (mmm) cc_final: 0.7467 (mmm) REVERT: E 545 MET cc_start: 0.8458 (mtm) cc_final: 0.8176 (mtm) REVERT: F 207 LEU cc_start: 0.7235 (pp) cc_final: 0.6341 (tp) REVERT: F 425 ASP cc_start: 0.8171 (p0) cc_final: 0.6608 (t0) REVERT: F 645 SER cc_start: 0.7536 (t) cc_final: 0.7335 (p) REVERT: F 717 ASN cc_start: 0.7233 (t0) cc_final: 0.6757 (m110) outliers start: 79 outliers final: 63 residues processed: 333 average time/residue: 0.7199 time to fit residues: 406.2295 Evaluate side-chains 335 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 265 time to evaluate : 3.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 347 ASN Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 508 ASN Chi-restraints excluded: chain B residue 573 PHE Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 672 ASN Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 157 MET Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 397 ASN Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 723 ASP Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 347 ASN Chi-restraints excluded: chain C residue 378 TYR Chi-restraints excluded: chain C residue 508 ASN Chi-restraints excluded: chain C residue 514 ASP Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 271 GLN Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 413 ASP Chi-restraints excluded: chain D residue 480 ASN Chi-restraints excluded: chain D residue 573 PHE Chi-restraints excluded: chain D residue 680 LEU Chi-restraints excluded: chain D residue 681 LEU Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 77 PHE Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 168 ASN Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 347 ASN Chi-restraints excluded: chain E residue 396 LEU Chi-restraints excluded: chain E residue 398 LEU Chi-restraints excluded: chain E residue 413 ASP Chi-restraints excluded: chain E residue 430 ASP Chi-restraints excluded: chain E residue 479 THR Chi-restraints excluded: chain E residue 532 LEU Chi-restraints excluded: chain E residue 573 PHE Chi-restraints excluded: chain E residue 680 LEU Chi-restraints excluded: chain E residue 710 VAL Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 114 ASN Chi-restraints excluded: chain F residue 202 LEU Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 349 VAL Chi-restraints excluded: chain F residue 573 PHE Chi-restraints excluded: chain F residue 593 THR Chi-restraints excluded: chain F residue 716 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 228 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 220 optimal weight: 0.7980 chunk 111 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 234 optimal weight: 2.9990 chunk 251 optimal weight: 2.9990 chunk 182 optimal weight: 6.9990 chunk 34 optimal weight: 0.8980 chunk 290 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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** ** C 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 168 ASN ** 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: 0.7873 moved from start: 0.4642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 30635 Z= 0.221 Angle : 0.526 7.772 41696 Z= 0.263 Chirality : 0.045 0.362 4680 Planarity : 0.004 0.090 5533 Dihedral : 4.626 55.209 4157 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 2.52 % Allowed : 16.26 % Favored : 81.22 % 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: -1.36 (0.14), residues: 3842 helix: 2.57 (0.24), residues: 521 sheet: -0.97 (0.15), residues: 1092 loop : -1.80 (0.13), residues: 2229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 260 HIS 0.005 0.001 HIS B 306 PHE 0.020 0.001 PHE A 289 TYR 0.011 0.001 TYR E 204 ARG 0.002 0.000 ARG C 103 *********************** 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 352 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 268 time to evaluate : 3.635 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: B 77 PHE cc_start: 0.8845 (OUTLIER) cc_final: 0.8085 (t80) REVERT: B 102 MET cc_start: 0.7235 (mmm) cc_final: 0.6955 (ttp) REVERT: B 318 PHE cc_start: 0.8263 (OUTLIER) cc_final: 0.7295 (m-80) REVERT: B 468 ASP cc_start: 0.8365 (t0) cc_final: 0.7905 (m-30) REVERT: B 523 TYR cc_start: 0.8721 (m-80) cc_final: 0.8432 (m-80) REVERT: A 123 LEU cc_start: 0.7923 (OUTLIER) cc_final: 0.7664 (pp) REVERT: A 222 ASP cc_start: 0.8528 (OUTLIER) cc_final: 0.8168 (p0) REVERT: A 234 VAL cc_start: 0.8294 (OUTLIER) cc_final: 0.8046 (p) REVERT: A 263 GLN cc_start: 0.7018 (mp10) cc_final: 0.6701 (mp10) REVERT: A 397 ASN cc_start: 0.8472 (OUTLIER) cc_final: 0.8006 (p0) REVERT: A 481 GLN cc_start: 0.7961 (pt0) cc_final: 0.7657 (pt0) REVERT: A 717 ASN cc_start: 0.7606 (m-40) cc_final: 0.7178 (t0) REVERT: C 102 MET cc_start: 0.8107 (tpp) cc_final: 0.7771 (tpt) REVERT: C 405 MET cc_start: 0.7757 (mmp) cc_final: 0.6651 (mtt) REVERT: C 425 ASP cc_start: 0.7276 (p0) cc_final: 0.7056 (p0) REVERT: C 529 MET cc_start: 0.7179 (ttm) cc_final: 0.6918 (tpt) REVERT: C 661 MET cc_start: 0.8978 (ttp) cc_final: 0.8404 (ttt) REVERT: C 673 ASP cc_start: 0.7964 (t70) cc_final: 0.7749 (t0) REVERT: D 404 LEU cc_start: 0.4252 (OUTLIER) cc_final: 0.4031 (pt) REVERT: D 405 MET cc_start: 0.6434 (ptt) cc_final: 0.5917 (tpt) REVERT: D 420 MET cc_start: 0.8344 (mmm) cc_final: 0.7977 (tpt) REVERT: E 110 LYS cc_start: 0.7732 (ttpt) cc_final: 0.7364 (tmtt) REVERT: E 325 LEU cc_start: 0.7974 (OUTLIER) cc_final: 0.7680 (tt) REVERT: E 420 MET cc_start: 0.7649 (mmm) cc_final: 0.7432 (mmm) REVERT: E 545 MET cc_start: 0.8464 (mtm) cc_final: 0.8190 (mtm) REVERT: F 207 LEU cc_start: 0.7244 (pp) cc_final: 0.6339 (tp) REVERT: F 425 ASP cc_start: 0.8182 (p0) cc_final: 0.6610 (t0) REVERT: F 717 ASN cc_start: 0.7223 (t0) cc_final: 0.6809 (m110) outliers start: 84 outliers final: 66 residues processed: 337 average time/residue: 0.6827 time to fit residues: 389.1322 Evaluate side-chains 336 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 262 time to evaluate : 3.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 77 PHE Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 347 ASN Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 508 ASN Chi-restraints excluded: chain B residue 573 PHE Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 672 ASN Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 157 MET Chi-restraints excluded: chain A residue 179 GLN Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 397 ASN Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 723 ASP Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 347 ASN Chi-restraints excluded: chain C residue 378 TYR Chi-restraints excluded: chain C residue 508 ASN Chi-restraints excluded: chain C residue 514 ASP Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 201 ASP Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 271 GLN Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 404 LEU Chi-restraints excluded: chain D residue 413 ASP Chi-restraints excluded: chain D residue 480 ASN Chi-restraints excluded: chain D residue 573 PHE Chi-restraints excluded: chain D residue 680 LEU Chi-restraints excluded: chain D residue 681 LEU Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 77 PHE Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 168 ASN Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 347 ASN Chi-restraints excluded: chain E residue 396 LEU Chi-restraints excluded: chain E residue 398 LEU Chi-restraints excluded: chain E residue 413 ASP Chi-restraints excluded: chain E residue 430 ASP Chi-restraints excluded: chain E residue 479 THR Chi-restraints excluded: chain E residue 516 SER Chi-restraints excluded: chain E residue 532 LEU Chi-restraints excluded: chain E residue 573 PHE Chi-restraints excluded: chain E residue 680 LEU Chi-restraints excluded: chain E residue 710 VAL Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 114 ASN Chi-restraints excluded: chain F residue 202 LEU Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 349 VAL Chi-restraints excluded: chain F residue 573 PHE Chi-restraints excluded: chain F residue 593 THR Chi-restraints excluded: chain F residue 716 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 335 optimal weight: 2.9990 chunk 353 optimal weight: 1.9990 chunk 322 optimal weight: 0.6980 chunk 344 optimal weight: 6.9990 chunk 207 optimal weight: 2.9990 chunk 149 optimal weight: 0.5980 chunk 270 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 310 optimal weight: 0.6980 chunk 325 optimal weight: 0.5980 chunk 342 optimal weight: 7.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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** ** C 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.4659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 30635 Z= 0.160 Angle : 0.509 7.890 41696 Z= 0.253 Chirality : 0.045 0.357 4680 Planarity : 0.004 0.089 5533 Dihedral : 4.505 52.535 4157 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.31 % Allowed : 16.47 % Favored : 81.22 % 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: -1.20 (0.14), residues: 3842 helix: 2.86 (0.24), residues: 508 sheet: -0.87 (0.15), residues: 1091 loop : -1.71 (0.13), residues: 2243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 260 HIS 0.006 0.001 HIS F 293 PHE 0.017 0.001 PHE A 289 TYR 0.009 0.001 TYR E 204 ARG 0.001 0.000 ARG E 365 *********************** 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 350 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 273 time to evaluate : 3.759 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: B 77 PHE cc_start: 0.8830 (OUTLIER) cc_final: 0.8046 (t80) REVERT: B 210 LYS cc_start: 0.8905 (tppt) cc_final: 0.8503 (tmtt) REVERT: B 318 PHE cc_start: 0.8218 (OUTLIER) cc_final: 0.7253 (m-80) REVERT: B 468 ASP cc_start: 0.8407 (t0) cc_final: 0.7946 (m-30) REVERT: A 234 VAL cc_start: 0.8288 (OUTLIER) cc_final: 0.8041 (p) REVERT: A 263 GLN cc_start: 0.7013 (mp10) cc_final: 0.6716 (mp10) REVERT: A 397 ASN cc_start: 0.8475 (OUTLIER) cc_final: 0.8014 (p0) REVERT: A 481 GLN cc_start: 0.7938 (pt0) cc_final: 0.7628 (pt0) REVERT: A 555 MET cc_start: 0.9318 (mmm) cc_final: 0.9084 (tpt) REVERT: A 717 ASN cc_start: 0.7589 (m-40) cc_final: 0.7160 (t0) REVERT: C 102 MET cc_start: 0.8102 (tpp) cc_final: 0.7095 (ttt) REVERT: C 405 MET cc_start: 0.7786 (mmp) cc_final: 0.6634 (mtt) REVERT: C 425 ASP cc_start: 0.7166 (p0) cc_final: 0.6965 (p0) REVERT: C 661 MET cc_start: 0.8940 (ttp) cc_final: 0.8398 (ttt) REVERT: C 673 ASP cc_start: 0.7862 (t70) cc_final: 0.7651 (t0) REVERT: D 404 LEU cc_start: 0.4272 (OUTLIER) cc_final: 0.4052 (pt) REVERT: D 405 MET cc_start: 0.6503 (ptt) cc_final: 0.5916 (tpt) REVERT: D 420 MET cc_start: 0.8315 (mmm) cc_final: 0.7937 (tpt) REVERT: D 529 MET cc_start: 0.7601 (tmm) cc_final: 0.7214 (tmm) REVERT: E 110 LYS cc_start: 0.7686 (ttpt) cc_final: 0.7345 (tmtt) REVERT: E 193 ASP cc_start: 0.7790 (p0) cc_final: 0.7416 (p0) REVERT: E 325 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7679 (tt) REVERT: E 420 MET cc_start: 0.7631 (mmm) cc_final: 0.7414 (mmm) REVERT: F 207 LEU cc_start: 0.7231 (pp) cc_final: 0.6323 (tp) REVERT: F 332 ILE cc_start: 0.8437 (tt) cc_final: 0.8206 (pt) REVERT: F 425 ASP cc_start: 0.8138 (p0) cc_final: 0.6581 (t0) REVERT: F 717 ASN cc_start: 0.7123 (t0) cc_final: 0.6756 (m110) outliers start: 77 outliers final: 64 residues processed: 332 average time/residue: 0.6915 time to fit residues: 388.7623 Evaluate side-chains 333 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 263 time to evaluate : 3.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 77 PHE Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 347 ASN Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 508 ASN Chi-restraints excluded: chain B residue 573 PHE Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 672 ASN Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 157 MET Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 397 ASN Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 347 ASN Chi-restraints excluded: chain C residue 378 TYR Chi-restraints excluded: chain C residue 508 ASN Chi-restraints excluded: chain C residue 514 ASP Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 704 MET Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 271 GLN Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 404 LEU Chi-restraints excluded: chain D residue 413 ASP Chi-restraints excluded: chain D residue 480 ASN Chi-restraints excluded: chain D residue 573 PHE Chi-restraints excluded: chain D residue 680 LEU Chi-restraints excluded: chain D residue 681 LEU Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 77 PHE Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 168 ASN Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 347 ASN Chi-restraints excluded: chain E residue 396 LEU Chi-restraints excluded: chain E residue 398 LEU Chi-restraints excluded: chain E residue 413 ASP Chi-restraints excluded: chain E residue 430 ASP Chi-restraints excluded: chain E residue 479 THR Chi-restraints excluded: chain E residue 532 LEU Chi-restraints excluded: chain E residue 573 PHE Chi-restraints excluded: chain E residue 680 LEU Chi-restraints excluded: chain E residue 710 VAL Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 114 ASN Chi-restraints excluded: chain F residue 202 LEU Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 349 VAL Chi-restraints excluded: chain F residue 573 PHE Chi-restraints excluded: chain F residue 593 THR Chi-restraints excluded: chain F residue 716 ILE Chi-restraints excluded: chain F residue 718 SER 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: 0.6980 chunk 172 optimal weight: 0.9990 chunk 252 optimal weight: 2.9990 chunk 381 optimal weight: 0.7980 chunk 351 optimal weight: 0.7980 chunk 303 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 234 optimal weight: 2.9990 chunk 186 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 276 ASN ** C 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7866 moved from start: 0.4754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 30635 Z= 0.208 Angle : 0.520 8.484 41696 Z= 0.259 Chirality : 0.045 0.361 4680 Planarity : 0.004 0.090 5533 Dihedral : 4.513 51.942 4157 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 2.28 % Allowed : 16.41 % Favored : 81.31 % 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: -1.18 (0.14), residues: 3842 helix: 2.87 (0.24), residues: 509 sheet: -0.86 (0.15), residues: 1108 loop : -1.69 (0.13), residues: 2225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 260 HIS 0.005 0.001 HIS F 293 PHE 0.017 0.001 PHE E 503 TYR 0.010 0.001 TYR E 204 ARG 0.001 0.000 ARG D 544 ********************** 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 343 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 267 time to evaluate : 3.752 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: B 77 PHE cc_start: 0.8838 (OUTLIER) cc_final: 0.8064 (t80) REVERT: B 318 PHE cc_start: 0.8256 (OUTLIER) cc_final: 0.7279 (m-80) REVERT: B 468 ASP cc_start: 0.8338 (t0) cc_final: 0.7890 (m-30) REVERT: B 523 TYR cc_start: 0.8812 (m-80) cc_final: 0.8511 (m-80) REVERT: A 234 VAL cc_start: 0.8308 (OUTLIER) cc_final: 0.8067 (p) REVERT: A 263 GLN cc_start: 0.7032 (mp10) cc_final: 0.6751 (mp10) REVERT: A 397 ASN cc_start: 0.8483 (OUTLIER) cc_final: 0.8005 (p0) REVERT: A 481 GLN cc_start: 0.7962 (pt0) cc_final: 0.7640 (pt0) REVERT: A 555 MET cc_start: 0.9184 (mmm) cc_final: 0.8774 (tpt) REVERT: A 661 MET cc_start: 0.6462 (mmt) cc_final: 0.6229 (mmt) REVERT: A 717 ASN cc_start: 0.7656 (m-40) cc_final: 0.7164 (t0) REVERT: C 102 MET cc_start: 0.8136 (tpp) cc_final: 0.7178 (ttt) REVERT: C 405 MET cc_start: 0.7800 (mmp) cc_final: 0.6597 (mtt) REVERT: C 425 ASP cc_start: 0.7192 (p0) cc_final: 0.6982 (p0) REVERT: C 661 MET cc_start: 0.8991 (ttp) cc_final: 0.8444 (ttt) REVERT: C 673 ASP cc_start: 0.7915 (t70) cc_final: 0.7702 (t0) REVERT: D 404 LEU cc_start: 0.4370 (OUTLIER) cc_final: 0.4150 (pt) REVERT: D 405 MET cc_start: 0.6510 (ptt) cc_final: 0.5921 (tpt) REVERT: D 420 MET cc_start: 0.8320 (mmm) cc_final: 0.7999 (tpt) REVERT: D 529 MET cc_start: 0.7600 (tmm) cc_final: 0.7186 (tmm) REVERT: E 110 LYS cc_start: 0.7683 (ttpt) cc_final: 0.7343 (tmtt) REVERT: E 193 ASP cc_start: 0.7820 (p0) cc_final: 0.7433 (p0) REVERT: E 325 LEU cc_start: 0.7963 (OUTLIER) cc_final: 0.7689 (tt) REVERT: E 420 MET cc_start: 0.7665 (mmm) cc_final: 0.7461 (mmm) REVERT: E 545 MET cc_start: 0.8444 (mtm) cc_final: 0.7157 (mtt) REVERT: E 550 GLN cc_start: 0.7718 (mt0) cc_final: 0.7400 (mt0) REVERT: F 207 LEU cc_start: 0.7229 (pp) cc_final: 0.6364 (tp) REVERT: F 332 ILE cc_start: 0.8436 (tt) cc_final: 0.8219 (pt) REVERT: F 717 ASN cc_start: 0.7109 (t0) cc_final: 0.6789 (m110) outliers start: 76 outliers final: 60 residues processed: 325 average time/residue: 0.7078 time to fit residues: 389.4885 Evaluate side-chains 332 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 266 time to evaluate : 3.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 77 PHE Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 347 ASN Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 508 ASN Chi-restraints excluded: chain B residue 573 PHE Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 672 ASN Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 157 MET Chi-restraints excluded: chain A residue 179 GLN Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 397 ASN Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 347 ASN Chi-restraints excluded: chain C residue 378 TYR Chi-restraints excluded: chain C residue 508 ASN Chi-restraints excluded: chain C residue 514 ASP Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain C residue 704 MET Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 271 GLN Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 404 LEU Chi-restraints excluded: chain D residue 413 ASP Chi-restraints excluded: chain D residue 480 ASN Chi-restraints excluded: chain D residue 573 PHE Chi-restraints excluded: chain D residue 680 LEU Chi-restraints excluded: chain D residue 681 LEU Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 77 PHE Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 168 ASN Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 347 ASN Chi-restraints excluded: chain E residue 396 LEU Chi-restraints excluded: chain E residue 398 LEU Chi-restraints excluded: chain E residue 430 ASP Chi-restraints excluded: chain E residue 479 THR Chi-restraints excluded: chain E residue 532 LEU Chi-restraints excluded: chain E residue 573 PHE Chi-restraints excluded: chain E residue 680 LEU Chi-restraints excluded: chain E residue 710 VAL Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 114 ASN Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 349 VAL Chi-restraints excluded: chain F residue 573 PHE Chi-restraints excluded: chain F residue 593 THR Chi-restraints excluded: chain F residue 716 ILE Chi-restraints excluded: chain F residue 718 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 241 optimal weight: 1.9990 chunk 323 optimal weight: 6.9990 chunk 93 optimal weight: 2.9990 chunk 280 optimal weight: 4.9990 chunk 44 optimal weight: 0.5980 chunk 84 optimal weight: 0.9980 chunk 304 optimal weight: 3.9990 chunk 127 optimal weight: 0.9990 chunk 312 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 56 optimal weight: 7.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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** ** C 415 ASN ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.103113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.079154 restraints weight = 178931.865| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 2.81 r_work: 0.2999 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.4832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 30635 Z= 0.211 Angle : 0.522 8.908 41696 Z= 0.260 Chirality : 0.045 0.360 4680 Planarity : 0.004 0.089 5533 Dihedral : 4.522 52.591 4157 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 2.28 % Allowed : 16.41 % Favored : 81.31 % 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: -1.15 (0.14), residues: 3842 helix: 2.87 (0.24), residues: 508 sheet: -0.82 (0.15), residues: 1094 loop : -1.67 (0.13), residues: 2240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 260 HIS 0.008 0.001 HIS F 293 PHE 0.017 0.001 PHE A 289 TYR 0.010 0.001 TYR E 204 ARG 0.002 0.000 ARG C 712 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10569.35 seconds wall clock time: 183 minutes 4.73 seconds (10984.73 seconds total)