Starting phenix.real_space_refine on Thu Apr 11 12:58:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uiw_26555/04_2024/7uiw_26555_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uiw_26555/04_2024/7uiw_26555.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uiw_26555/04_2024/7uiw_26555.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uiw_26555/04_2024/7uiw_26555.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uiw_26555/04_2024/7uiw_26555_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uiw_26555/04_2024/7uiw_26555_trim_updated.pdb" } resolution = 3.33 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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: 7 Type Number sf(0) Gaussians P 29 5.49 5 Mg 7 5.21 5 S 171 5.16 5 C 23703 2.51 5 N 6677 2.21 5 O 7189 1.98 5 H 38115 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 186": "OD1" <-> "OD2" Residue "A GLU 194": "OE1" <-> "OE2" Residue "A GLU 225": "OE1" <-> "OE2" Residue "A TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 249": "OD1" <-> "OD2" Residue "A PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 275": "OE1" <-> "OE2" Residue "A GLU 286": "OE1" <-> "OE2" Residue "A ASP 302": "OD1" <-> "OD2" Residue "A GLU 326": "OE1" <-> "OE2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 383": "OE1" <-> "OE2" Residue "A ASP 400": "OD1" <-> "OD2" Residue "A GLU 404": "OE1" <-> "OE2" Residue "A PHE 461": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 484": "OE1" <-> "OE2" Residue "A PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 503": "OE1" <-> "OE2" Residue "A PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 540": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 627": "OD1" <-> "OD2" Residue "A GLU 631": "OE1" <-> "OE2" Residue "A PHE 636": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 650": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 665": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 238": "OE1" <-> "OE2" Residue "B TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 262": "OD1" <-> "OD2" Residue "B ASP 302": "OD1" <-> "OD2" Residue "B TYR 373": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 388": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 396": "OD1" <-> "OD2" Residue "B ASP 403": "OD1" <-> "OD2" Residue "B GLU 404": "OE1" <-> "OE2" Residue "B PHE 461": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 524": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 588": "OD1" <-> "OD2" Residue "B GLU 613": "OE1" <-> "OE2" Residue "B PHE 636": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 640": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 650": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 665": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 277": "OD1" <-> "OD2" Residue "C PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 373": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 400": "OD1" <-> "OD2" Residue "C PHE 461": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 472": "OE1" <-> "OE2" Residue "C GLU 503": "OE1" <-> "OE2" Residue "C TYR 524": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 540": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 627": "OD1" <-> "OD2" Residue "C GLU 630": "OE1" <-> "OE2" Residue "C PHE 636": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 640": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 665": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 746": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 262": "OD1" <-> "OD2" Residue "D PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 388": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 391": "OD1" <-> "OD2" Residue "D ASP 403": "OD1" <-> "OD2" Residue "D GLU 427": "OE1" <-> "OE2" Residue "D ASP 447": "OD1" <-> "OD2" Residue "D PHE 461": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 636": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 640": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 668": "OE1" <-> "OE2" Residue "D GLU 692": "OE1" <-> "OE2" Residue "D GLU 741": "OE1" <-> "OE2" Residue "E PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 215": "OE1" <-> "OE2" Residue "E ASP 242": "OD1" <-> "OD2" Residue "E TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 260": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 264": "OE1" <-> "OE2" Residue "E PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 391": "OD1" <-> "OD2" Residue "E GLU 427": "OE1" <-> "OE2" Residue "E ASP 445": "OD1" <-> "OD2" Residue "E ASP 454": "OD1" <-> "OD2" Residue "E GLU 503": "OE1" <-> "OE2" Residue "E PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 524": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 565": "OE1" <-> "OE2" Residue "E PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 611": "OE1" <-> "OE2" Residue "E ASP 627": "OD1" <-> "OD2" Residue "E GLU 639": "OE1" <-> "OE2" Residue "E PHE 650": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 651": "OD1" <-> "OD2" Residue "E GLU 685": "OE1" <-> "OE2" Residue "E TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 738": "OE1" <-> "OE2" Residue "E TYR 744": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 746": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 194": "OE1" <-> "OE2" Residue "F ARG 197": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ASP 262": "OD1" <-> "OD2" Residue "F PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 286": "OE1" <-> "OE2" Residue "F ASP 302": "OD1" <-> "OD2" Residue "F GLU 326": "OE1" <-> "OE2" Residue "F PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 353": "OE1" <-> "OE2" Residue "F GLU 383": "OE1" <-> "OE2" Residue "F TYR 388": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 400": "OD1" <-> "OD2" Residue "F ASP 454": "OD1" <-> "OD2" Residue "F GLU 468": "OE1" <-> "OE2" Residue "F GLU 472": "OE1" <-> "OE2" Residue "F PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 524": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 565": "OE1" <-> "OE2" Residue "F ASP 582": "OD1" <-> "OD2" Residue "F ASP 588": "OD1" <-> "OD2" Residue "F GLU 611": "OE1" <-> "OE2" Residue "F PHE 650": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 651": "OD1" <-> "OD2" Residue "F PHE 665": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 674": "OD1" <-> "OD2" Residue "F GLU 692": "OE1" <-> "OE2" Residue "F TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 696": "OD1" <-> "OD2" Residue "F ASP 736": "OD1" <-> "OD2" Residue "H ARG 12": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H GLU 14": "OE1" <-> "OE2" Residue "H ASP 18": "OD1" <-> "OD2" Residue "H ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 53": "OE1" <-> "OE2" Residue "H ASP 58": "OD1" <-> "OD2" Residue "H ASP 86": "OD1" <-> "OD2" Residue "H PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ARG 118": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H GLU 141": "OE1" <-> "OE2" Residue "H ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H GLU 169": "OE1" <-> "OE2" Residue "H ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ASP 171": "OD1" <-> "OD2" Residue "H PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 181": "OE1" <-> "OE2" Residue "H TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I ARG 12": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I GLU 14": "OE1" <-> "OE2" Residue "I ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I GLU 53": "OE1" <-> "OE2" Residue "I ASP 58": "OD1" <-> "OD2" Residue "I PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I GLU 136": "OE1" <-> "OE2" Residue "I GLU 141": "OE1" <-> "OE2" Residue "I ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I GLU 165": "OE1" <-> "OE2" Residue "I ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I GLU 181": "OE1" <-> "OE2" Residue "J ARG 12": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J ASP 58": "OD1" <-> "OD2" Residue "J TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J GLU 141": "OE1" <-> "OE2" Residue "J ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J GLU 162": "OE1" <-> "OE2" Residue "J ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J ASP 186": "OD1" <-> "OD2" Residue "K ARG 12": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K GLU 151": "OE1" <-> "OE2" Residue "K GLU 165": "OE1" <-> "OE2" Residue "K ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K GLU 169": "OE1" <-> "OE2" Residue "K ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L GLU 8": "OE1" <-> "OE2" Residue "L ARG 12": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L GLU 26": "OE1" <-> "OE2" Residue "L ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L GLU 56": "OE1" <-> "OE2" Residue "L TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ASP 78": "OD1" <-> "OD2" Residue "L ASP 86": "OD1" <-> "OD2" Residue "L ARG 118": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L GLU 141": "OE1" <-> "OE2" Residue "L ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ASP 167": "OD1" <-> "OD2" Residue "L ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M ARG 12": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M GLU 36": "OE1" <-> "OE2" Residue "M ASP 37": "OD1" <-> "OD2" Residue "M GLU 51": "OE1" <-> "OE2" Residue "M GLU 53": "OE1" <-> "OE2" Residue "M GLU 56": "OE1" <-> "OE2" Residue "M ASP 58": "OD1" <-> "OD2" Residue "M TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M GLU 136": "OE1" <-> "OE2" Residue "M ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M GLU 169": "OE1" <-> "OE2" Residue "M ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ASP 171": "OD1" <-> "OD2" Residue "M PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M GLU 181": "OE1" <-> "OE2" Residue "N ARG 12": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N GLU 26": "OE1" <-> "OE2" Residue "N ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N ASP 37": "OD1" <-> "OD2" Residue "N GLU 51": "OE1" <-> "OE2" Residue "N GLU 56": "OE1" <-> "OE2" Residue "N TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N ASP 78": "OD1" <-> "OD2" Residue "N ASP 134": "OD1" <-> "OD2" Residue "N ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N GLU 178": "OE1" <-> "OE2" Residue "N GLU 181": "OE1" <-> "OE2" Residue "N TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 75891 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 9019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 9019 Classifications: {'peptide': 570} Link IDs: {'PTRANS': 17, 'TRANS': 552} Chain breaks: 2 Chain: "B" Number of atoms: 9141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 580, 9141 Classifications: {'peptide': 580} Link IDs: {'PTRANS': 18, 'TRANS': 561} Chain: "C" Number of atoms: 9154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 581, 9154 Classifications: {'peptide': 581} Link IDs: {'PTRANS': 18, 'TRANS': 562} Chain: "D" Number of atoms: 9144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 580, 9144 Classifications: {'peptide': 580} Link IDs: {'PTRANS': 18, 'TRANS': 561} Chain: "E" Number of atoms: 9143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 580, 9143 Classifications: {'peptide': 580} Link IDs: {'PTRANS': 18, 'TRANS': 561} Chain: "F" Number of atoms: 8621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 8621 Classifications: {'peptide': 541} Link IDs: {'PTRANS': 15, 'TRANS': 525} Chain breaks: 4 Chain: "H" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 3001 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 7, 'TRANS': 183} Chain: "I" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 3001 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 7, 'TRANS': 183} Chain: "J" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 3001 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 7, 'TRANS': 183} Chain: "K" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 3001 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 7, 'TRANS': 183} Chain: "L" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 3001 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 7, 'TRANS': 183} Chain: "M" Number of atoms: 2977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 2977 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 7, 'TRANS': 182} Chain: "N" Number of atoms: 2978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 2978 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 7, 'TRANS': 182} Chain: "S" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 396 Classifications: {'peptide': 25} Link IDs: {'PTRANS': 2, 'TRANS': 22} Chain: "A" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'AGS': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 25.31, per 1000 atoms: 0.33 Number of scatterers: 75891 At special positions: 0 Unit cell: (150.51, 151.38, 169.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 171 16.00 P 29 15.00 Mg 7 11.99 O 7189 8.00 N 6677 7.00 C 23703 6.00 H 38115 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 51.53 Conformation dependent library (CDL) restraints added in 6.1 seconds 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8866 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 219 helices and 38 sheets defined 48.3% alpha, 8.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 11.37 Creating SS restraints... Processing helix chain 'A' and resid 176 through 182 Processing helix chain 'A' and resid 192 through 203 Processing helix chain 'A' and resid 220 through 233 removed outlier: 3.877A pdb=" N ALA A 228 " --> pdb=" O ALA A 224 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN A 233 " --> pdb=" O TRP A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 242 removed outlier: 3.500A pdb=" N ASP A 242 " --> pdb=" O VAL A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 255 Processing helix chain 'A' and resid 262 through 276 removed outlier: 3.510A pdb=" N ALA A 269 " --> pdb=" O LYS A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 290 No H-bonds generated for 'chain 'A' and resid 287 through 290' Processing helix chain 'A' and resid 299 through 312 removed outlier: 3.584A pdb=" N ALA A 303 " --> pdb=" O GLY A 299 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU A 306 " --> pdb=" O ASP A 302 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Proline residue: A 309 - end of helix Processing helix chain 'A' and resid 324 through 334 removed outlier: 3.619A pdb=" N ASN A 329 " --> pdb=" O GLN A 325 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LYS A 333 " --> pdb=" O ASN A 329 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ASP A 334 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 340 removed outlier: 3.522A pdb=" N ARG A 340 " --> pdb=" O ALA A 336 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 336 through 340' Processing helix chain 'A' and resid 351 through 369 removed outlier: 4.000A pdb=" N GLY A 360 " --> pdb=" O GLN A 356 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LEU A 361 " --> pdb=" O ILE A 357 " (cutoff:3.500A) Proline residue: A 363 - end of helix Processing helix chain 'A' and resid 375 through 388 removed outlier: 3.858A pdb=" N VAL A 382 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLU A 383 " --> pdb=" O ARG A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 411 removed outlier: 3.536A pdb=" N ILE A 399 " --> pdb=" O PRO A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 434 removed outlier: 3.635A pdb=" N ARG A 432 " --> pdb=" O SER A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 450 Processing helix chain 'A' and resid 452 through 459 removed outlier: 3.729A pdb=" N LEU A 459 " --> pdb=" O ARG A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 479 Processing helix chain 'A' and resid 501 through 512 removed outlier: 3.633A pdb=" N THR A 505 " --> pdb=" O LYS A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 534 removed outlier: 3.677A pdb=" N ILE A 534 " --> pdb=" O SER A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 555 removed outlier: 3.600A pdb=" N ALA A 552 " --> pdb=" O LEU A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 568 No H-bonds generated for 'chain 'A' and resid 566 through 568' Processing helix chain 'A' and resid 572 through 583 removed outlier: 3.663A pdb=" N ILE A 576 " --> pdb=" O ASP A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 635 removed outlier: 3.581A pdb=" N LYS A 634 " --> pdb=" O GLU A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 643 Processing helix chain 'A' and resid 655 through 675 removed outlier: 3.558A pdb=" N GLN A 660 " --> pdb=" O ASP A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 684 through 694 Processing helix chain 'A' and resid 702 through 711 Processing helix chain 'A' and resid 713 through 722 Processing helix chain 'A' and resid 724 through 726 No H-bonds generated for 'chain 'A' and resid 724 through 726' Processing helix chain 'B' and resid 176 through 181 Processing helix chain 'B' and resid 192 through 203 Processing helix chain 'B' and resid 220 through 233 removed outlier: 3.729A pdb=" N ALA B 228 " --> pdb=" O ALA B 224 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TRP B 229 " --> pdb=" O GLU B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 256 removed outlier: 4.346A pdb=" N GLY B 256 " --> pdb=" O SER B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 277 Processing helix chain 'B' and resid 287 through 292 Processing helix chain 'B' and resid 303 through 313 Proline residue: B 309 - end of helix Processing helix chain 'B' and resid 324 through 329 Processing helix chain 'B' and resid 335 through 340 Processing helix chain 'B' and resid 351 through 369 removed outlier: 3.666A pdb=" N GLN B 356 " --> pdb=" O GLU B 352 " (cutoff:3.500A) Proline residue: B 363 - end of helix Processing helix chain 'B' and resid 375 through 388 removed outlier: 3.855A pdb=" N ARG B 379 " --> pdb=" O ALA B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 410 Processing helix chain 'B' and resid 426 through 434 Processing helix chain 'B' and resid 443 through 450 removed outlier: 3.600A pdb=" N THR B 448 " --> pdb=" O SER B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 459 Processing helix chain 'B' and resid 464 through 479 Processing helix chain 'B' and resid 502 through 512 Processing helix chain 'B' and resid 521 through 524 Processing helix chain 'B' and resid 527 through 534 removed outlier: 3.605A pdb=" N SER B 531 " --> pdb=" O HIS B 528 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE B 534 " --> pdb=" O SER B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 555 Processing helix chain 'B' and resid 566 through 568 No H-bonds generated for 'chain 'B' and resid 566 through 568' Processing helix chain 'B' and resid 571 through 582 removed outlier: 4.023A pdb=" N GLN B 579 " --> pdb=" O ASN B 575 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL B 580 " --> pdb=" O ILE B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 613 Processing helix chain 'B' and resid 625 through 635 Processing helix chain 'B' and resid 638 through 643 Processing helix chain 'B' and resid 655 through 675 removed outlier: 3.514A pdb=" N GLN B 660 " --> pdb=" O ASP B 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 684 through 693 Processing helix chain 'B' and resid 697 through 699 No H-bonds generated for 'chain 'B' and resid 697 through 699' Processing helix chain 'B' and resid 702 through 711 removed outlier: 3.671A pdb=" N VAL B 707 " --> pdb=" O MET B 704 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP B 710 " --> pdb=" O VAL B 707 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ASN B 711 " --> pdb=" O ILE B 708 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 721 Processing helix chain 'B' and resid 724 through 726 No H-bonds generated for 'chain 'B' and resid 724 through 726' Processing helix chain 'C' and resid 176 through 182 Processing helix chain 'C' and resid 192 through 202 Processing helix chain 'C' and resid 220 through 233 removed outlier: 3.823A pdb=" N ALA C 228 " --> pdb=" O ALA C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 240 No H-bonds generated for 'chain 'C' and resid 238 through 240' Processing helix chain 'C' and resid 250 through 254 Processing helix chain 'C' and resid 262 through 277 removed outlier: 3.540A pdb=" N LEU C 274 " --> pdb=" O LEU C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 291 Processing helix chain 'C' and resid 303 through 313 Proline residue: C 309 - end of helix Processing helix chain 'C' and resid 324 through 329 Processing helix chain 'C' and resid 335 through 340 removed outlier: 3.538A pdb=" N ARG C 340 " --> pdb=" O ALA C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 369 Proline residue: C 363 - end of helix Processing helix chain 'C' and resid 375 through 388 Processing helix chain 'C' and resid 394 through 411 removed outlier: 3.586A pdb=" N VAL C 401 " --> pdb=" O LYS C 397 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA C 409 " --> pdb=" O ALA C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 423 through 434 Processing helix chain 'C' and resid 443 through 450 Processing helix chain 'C' and resid 452 through 459 Processing helix chain 'C' and resid 464 through 479 Processing helix chain 'C' and resid 503 through 512 removed outlier: 3.699A pdb=" N LYS C 510 " --> pdb=" O VAL C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 527 through 534 removed outlier: 3.705A pdb=" N SER C 531 " --> pdb=" O HIS C 528 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE C 534 " --> pdb=" O SER C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 555 Processing helix chain 'C' and resid 566 through 568 No H-bonds generated for 'chain 'C' and resid 566 through 568' Processing helix chain 'C' and resid 571 through 583 removed outlier: 3.832A pdb=" N ASN C 575 " --> pdb=" O PRO C 571 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ILE C 576 " --> pdb=" O ASP C 572 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU C 577 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU C 578 " --> pdb=" O PHE C 574 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLN C 579 " --> pdb=" O ASN C 575 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL C 580 " --> pdb=" O ILE C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 609 through 613 Processing helix chain 'C' and resid 625 through 635 removed outlier: 3.671A pdb=" N MET C 629 " --> pdb=" O SER C 625 " (cutoff:3.500A) Processing helix chain 'C' and resid 638 through 643 Processing helix chain 'C' and resid 655 through 676 removed outlier: 3.783A pdb=" N GLN C 660 " --> pdb=" O ASP C 656 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS C 676 " --> pdb=" O GLN C 672 " (cutoff:3.500A) Processing helix chain 'C' and resid 684 through 694 Processing helix chain 'C' and resid 702 through 711 removed outlier: 3.709A pdb=" N ARG C 706 " --> pdb=" O ARG C 702 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 722 Processing helix chain 'C' and resid 724 through 726 No H-bonds generated for 'chain 'C' and resid 724 through 726' Processing helix chain 'D' and resid 176 through 181 removed outlier: 3.519A pdb=" N ARG D 181 " --> pdb=" O ASN D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 202 Processing helix chain 'D' and resid 220 through 233 removed outlier: 3.760A pdb=" N ALA D 228 " --> pdb=" O ALA D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 253 No H-bonds generated for 'chain 'D' and resid 250 through 253' Processing helix chain 'D' and resid 262 through 277 Processing helix chain 'D' and resid 287 through 292 Processing helix chain 'D' and resid 303 through 313 Proline residue: D 309 - end of helix Processing helix chain 'D' and resid 324 through 329 Processing helix chain 'D' and resid 335 through 340 removed outlier: 3.542A pdb=" N ARG D 340 " --> pdb=" O ALA D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 369 removed outlier: 3.690A pdb=" N GLN D 356 " --> pdb=" O GLU D 352 " (cutoff:3.500A) Proline residue: D 363 - end of helix Processing helix chain 'D' and resid 375 through 388 Processing helix chain 'D' and resid 394 through 411 Processing helix chain 'D' and resid 423 through 434 Processing helix chain 'D' and resid 443 through 459 removed outlier: 4.555A pdb=" N GLY D 453 " --> pdb=" O LEU D 449 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N ASP D 454 " --> pdb=" O LYS D 450 " (cutoff:3.500A) Processing helix chain 'D' and resid 464 through 479 Processing helix chain 'D' and resid 503 through 512 Processing helix chain 'D' and resid 527 through 534 removed outlier: 3.985A pdb=" N ILE D 534 " --> pdb=" O SER D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 555 Processing helix chain 'D' and resid 566 through 568 No H-bonds generated for 'chain 'D' and resid 566 through 568' Processing helix chain 'D' and resid 571 through 582 removed outlier: 3.778A pdb=" N GLN D 579 " --> pdb=" O ILE D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 609 through 613 Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 642 Processing helix chain 'D' and resid 655 through 676 removed outlier: 3.574A pdb=" N GLN D 660 " --> pdb=" O ASP D 656 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS D 676 " --> pdb=" O GLN D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 684 through 694 Processing helix chain 'D' and resid 702 through 711 Processing helix chain 'D' and resid 713 through 721 removed outlier: 3.736A pdb=" N ASN D 718 " --> pdb=" O LYS D 714 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU D 719 " --> pdb=" O PRO D 715 " (cutoff:3.500A) Processing helix chain 'D' and resid 724 through 726 No H-bonds generated for 'chain 'D' and resid 724 through 726' Processing helix chain 'E' and resid 176 through 182 Processing helix chain 'E' and resid 192 through 202 Processing helix chain 'E' and resid 220 through 233 removed outlier: 3.839A pdb=" N ALA E 224 " --> pdb=" O LYS E 220 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA E 228 " --> pdb=" O ALA E 224 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N TRP E 229 " --> pdb=" O GLU E 225 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 254 Processing helix chain 'E' and resid 262 through 276 Processing helix chain 'E' and resid 288 through 293 removed outlier: 4.104A pdb=" N GLY E 292 " --> pdb=" O HIS E 288 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA E 293 " --> pdb=" O THR E 289 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 288 through 293' Processing helix chain 'E' and resid 303 through 313 Proline residue: E 309 - end of helix Processing helix chain 'E' and resid 324 through 329 Processing helix chain 'E' and resid 335 through 340 removed outlier: 3.813A pdb=" N ARG E 340 " --> pdb=" O ALA E 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 369 removed outlier: 3.846A pdb=" N VAL E 355 " --> pdb=" O ILE E 351 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN E 356 " --> pdb=" O GLU E 352 " (cutoff:3.500A) Proline residue: E 363 - end of helix Processing helix chain 'E' and resid 375 through 388 Processing helix chain 'E' and resid 394 through 411 Processing helix chain 'E' and resid 423 through 434 Processing helix chain 'E' and resid 447 through 459 removed outlier: 4.338A pdb=" N GLY E 453 " --> pdb=" O LEU E 449 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ASP E 454 " --> pdb=" O LYS E 450 " (cutoff:3.500A) Processing helix chain 'E' and resid 464 through 478 Processing helix chain 'E' and resid 503 through 512 Processing helix chain 'E' and resid 527 through 534 removed outlier: 4.007A pdb=" N VAL E 530 " --> pdb=" O ARG E 527 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ILE E 534 " --> pdb=" O SER E 531 " (cutoff:3.500A) Processing helix chain 'E' and resid 548 through 555 removed outlier: 3.538A pdb=" N ALA E 552 " --> pdb=" O LEU E 548 " (cutoff:3.500A) Processing helix chain 'E' and resid 566 through 568 No H-bonds generated for 'chain 'E' and resid 566 through 568' Processing helix chain 'E' and resid 571 through 582 removed outlier: 3.994A pdb=" N GLN E 579 " --> pdb=" O ASN E 575 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL E 580 " --> pdb=" O ILE E 576 " (cutoff:3.500A) Processing helix chain 'E' and resid 607 through 613 removed outlier: 4.071A pdb=" N GLU E 611 " --> pdb=" O ALA E 607 " (cutoff:3.500A) Processing helix chain 'E' and resid 627 through 635 Processing helix chain 'E' and resid 638 through 643 Processing helix chain 'E' and resid 655 through 676 removed outlier: 3.734A pdb=" N HIS E 659 " --> pdb=" O THR E 655 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS E 676 " --> pdb=" O GLN E 672 " (cutoff:3.500A) Processing helix chain 'E' and resid 684 through 694 removed outlier: 3.733A pdb=" N ASN E 688 " --> pdb=" O GLN E 684 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS E 693 " --> pdb=" O TRP E 689 " (cutoff:3.500A) Processing helix chain 'E' and resid 702 through 711 removed outlier: 3.823A pdb=" N ALA E 705 " --> pdb=" O ARG E 702 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLN E 709 " --> pdb=" O ARG E 706 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ASN E 711 " --> pdb=" O ILE E 708 " (cutoff:3.500A) Processing helix chain 'E' and resid 713 through 721 Processing helix chain 'F' and resid 176 through 179 No H-bonds generated for 'chain 'F' and resid 176 through 179' Processing helix chain 'F' and resid 196 through 202 removed outlier: 3.790A pdb=" N LEU F 202 " --> pdb=" O ALA F 198 " (cutoff:3.500A) Processing helix chain 'F' and resid 218 through 233 removed outlier: 4.073A pdb=" N ILE F 223 " --> pdb=" O GLY F 219 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ALA F 224 " --> pdb=" O LYS F 220 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N TRP F 229 " --> pdb=" O GLU F 225 " (cutoff:3.500A) Processing helix chain 'F' and resid 238 through 241 No H-bonds generated for 'chain 'F' and resid 238 through 241' Processing helix chain 'F' and resid 250 through 253 No H-bonds generated for 'chain 'F' and resid 250 through 253' Processing helix chain 'F' and resid 262 through 274 removed outlier: 4.301A pdb=" N LEU F 271 " --> pdb=" O PHE F 267 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LYS F 272 " --> pdb=" O LYS F 268 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N GLN F 273 " --> pdb=" O ALA F 269 " (cutoff:3.500A) Processing helix chain 'F' and resid 287 through 289 No H-bonds generated for 'chain 'F' and resid 287 through 289' Processing helix chain 'F' and resid 305 through 313 Proline residue: F 309 - end of helix removed outlier: 3.538A pdb=" N SER F 312 " --> pdb=" O LYS F 308 " (cutoff:3.500A) Processing helix chain 'F' and resid 325 through 331 removed outlier: 3.530A pdb=" N ILE F 330 " --> pdb=" O GLU F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 353 through 369 removed outlier: 3.593A pdb=" N ILE F 358 " --> pdb=" O VAL F 355 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN F 359 " --> pdb=" O GLN F 356 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLY F 360 " --> pdb=" O ILE F 357 " (cutoff:3.500A) Proline residue: F 363 - end of helix removed outlier: 3.774A pdb=" N HIS F 369 " --> pdb=" O GLU F 366 " (cutoff:3.500A) Processing helix chain 'F' and resid 376 through 381 Processing helix chain 'F' and resid 394 through 412 removed outlier: 3.648A pdb=" N ASP F 400 " --> pdb=" O ASP F 396 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ASP F 403 " --> pdb=" O ILE F 399 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLU F 404 " --> pdb=" O ASP F 400 " (cutoff:3.500A) Processing helix chain 'F' and resid 423 through 434 removed outlier: 3.593A pdb=" N SER F 428 " --> pdb=" O ALA F 424 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL F 429 " --> pdb=" O ASP F 425 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG F 432 " --> pdb=" O SER F 428 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE F 433 " --> pdb=" O VAL F 429 " (cutoff:3.500A) Processing helix chain 'F' and resid 438 through 441 No H-bonds generated for 'chain 'F' and resid 438 through 441' Processing helix chain 'F' and resid 445 through 459 removed outlier: 4.199A pdb=" N GLY F 453 " --> pdb=" O LEU F 449 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N ASP F 454 " --> pdb=" O LYS F 450 " (cutoff:3.500A) Processing helix chain 'F' and resid 464 through 479 Processing helix chain 'F' and resid 501 through 512 removed outlier: 3.909A pdb=" N THR F 505 " --> pdb=" O LYS F 501 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N VAL F 506 " --> pdb=" O THR F 502 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU F 512 " --> pdb=" O LEU F 508 " (cutoff:3.500A) Processing helix chain 'F' and resid 527 through 530 No H-bonds generated for 'chain 'F' and resid 527 through 530' Processing helix chain 'F' and resid 573 through 576 No H-bonds generated for 'chain 'F' and resid 573 through 576' Processing helix chain 'F' and resid 578 through 583 Processing helix chain 'F' and resid 628 through 635 removed outlier: 3.882A pdb=" N ILE F 632 " --> pdb=" O ALA F 628 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS F 633 " --> pdb=" O MET F 629 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 643 Processing helix chain 'F' and resid 655 through 676 removed outlier: 3.591A pdb=" N HIS F 659 " --> pdb=" O THR F 655 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN F 660 " --> pdb=" O ASP F 656 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE F 665 " --> pdb=" O VAL F 661 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS F 676 " --> pdb=" O GLN F 672 " (cutoff:3.500A) Processing helix chain 'F' and resid 684 through 694 removed outlier: 3.692A pdb=" N TRP F 689 " --> pdb=" O GLU F 685 " (cutoff:3.500A) Processing helix chain 'F' and resid 702 through 704 No H-bonds generated for 'chain 'F' and resid 702 through 704' Processing helix chain 'F' and resid 713 through 721 removed outlier: 3.551A pdb=" N ASN F 718 " --> pdb=" O LYS F 714 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU F 719 " --> pdb=" O PRO F 715 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU F 720 " --> pdb=" O LEU F 716 " (cutoff:3.500A) Processing helix chain 'H' and resid 19 through 26 removed outlier: 3.809A pdb=" N GLU H 26 " --> pdb=" O ARG H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 53 removed outlier: 3.541A pdb=" N ALA H 52 " --> pdb=" O LEU H 48 " (cutoff:3.500A) Processing helix chain 'H' and resid 70 through 82 removed outlier: 3.774A pdb=" N SER H 75 " --> pdb=" O THR H 71 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE H 76 " --> pdb=" O ALA H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 104 Processing helix chain 'H' and resid 132 through 157 removed outlier: 3.615A pdb=" N ILE H 142 " --> pdb=" O HIS H 138 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU H 143 " --> pdb=" O ALA H 139 " (cutoff:3.500A) Processing helix chain 'H' and resid 161 through 169 Processing helix chain 'H' and resid 176 through 182 removed outlier: 3.594A pdb=" N VAL H 180 " --> pdb=" O ALA H 176 " (cutoff:3.500A) Processing helix chain 'I' and resid 19 through 26 removed outlier: 3.883A pdb=" N GLU I 26 " --> pdb=" O ARG I 22 " (cutoff:3.500A) Processing helix chain 'I' and resid 37 through 53 Processing helix chain 'I' and resid 70 through 82 removed outlier: 3.846A pdb=" N SER I 75 " --> pdb=" O THR I 71 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE I 76 " --> pdb=" O ALA I 72 " (cutoff:3.500A) Processing helix chain 'I' and resid 97 through 103 Processing helix chain 'I' and resid 132 through 157 Processing helix chain 'I' and resid 161 through 168 Processing helix chain 'I' and resid 176 through 182 Processing helix chain 'J' and resid 19 through 26 removed outlier: 3.716A pdb=" N GLU J 26 " --> pdb=" O ARG J 22 " (cutoff:3.500A) Processing helix chain 'J' and resid 37 through 53 removed outlier: 3.751A pdb=" N ASN J 41 " --> pdb=" O ASP J 37 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU J 42 " --> pdb=" O HIS J 38 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE J 43 " --> pdb=" O MET J 39 " (cutoff:3.500A) Processing helix chain 'J' and resid 70 through 82 removed outlier: 3.928A pdb=" N SER J 75 " --> pdb=" O THR J 71 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILE J 76 " --> pdb=" O ALA J 72 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR J 77 " --> pdb=" O GLY J 73 " (cutoff:3.500A) Processing helix chain 'J' and resid 132 through 157 removed outlier: 3.537A pdb=" N ILE J 142 " --> pdb=" O HIS J 138 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU J 155 " --> pdb=" O GLU J 151 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N HIS J 156 " --> pdb=" O LEU J 152 " (cutoff:3.500A) Processing helix chain 'J' and resid 161 through 169 Processing helix chain 'J' and resid 176 through 182 removed outlier: 3.680A pdb=" N VAL J 180 " --> pdb=" O ALA J 176 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU J 181 " --> pdb=" O PRO J 177 " (cutoff:3.500A) Processing helix chain 'K' and resid 19 through 25 Processing helix chain 'K' and resid 37 through 53 Processing helix chain 'K' and resid 70 through 82 removed outlier: 3.508A pdb=" N MET K 74 " --> pdb=" O ILE K 70 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N SER K 75 " --> pdb=" O THR K 71 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ILE K 76 " --> pdb=" O ALA K 72 " (cutoff:3.500A) Processing helix chain 'K' and resid 100 through 104 Processing helix chain 'K' and resid 132 through 157 removed outlier: 3.527A pdb=" N HIS K 156 " --> pdb=" O LEU K 152 " (cutoff:3.500A) Processing helix chain 'K' and resid 161 through 168 removed outlier: 3.533A pdb=" N GLU K 165 " --> pdb=" O LEU K 161 " (cutoff:3.500A) Processing helix chain 'K' and resid 176 through 182 removed outlier: 3.536A pdb=" N VAL K 180 " --> pdb=" O ALA K 176 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU K 181 " --> pdb=" O PRO K 177 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 26 removed outlier: 3.858A pdb=" N GLU L 26 " --> pdb=" O ARG L 22 " (cutoff:3.500A) Processing helix chain 'L' and resid 37 through 53 removed outlier: 3.599A pdb=" N PHE L 49 " --> pdb=" O ALA L 45 " (cutoff:3.500A) Processing helix chain 'L' and resid 70 through 82 removed outlier: 4.008A pdb=" N SER L 75 " --> pdb=" O THR L 71 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE L 76 " --> pdb=" O ALA L 72 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLN L 81 " --> pdb=" O TYR L 77 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE L 82 " --> pdb=" O ASP L 78 " (cutoff:3.500A) Processing helix chain 'L' and resid 97 through 105 Processing helix chain 'L' and resid 132 through 157 removed outlier: 3.819A pdb=" N ASN L 150 " --> pdb=" O LYS L 146 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU L 155 " --> pdb=" O GLU L 151 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N HIS L 156 " --> pdb=" O LEU L 152 " (cutoff:3.500A) Processing helix chain 'L' and resid 161 through 168 removed outlier: 3.731A pdb=" N ARG L 166 " --> pdb=" O GLU L 162 " (cutoff:3.500A) Processing helix chain 'L' and resid 176 through 182 removed outlier: 3.817A pdb=" N GLU L 181 " --> pdb=" O PRO L 177 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYR L 182 " --> pdb=" O GLU L 178 " (cutoff:3.500A) Processing helix chain 'M' and resid 19 through 26 removed outlier: 3.841A pdb=" N GLU M 26 " --> pdb=" O ARG M 22 " (cutoff:3.500A) Processing helix chain 'M' and resid 37 through 53 Processing helix chain 'M' and resid 70 through 82 removed outlier: 3.580A pdb=" N ILE M 76 " --> pdb=" O ALA M 72 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR M 79 " --> pdb=" O SER M 75 " (cutoff:3.500A) Processing helix chain 'M' and resid 97 through 104 Processing helix chain 'M' and resid 132 through 157 removed outlier: 3.543A pdb=" N GLU M 151 " --> pdb=" O GLY M 147 " (cutoff:3.500A) Processing helix chain 'M' and resid 161 through 168 Processing helix chain 'M' and resid 176 through 182 Processing helix chain 'N' and resid 19 through 26 removed outlier: 3.760A pdb=" N GLU N 26 " --> pdb=" O ARG N 22 " (cutoff:3.500A) Processing helix chain 'N' and resid 37 through 53 removed outlier: 3.766A pdb=" N ALA N 52 " --> pdb=" O LEU N 48 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU N 53 " --> pdb=" O PHE N 49 " (cutoff:3.500A) Processing helix chain 'N' and resid 70 through 82 removed outlier: 3.509A pdb=" N SER N 75 " --> pdb=" O THR N 71 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ILE N 76 " --> pdb=" O ALA N 72 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR N 77 " --> pdb=" O GLY N 73 " (cutoff:3.500A) Processing helix chain 'N' and resid 97 through 104 Processing helix chain 'N' and resid 132 through 157 removed outlier: 3.656A pdb=" N HIS N 156 " --> pdb=" O LEU N 152 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR N 157 " --> pdb=" O MET N 153 " (cutoff:3.500A) Processing helix chain 'N' and resid 161 through 169 Processing helix chain 'N' and resid 176 through 182 removed outlier: 3.595A pdb=" N VAL N 180 " --> pdb=" O ALA N 176 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU N 181 " --> pdb=" O PRO N 177 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 209 through 212 Processing sheet with id= B, first strand: chain 'A' and resid 601 through 605 removed outlier: 3.916A pdb=" N GLY A 495 " --> pdb=" O THR A 605 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N ASN A 646 " --> pdb=" O LEU A 492 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N ALA A 494 " --> pdb=" O ASN A 646 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ILE A 648 " --> pdb=" O ALA A 494 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 515 through 520 Processing sheet with id= D, first strand: chain 'A' and resid 679 through 682 removed outlier: 3.540A pdb=" N GLU A 741 " --> pdb=" O ASP A 736 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 342 through 345 removed outlier: 6.286A pdb=" N VAL B 318 " --> pdb=" O PRO B 210 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N LEU B 212 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N GLY B 320 " --> pdb=" O LEU B 212 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LEU B 282 " --> pdb=" O ILE B 319 " (cutoff:3.500A) removed outlier: 8.568A pdb=" N SER B 321 " --> pdb=" O LEU B 282 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N ILE B 284 " --> pdb=" O SER B 321 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 646 through 650 removed outlier: 3.855A pdb=" N ASN B 646 " --> pdb=" O SER B 490 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY B 495 " --> pdb=" O THR B 605 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 585 through 587 Processing sheet with id= H, first strand: chain 'B' and resid 680 through 682 removed outlier: 6.932A pdb=" N VAL B 731 " --> pdb=" O GLU B 681 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 173 through 175 removed outlier: 4.961A pdb=" N ASP C 285 " --> pdb=" O LEU C 248 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ARG C 317 " --> pdb=" O LEU C 282 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N ILE C 284 " --> pdb=" O ARG C 317 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ILE C 319 " --> pdb=" O ILE C 284 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N GLN C 342 " --> pdb=" O LEU C 211 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL C 213 " --> pdb=" O GLN C 342 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N ILE C 344 " --> pdb=" O VAL C 213 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 646 through 650 removed outlier: 3.907A pdb=" N ASN C 646 " --> pdb=" O SER C 490 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU C 492 " --> pdb=" O ASN C 646 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR C 604 " --> pdb=" O LEU C 563 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 680 through 682 removed outlier: 6.594A pdb=" N VAL C 731 " --> pdb=" O GLU C 681 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 173 through 175 removed outlier: 6.632A pdb=" N ILE D 281 " --> pdb=" O TYR D 246 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N LEU D 248 " --> pdb=" O ILE D 281 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N PHE D 283 " --> pdb=" O LEU D 248 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ARG D 317 " --> pdb=" O LEU D 282 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N ILE D 284 " --> pdb=" O ARG D 317 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ILE D 319 " --> pdb=" O ILE D 284 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N GLN D 342 " --> pdb=" O LEU D 211 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N VAL D 213 " --> pdb=" O GLN D 342 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N ILE D 344 " --> pdb=" O VAL D 213 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 646 through 650 Processing sheet with id= N, first strand: chain 'D' and resid 680 through 682 removed outlier: 6.876A pdb=" N VAL D 731 " --> pdb=" O GLU D 681 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 173 through 175 removed outlier: 6.679A pdb=" N ILE E 281 " --> pdb=" O TYR E 246 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N LEU E 248 " --> pdb=" O ILE E 281 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N PHE E 283 " --> pdb=" O LEU E 248 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ARG E 317 " --> pdb=" O LEU E 282 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N ILE E 284 " --> pdb=" O ARG E 317 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N ILE E 319 " --> pdb=" O ILE E 284 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 646 through 649 removed outlier: 3.645A pdb=" N ASN E 646 " --> pdb=" O SER E 490 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU E 492 " --> pdb=" O ASN E 646 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N LEU E 601 " --> pdb=" O PHE E 491 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N PHE E 493 " --> pdb=" O LEU E 601 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N MET E 603 " --> pdb=" O PHE E 493 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR E 604 " --> pdb=" O LEU E 563 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLU E 515 " --> pdb=" O VAL E 560 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N LEU E 562 " --> pdb=" O GLU E 515 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU E 517 " --> pdb=" O LEU E 562 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ASP E 564 " --> pdb=" O LEU E 517 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N PHE E 519 " --> pdb=" O ASP E 564 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 585 through 587 Processing sheet with id= R, first strand: chain 'E' and resid 679 through 682 removed outlier: 5.585A pdb=" N GLU E 681 " --> pdb=" O GLN E 730 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N THR E 732 " --> pdb=" O GLU E 681 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 209 through 213 Processing sheet with id= T, first strand: chain 'F' and resid 245 through 247 removed outlier: 6.387A pdb=" N ILE F 281 " --> pdb=" O TYR F 246 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ARG F 317 " --> pdb=" O LEU F 282 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ILE F 284 " --> pdb=" O ARG F 317 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ILE F 319 " --> pdb=" O ILE F 284 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'F' and resid 490 through 494 removed outlier: 6.864A pdb=" N LEU F 601 " --> pdb=" O PHE F 491 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N PHE F 493 " --> pdb=" O LEU F 601 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N MET F 603 " --> pdb=" O PHE F 493 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N LEU F 561 " --> pdb=" O VAL F 602 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N THR F 604 " --> pdb=" O LEU F 561 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N LEU F 563 " --> pdb=" O THR F 604 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'H' and resid 5 through 7 Processing sheet with id= W, first strand: chain 'H' and resid 28 through 32 removed outlier: 6.395A pdb=" N TYR H 60 " --> pdb=" O ILE H 29 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N LEU H 31 " --> pdb=" O TYR H 60 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N TYR H 62 " --> pdb=" O LEU H 31 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N SER H 88 " --> pdb=" O LEU H 61 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ILE H 63 " --> pdb=" O SER H 88 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N ILE H 90 " --> pdb=" O ILE H 63 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'H' and resid 118 through 121 Processing sheet with id= Y, first strand: chain 'I' and resid 5 through 9 Processing sheet with id= Z, first strand: chain 'I' and resid 60 through 63 removed outlier: 6.121A pdb=" N SER I 88 " --> pdb=" O LEU I 61 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ILE I 63 " --> pdb=" O SER I 88 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ILE I 90 " --> pdb=" O ILE I 63 " (cutoff:3.500A) No H-bonds generated for sheet with id= Z Processing sheet with id= AA, first strand: chain 'J' and resid 5 through 9 removed outlier: 3.543A pdb=" N ARG J 15 " --> pdb=" O GLU J 8 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'J' and resid 28 through 32 removed outlier: 6.519A pdb=" N TYR J 60 " --> pdb=" O ILE J 29 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N LEU J 31 " --> pdb=" O TYR J 60 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N TYR J 62 " --> pdb=" O LEU J 31 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'K' and resid 5 through 8 removed outlier: 3.573A pdb=" N ARG K 15 " --> pdb=" O GLU K 8 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'K' and resid 28 through 32 removed outlier: 6.640A pdb=" N TYR K 60 " --> pdb=" O ILE K 29 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N LEU K 31 " --> pdb=" O TYR K 60 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N TYR K 62 " --> pdb=" O LEU K 31 " (cutoff:3.500A) No H-bonds generated for sheet with id= AD Processing sheet with id= AE, first strand: chain 'K' and resid 119 through 121 removed outlier: 3.664A pdb=" N VAL K 119 " --> pdb=" O LEU K 174 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE K 121 " --> pdb=" O ARG K 172 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG K 172 " --> pdb=" O ILE K 121 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'L' and resid 6 through 9 removed outlier: 3.938A pdb=" N GLU L 8 " --> pdb=" O ARG L 15 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG L 15 " --> pdb=" O GLU L 8 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'L' and resid 59 through 63 removed outlier: 3.554A pdb=" N ILE L 63 " --> pdb=" O ILE L 90 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'L' and resid 118 through 121 Processing sheet with id= AI, first strand: chain 'M' and resid 119 through 121 Processing sheet with id= AJ, first strand: chain 'N' and resid 6 through 8 Processing sheet with id= AK, first strand: chain 'N' and resid 59 through 63 Processing sheet with id= AL, first strand: chain 'N' and resid 118 through 120 1419 hydrogen bonds defined for protein. 4068 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: 29.82 Time building geometry restraints manager: 54.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.06: 38089 1.06 - 1.28: 6511 1.28 - 1.50: 15369 1.50 - 1.73: 16182 1.73 - 1.95: 307 Bond restraints: 76458 Sorted by residual: bond pdb=" C4 ADP E 801 " pdb=" C5 ADP E 801 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.95e+01 bond pdb=" C5 ADP E 801 " pdb=" C6 ADP E 801 " ideal model delta sigma weight residual 1.490 1.407 0.083 2.00e-02 2.50e+03 1.71e+01 bond pdb=" O3B AGS E 802 " pdb=" PG AGS E 802 " ideal model delta sigma weight residual 1.559 1.614 -0.055 2.00e-02 2.50e+03 7.58e+00 bond pdb=" O3B AGS A 801 " pdb=" PG AGS A 801 " ideal model delta sigma weight residual 1.559 1.614 -0.055 2.00e-02 2.50e+03 7.50e+00 bond pdb=" O3B AGS D 802 " pdb=" PG AGS D 802 " ideal model delta sigma weight residual 1.559 1.614 -0.055 2.00e-02 2.50e+03 7.49e+00 ... (remaining 76453 not shown) Histogram of bond angle deviations from ideal: 79.36 - 90.51: 4 90.51 - 101.66: 145 101.66 - 112.81: 91799 112.81 - 123.96: 41619 123.96 - 135.11: 5007 Bond angle restraints: 138574 Sorted by residual: angle pdb="HG21 ILE F 576 " pdb=" CG2 ILE F 576 " pdb="HG22 ILE F 576 " ideal model delta sigma weight residual 110.00 79.36 30.64 3.00e+00 1.11e-01 1.04e+02 angle pdb="HG22 ILE F 576 " pdb=" CG2 ILE F 576 " pdb="HG23 ILE F 576 " ideal model delta sigma weight residual 110.00 79.89 30.11 3.00e+00 1.11e-01 1.01e+02 angle pdb=" CB ILE F 576 " pdb=" CG2 ILE F 576 " pdb="HG21 ILE F 576 " ideal model delta sigma weight residual 109.00 81.58 27.42 3.00e+00 1.11e-01 8.35e+01 angle pdb=" CB ILE F 576 " pdb=" CG2 ILE F 576 " pdb="HG23 ILE F 576 " ideal model delta sigma weight residual 109.00 82.60 26.40 3.00e+00 1.11e-01 7.74e+01 angle pdb="HG21 ILE F 576 " pdb=" CG2 ILE F 576 " pdb="HG23 ILE F 576 " ideal model delta sigma weight residual 110.00 135.11 -25.11 3.00e+00 1.11e-01 7.01e+01 ... (remaining 138569 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.72: 34525 35.72 - 71.44: 839 71.44 - 107.15: 43 107.15 - 142.87: 8 142.87 - 178.59: 2 Dihedral angle restraints: 35417 sinusoidal: 19982 harmonic: 15435 Sorted by residual: dihedral pdb=" O1B ADP E 801 " pdb=" O3A ADP E 801 " pdb=" PB ADP E 801 " pdb=" PA ADP E 801 " ideal model delta sinusoidal sigma weight residual 300.00 121.41 178.59 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' ADP E 801 " pdb=" O5' ADP E 801 " pdb=" PA ADP E 801 " pdb=" O2A ADP E 801 " ideal model delta sinusoidal sigma weight residual -60.00 50.96 -110.96 1 2.00e+01 2.50e-03 3.26e+01 dihedral pdb=" O2A ADP E 801 " pdb=" O3A ADP E 801 " pdb=" PA ADP E 801 " pdb=" PB ADP E 801 " ideal model delta sinusoidal sigma weight residual -60.00 49.12 -109.12 1 2.00e+01 2.50e-03 3.19e+01 ... (remaining 35414 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 4000 0.034 - 0.068: 1306 0.068 - 0.102: 427 0.102 - 0.136: 191 0.136 - 0.170: 27 Chirality restraints: 5951 Sorted by residual: chirality pdb=" CA ILE F 319 " pdb=" N ILE F 319 " pdb=" C ILE F 319 " pdb=" CB ILE F 319 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.19e-01 chirality pdb=" C3' ADP E 801 " pdb=" C2' ADP E 801 " pdb=" C4' ADP E 801 " pdb=" O3' ADP E 801 " both_signs ideal model delta sigma weight residual False -2.51 -2.68 0.17 2.00e-01 2.50e+01 7.03e-01 chirality pdb=" CA PRO A 309 " pdb=" N PRO A 309 " pdb=" C PRO A 309 " pdb=" CB PRO A 309 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.02e-01 ... (remaining 5948 not shown) Planarity restraints: 11294 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG C 702 " -0.036 5.00e-02 4.00e+02 5.43e-02 4.73e+00 pdb=" N PRO C 703 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO C 703 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 703 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS H 84 " -0.035 5.00e-02 4.00e+02 5.23e-02 4.38e+00 pdb=" N PRO H 85 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO H 85 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO H 85 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 284 " -0.010 2.00e-02 2.50e+03 2.02e-02 4.10e+00 pdb=" C ILE A 284 " 0.035 2.00e-02 2.50e+03 pdb=" O ILE A 284 " -0.013 2.00e-02 2.50e+03 pdb=" N ASP A 285 " -0.012 2.00e-02 2.50e+03 ... (remaining 11291 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.25: 8506 2.25 - 2.84: 175143 2.84 - 3.43: 198957 3.43 - 4.01: 273838 4.01 - 4.60: 421354 Nonbonded interactions: 1077798 Sorted by model distance: nonbonded pdb=" O ALA F 381 " pdb=" HZ2 LYS F 397 " model vdw 1.665 1.850 nonbonded pdb=" O ALA N 96 " pdb=" H ALA N 100 " model vdw 1.683 1.850 nonbonded pdb=" OE1 GLU E 484 " pdb=" H GLU E 484 " model vdw 1.698 1.850 nonbonded pdb=" O ALA M 96 " pdb=" H ALA M 100 " model vdw 1.701 1.850 nonbonded pdb=" O ILE E 708 " pdb=" H LYS E 713 " model vdw 1.707 1.850 ... (remaining 1077793 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 172 through 291 or (resid 302 and (name N or name CA or na \ me C or name O or name CB or name CG or name OD1 or name OD2 or name HA or name \ HB2 or name HB3)) or resid 303 through 323 or (resid 324 and (name N or name CA \ or name C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or \ name CE2 or name CZ or name OH or name H or name HA or name HB2 or name HB3 or \ name HD1 or name HD2 or name HE1 or name HE2)) or resid 325 through 533 or (resi \ d 549 and (name N or name CA or name C or name O or name CB or name CG or name C \ D1 or name CD2 or name HA or name HB2 or name HB3 or name HG or name HD11 or nam \ e HD12 or name HD13 or name HD21 or name HD22 or name HD23)) or resid 550 throug \ h 568 or resid 572 through 613 or resid 624 through 748)) selection = (chain 'B' and ((resid 172 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name H \ A or name HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name HE2 or nam \ e HZ )) or resid 173 through 291 or (resid 302 and (name N or name CA or name C \ or name O or name CB or name CG or name OD1 or name OD2 or name HA or name HB2 o \ r name HB3)) or resid 303 through 323 or (resid 324 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name \ CE2 or name CZ or name OH or name H or name HA or name HB2 or name HB3 or name \ HD1 or name HD2 or name HE1 or name HE2)) or resid 325 through 435 or resid 438 \ through 533 or (resid 549 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name HG \ or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23)) \ or resid 550 through 568 or resid 572 through 613 or resid 624 through 748)) selection = (chain 'C' and ((resid 172 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name H \ A or name HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name HE2 or nam \ e HZ )) or resid 173 through 291 or (resid 302 and (name N or name CA or name C \ or name O or name CB or name CG or name OD1 or name OD2 or name HA or name HB2 o \ r name HB3)) or resid 303 through 323 or (resid 324 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name \ CE2 or name CZ or name OH or name H or name HA or name HB2 or name HB3 or name \ HD1 or name HD2 or name HE1 or name HE2)) or resid 325 through 435 or resid 438 \ through 533 or (resid 549 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name HG \ or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23)) \ or resid 550 through 568 or resid 572 through 613 or resid 624 through 748)) selection = (chain 'D' and ((resid 172 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name H \ A or name HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name HE2 or nam \ e HZ )) or resid 173 through 291 or (resid 302 and (name N or name CA or name C \ or name O or name CB or name CG or name OD1 or name OD2 or name HA or name HB2 o \ r name HB3)) or resid 303 through 323 or (resid 324 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name \ CE2 or name CZ or name OH or name H or name HA or name HB2 or name HB3 or name \ HD1 or name HD2 or name HE1 or name HE2)) or resid 325 through 435 or resid 438 \ through 533 or (resid 549 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name HG \ or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23)) \ or resid 550 through 568 or resid 572 through 613 or resid 624 through 748)) selection = (chain 'E' and ((resid 172 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name H \ A or name HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name HE2 or nam \ e HZ )) or resid 173 through 291 or (resid 302 and (name N or name CA or name C \ or name O or name CB or name CG or name OD1 or name OD2 or name HA or name HB2 o \ r name HB3)) or resid 303 through 435 or resid 438 through 533 or (resid 549 and \ (name N or name CA or name C or name O or name CB or name CG or name CD1 or nam \ e CD2 or name HA or name HB2 or name HB3 or name HG or name HD11 or name HD12 or \ name HD13 or name HD21 or name HD22 or name HD23)) or resid 550 through 568 or \ resid 572 through 613 or resid 624 through 748)) selection = (chain 'F' and ((resid 172 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name H \ A or name HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name HE2 or nam \ e HZ )) or resid 173 through 323 or (resid 324 and (name N or name CA or name C \ or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 \ or name CZ or name OH or name H or name HA or name HB2 or name HB3 or name HD1 o \ r name HD2 or name HE1 or name HE2)) or resid 325 through 435 or resid 438 throu \ gh 748)) } ncs_group { reference = (chain 'H' and resid 2 through 191) selection = (chain 'I' and resid 2 through 191) selection = (chain 'J' and resid 2 through 191) selection = (chain 'K' and resid 2 through 191) selection = (chain 'L' and resid 2 through 191) selection = chain 'M' selection = (chain 'N' and (resid 2 through 186 or (resid 187 and (name N or name CA or name \ C or name O or name CB or name OG or name HA or name HB2 or name HB3 or name HG \ )) or resid 188 through 191)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.300 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: 0.850 Extract box with map and model: 4.850 Check model and map are aligned: 0.860 Set scattering table: 0.540 Process input model: 200.030 Find NCS groups from input model: 3.690 Set up NCS constraints: 0.220 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: 0.020 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 214.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.109 38343 Z= 0.269 Angle : 0.774 13.427 51789 Z= 0.398 Chirality : 0.042 0.170 5951 Planarity : 0.004 0.054 6683 Dihedral : 14.066 178.591 14628 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Rotamer: Outliers : 0.02 % Allowed : 1.58 % Favored : 98.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.11), residues: 4752 helix: 0.94 (0.10), residues: 2267 sheet: -1.72 (0.19), residues: 679 loop : -0.69 (0.13), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP S 7 HIS 0.007 0.001 HIS D 393 PHE 0.023 0.001 PHE A 263 TYR 0.010 0.001 TYR C 324 ARG 0.005 0.000 ARG A 204 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 324 is missing expected H atoms. Skipping. Evaluate side-chains 1306 residues out of total 4045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1305 time to evaluate : 4.870 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 515 GLU cc_start: 0.7699 (tt0) cc_final: 0.7248 (mm-30) REVERT: B 210 PRO cc_start: 0.8759 (Cg_endo) cc_final: 0.8362 (Cg_exo) REVERT: B 588 ASP cc_start: 0.8164 (p0) cc_final: 0.7934 (p0) REVERT: C 215 GLU cc_start: 0.7817 (mm-30) cc_final: 0.6770 (mm-30) REVERT: C 522 SER cc_start: 0.8723 (p) cc_final: 0.8234 (p) REVERT: D 348 GLU cc_start: 0.7853 (pt0) cc_final: 0.7191 (pt0) REVERT: D 366 GLU cc_start: 0.7164 (mt-10) cc_final: 0.6931 (mt-10) REVERT: D 454 ASP cc_start: 0.7181 (m-30) cc_final: 0.6846 (m-30) REVERT: E 323 THR cc_start: 0.8423 (m) cc_final: 0.7995 (m) REVERT: E 447 ASP cc_start: 0.6750 (p0) cc_final: 0.6357 (p0) REVERT: E 524 TYR cc_start: 0.8250 (m-80) cc_final: 0.7986 (m-80) REVERT: F 192 GLU cc_start: 0.6537 (mp0) cc_final: 0.6270 (mp0) REVERT: F 629 MET cc_start: 0.6650 (ptt) cc_final: 0.6416 (ptt) REVERT: H 2 LEU cc_start: 0.6625 (tp) cc_final: 0.6425 (tp) REVERT: H 5 MET cc_start: 0.7422 (mmt) cc_final: 0.7027 (mmt) REVERT: H 24 LEU cc_start: 0.8416 (tp) cc_final: 0.8033 (tp) REVERT: H 47 MET cc_start: 0.8071 (mtt) cc_final: 0.7778 (mtt) REVERT: H 77 TYR cc_start: 0.7739 (t80) cc_final: 0.7321 (t80) REVERT: H 112 PHE cc_start: 0.6214 (m-80) cc_final: 0.5997 (m-80) REVERT: H 136 GLU cc_start: 0.6990 (tm-30) cc_final: 0.6786 (tm-30) REVERT: H 148 ARG cc_start: 0.7161 (tpm170) cc_final: 0.6777 (tpm170) REVERT: H 165 GLU cc_start: 0.7591 (tm-30) cc_final: 0.7370 (tm-30) REVERT: J 165 GLU cc_start: 0.7649 (tp30) cc_final: 0.7030 (tt0) REVERT: J 174 LEU cc_start: 0.7921 (mt) cc_final: 0.7666 (mt) REVERT: K 104 THR cc_start: 0.7424 (t) cc_final: 0.7157 (t) REVERT: L 14 GLU cc_start: 0.5759 (pp20) cc_final: 0.4800 (pp20) REVERT: L 149 MET cc_start: 0.6338 (mmp) cc_final: 0.6066 (mmp) REVERT: L 153 MET cc_start: 0.6072 (ttm) cc_final: 0.5720 (ttm) REVERT: S 12 GLN cc_start: 0.6432 (tp40) cc_final: 0.6113 (tp40) outliers start: 1 outliers final: 0 residues processed: 1306 average time/residue: 1.1180 time to fit residues: 2275.9937 Evaluate side-chains 1109 residues out of total 4045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1109 time to evaluate : 4.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 478 random chunks: chunk 403 optimal weight: 7.9990 chunk 362 optimal weight: 2.9990 chunk 201 optimal weight: 5.9990 chunk 123 optimal weight: 7.9990 chunk 244 optimal weight: 10.0000 chunk 193 optimal weight: 10.0000 chunk 374 optimal weight: 6.9990 chunk 144 optimal weight: 0.0060 chunk 227 optimal weight: 9.9990 chunk 278 optimal weight: 7.9990 chunk 434 optimal weight: 40.0000 overall best weight: 4.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 HIS ** A 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 659 HIS A 688 ASN A 709 GLN B 325 GLN ** C 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 463 GLN C 660 GLN D 528 HIS ** D 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 642 ASN D 711 ASN ** D 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 368 HIS ** E 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 305 ASN F 329 ASN F 583 ASN F 718 ASN H 41 ASN H 81 GLN I 41 ASN ** I 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 159 GLN ** J 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 41 ASN K 150 ASN L 41 ASN L 156 HIS N 41 ASN N 46 GLN N 150 ASN ** N 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 38343 Z= 0.284 Angle : 0.556 6.122 51789 Z= 0.301 Chirality : 0.040 0.178 5951 Planarity : 0.004 0.074 6683 Dihedral : 9.050 173.668 5368 Min Nonbonded Distance : 1.694 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.36 % Allowed : 9.99 % Favored : 88.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.12), residues: 4752 helix: 1.05 (0.10), residues: 2367 sheet: -1.59 (0.19), residues: 671 loop : -0.55 (0.14), residues: 1714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 689 HIS 0.008 0.001 HIS E 393 PHE 0.025 0.001 PHE F 267 TYR 0.017 0.001 TYR J 77 ARG 0.008 0.000 ARG B 340 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 324 is missing expected H atoms. Skipping. Evaluate side-chains 1184 residues out of total 4045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 1129 time to evaluate : 4.529 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 364 LYS cc_start: 0.7342 (mmpt) cc_final: 0.7039 (tttm) REVERT: A 412 MET cc_start: 0.4940 (tmm) cc_final: 0.4684 (tmm) REVERT: A 484 GLU cc_start: 0.7414 (pm20) cc_final: 0.6886 (mp0) REVERT: A 503 GLU cc_start: 0.7847 (tp30) cc_final: 0.7596 (tp30) REVERT: B 355 VAL cc_start: 0.8978 (m) cc_final: 0.8733 (t) REVERT: B 623 ASP cc_start: 0.7459 (t0) cc_final: 0.7032 (t70) REVERT: C 565 GLU cc_start: 0.7533 (mm-30) cc_final: 0.7259 (mm-30) REVERT: C 633 LYS cc_start: 0.8396 (mttt) cc_final: 0.8191 (mttt) REVERT: D 564 ASP cc_start: 0.8467 (OUTLIER) cc_final: 0.8161 (m-30) REVERT: E 307 ILE cc_start: 0.8898 (pt) cc_final: 0.8362 (tt) REVERT: E 326 GLU cc_start: 0.7082 (mp0) cc_final: 0.6809 (mp0) REVERT: F 192 GLU cc_start: 0.6304 (mp0) cc_final: 0.5960 (mp0) REVERT: F 208 ASN cc_start: 0.6787 (p0) cc_final: 0.6557 (p0) REVERT: H 5 MET cc_start: 0.7188 (mmt) cc_final: 0.6898 (mmt) REVERT: H 24 LEU cc_start: 0.8474 (tp) cc_final: 0.8195 (tp) REVERT: H 47 MET cc_start: 0.8081 (mtt) cc_final: 0.7846 (mtt) REVERT: J 31 LEU cc_start: 0.7783 (tp) cc_final: 0.7537 (tt) REVERT: J 78 ASP cc_start: 0.6831 (m-30) cc_final: 0.6594 (m-30) REVERT: J 165 GLU cc_start: 0.7631 (tp30) cc_final: 0.6927 (tt0) REVERT: L 14 GLU cc_start: 0.5901 (pp20) cc_final: 0.4911 (pp20) REVERT: L 102 LEU cc_start: 0.5592 (mt) cc_final: 0.5292 (tp) REVERT: L 149 MET cc_start: 0.6622 (mmp) cc_final: 0.6296 (mmp) REVERT: L 153 MET cc_start: 0.6130 (ttm) cc_final: 0.5780 (ttm) outliers start: 55 outliers final: 41 residues processed: 1153 average time/residue: 1.1333 time to fit residues: 2034.5825 Evaluate side-chains 1093 residues out of total 4045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 1051 time to evaluate : 4.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 724 SER Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain B residue 656 ASP Chi-restraints excluded: chain B residue 679 SER Chi-restraints excluded: chain B residue 702 ARG Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 566 ILE Chi-restraints excluded: chain C residue 688 ASN Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 564 ASP Chi-restraints excluded: chain D residue 722 PHE Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 178 GLN Chi-restraints excluded: chain E residue 186 ASP Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 454 ASP Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 354 THR Chi-restraints excluded: chain F residue 561 LEU Chi-restraints excluded: chain F residue 578 LEU Chi-restraints excluded: chain F residue 667 VAL Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain I residue 88 SER Chi-restraints excluded: chain J residue 65 SER Chi-restraints excluded: chain J residue 88 SER Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain L residue 18 ASP Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 155 LEU Chi-restraints excluded: chain L residue 174 LEU Chi-restraints excluded: chain M residue 58 ASP Chi-restraints excluded: chain M residue 79 THR Chi-restraints excluded: chain M residue 82 PHE Chi-restraints excluded: chain S residue 5 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 478 random chunks: chunk 241 optimal weight: 10.0000 chunk 134 optimal weight: 6.9990 chunk 361 optimal weight: 10.0000 chunk 295 optimal weight: 20.0000 chunk 119 optimal weight: 4.9990 chunk 434 optimal weight: 30.0000 chunk 469 optimal weight: 50.0000 chunk 387 optimal weight: 9.9990 chunk 431 optimal weight: 30.0000 chunk 148 optimal weight: 5.9990 chunk 348 optimal weight: 5.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN B 175 ASN B 209 ASN B 276 GLN B 558 HIS ** B 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 GLN C 325 GLN C 329 ASN ** C 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 483 HIS D 356 GLN ** D 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 342 GLN ** E 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 718 ASN ** H 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 41 ASN ** J 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 54 ASN ** L 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 41 ASN N 122 HIS ** N 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.3438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 38343 Z= 0.381 Angle : 0.596 10.667 51789 Z= 0.318 Chirality : 0.042 0.195 5951 Planarity : 0.005 0.105 6683 Dihedral : 9.116 175.496 5368 Min Nonbonded Distance : 1.742 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.93 % Allowed : 12.39 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.12), residues: 4752 helix: 0.59 (0.10), residues: 2369 sheet: -1.54 (0.18), residues: 698 loop : -0.75 (0.14), residues: 1685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP D 229 HIS 0.011 0.001 HIS A 558 PHE 0.024 0.002 PHE F 267 TYR 0.031 0.002 TYR L 62 ARG 0.009 0.001 ARG H 148 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 324 is missing expected H atoms. Skipping. Evaluate side-chains 1192 residues out of total 4045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 1114 time to evaluate : 4.617 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 364 LYS cc_start: 0.7492 (mmpt) cc_final: 0.7082 (tttm) REVERT: A 412 MET cc_start: 0.5103 (tmm) cc_final: 0.4837 (tmm) REVERT: A 510 LYS cc_start: 0.8259 (mmtp) cc_final: 0.8032 (mmtp) REVERT: A 558 HIS cc_start: 0.6485 (m-70) cc_final: 0.6048 (m-70) REVERT: B 343 LYS cc_start: 0.8010 (ttpt) cc_final: 0.7745 (tttm) REVERT: B 675 GLN cc_start: 0.7686 (OUTLIER) cc_final: 0.7319 (mp10) REVERT: C 302 ASP cc_start: 0.7382 (p0) cc_final: 0.7154 (p0) REVERT: C 565 GLU cc_start: 0.7704 (mm-30) cc_final: 0.7461 (mm-30) REVERT: D 510 LYS cc_start: 0.8238 (mtpt) cc_final: 0.7996 (mtpt) REVERT: E 307 ILE cc_start: 0.9054 (pt) cc_final: 0.8565 (tt) REVERT: E 458 MET cc_start: 0.7464 (ppp) cc_final: 0.7109 (tmm) REVERT: E 659 HIS cc_start: 0.6230 (m-70) cc_final: 0.5955 (m-70) REVERT: F 188 LEU cc_start: 0.6816 (OUTLIER) cc_final: 0.6333 (tt) REVERT: F 305 ASN cc_start: 0.6080 (OUTLIER) cc_final: 0.5871 (t160) REVERT: F 512 LEU cc_start: 0.7026 (OUTLIER) cc_final: 0.6754 (mp) REVERT: F 578 LEU cc_start: 0.6773 (OUTLIER) cc_final: 0.6190 (mp) REVERT: F 664 LYS cc_start: 0.8539 (pttt) cc_final: 0.8224 (ttpt) REVERT: H 5 MET cc_start: 0.7198 (mmt) cc_final: 0.6857 (mmt) REVERT: H 47 MET cc_start: 0.8007 (mtt) cc_final: 0.7755 (mtt) REVERT: H 50 LEU cc_start: 0.8119 (mt) cc_final: 0.7898 (mt) REVERT: I 17 PHE cc_start: 0.6588 (m-80) cc_final: 0.6350 (m-80) REVERT: I 39 MET cc_start: 0.7206 (OUTLIER) cc_final: 0.6937 (ptm) REVERT: J 39 MET cc_start: 0.7950 (ppp) cc_final: 0.7677 (ptm) REVERT: J 78 ASP cc_start: 0.7065 (m-30) cc_final: 0.6794 (m-30) REVERT: J 165 GLU cc_start: 0.7636 (tp30) cc_final: 0.6972 (tt0) REVERT: L 14 GLU cc_start: 0.6150 (pp20) cc_final: 0.5025 (pp20) REVERT: L 102 LEU cc_start: 0.5806 (mt) cc_final: 0.5444 (tp) REVERT: L 149 MET cc_start: 0.6408 (mmp) cc_final: 0.6145 (mmp) REVERT: L 153 MET cc_start: 0.6112 (ttm) cc_final: 0.5795 (ttm) REVERT: N 123 GLN cc_start: 0.7943 (pp30) cc_final: 0.7726 (pp30) outliers start: 78 outliers final: 50 residues processed: 1149 average time/residue: 1.0926 time to fit residues: 1959.6070 Evaluate side-chains 1092 residues out of total 4045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 1036 time to evaluate : 4.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 527 ARG Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 724 SER Chi-restraints excluded: chain B residue 276 GLN Chi-restraints excluded: chain B residue 353 GLU Chi-restraints excluded: chain B residue 461 PHE Chi-restraints excluded: chain B residue 656 ASP Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 679 SER Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain C residue 286 GLU Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain C residue 657 VAL Chi-restraints excluded: chain C residue 688 ASN Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 302 ASP Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain D residue 321 SER Chi-restraints excluded: chain D residue 531 SER Chi-restraints excluded: chain D residue 722 PHE Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 186 ASP Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 302 ASP Chi-restraints excluded: chain E residue 324 TYR Chi-restraints excluded: chain E residue 331 PHE Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 454 ASP Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 305 ASN Chi-restraints excluded: chain F residue 354 THR Chi-restraints excluded: chain F residue 512 LEU Chi-restraints excluded: chain F residue 561 LEU Chi-restraints excluded: chain F residue 578 LEU Chi-restraints excluded: chain F residue 612 THR Chi-restraints excluded: chain F residue 667 VAL Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain I residue 39 MET Chi-restraints excluded: chain I residue 142 ILE Chi-restraints excluded: chain J residue 65 SER Chi-restraints excluded: chain J residue 88 SER Chi-restraints excluded: chain K residue 41 ASN Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain M residue 58 ASP Chi-restraints excluded: chain M residue 79 THR Chi-restraints excluded: chain M residue 82 PHE Chi-restraints excluded: chain S residue 5 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 478 random chunks: chunk 429 optimal weight: 30.0000 chunk 326 optimal weight: 20.0000 chunk 225 optimal weight: 9.9990 chunk 48 optimal weight: 5.9990 chunk 207 optimal weight: 5.9990 chunk 292 optimal weight: 9.9990 chunk 436 optimal weight: 20.0000 chunk 462 optimal weight: 7.9990 chunk 228 optimal weight: 8.9990 chunk 413 optimal weight: 20.0000 chunk 124 optimal weight: 8.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 558 HIS ** A 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 ASN B 606 ASN ** C 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 GLN C 329 ASN ** C 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 718 ASN D 356 GLN ** D 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 305 ASN ** F 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 116 ASN ** J 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 46 GLN L 94 GLN N 41 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.4004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 38343 Z= 0.399 Angle : 0.573 8.045 51789 Z= 0.307 Chirality : 0.041 0.199 5951 Planarity : 0.004 0.061 6683 Dihedral : 9.233 169.104 5368 Min Nonbonded Distance : 1.703 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.13 % Allowed : 14.44 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.12), residues: 4752 helix: 0.41 (0.10), residues: 2388 sheet: -1.47 (0.18), residues: 690 loop : -0.85 (0.14), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 689 HIS 0.007 0.001 HIS I 191 PHE 0.028 0.002 PHE B 172 TYR 0.020 0.001 TYR A 695 ARG 0.026 0.001 ARG B 410 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 324 is missing expected H atoms. Skipping. Evaluate side-chains 1152 residues out of total 4045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 1066 time to evaluate : 4.559 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 364 LYS cc_start: 0.7501 (mmpt) cc_final: 0.7044 (tttm) REVERT: A 412 MET cc_start: 0.5203 (tmm) cc_final: 0.4931 (tmm) REVERT: C 432 ARG cc_start: 0.8531 (mtp85) cc_final: 0.8195 (ttt90) REVERT: C 458 MET cc_start: 0.6714 (mmt) cc_final: 0.6481 (mmt) REVERT: C 527 ARG cc_start: 0.7635 (ttm-80) cc_final: 0.7360 (ttm-80) REVERT: C 565 GLU cc_start: 0.7744 (mm-30) cc_final: 0.7512 (mm-30) REVERT: D 472 GLU cc_start: 0.8257 (mm-30) cc_final: 0.7243 (mm-30) REVERT: E 307 ILE cc_start: 0.9120 (pt) cc_final: 0.8627 (tt) REVERT: F 240 MET cc_start: 0.4430 (tpp) cc_final: 0.4144 (tpp) REVERT: F 664 LYS cc_start: 0.8577 (pttt) cc_final: 0.8260 (ttpt) REVERT: H 5 MET cc_start: 0.7270 (mmt) cc_final: 0.6891 (mmt) REVERT: H 47 MET cc_start: 0.7976 (mtt) cc_final: 0.7765 (mtt) REVERT: H 74 MET cc_start: 0.7647 (mmp) cc_final: 0.6802 (mmp) REVERT: H 78 ASP cc_start: 0.6958 (m-30) cc_final: 0.6623 (m-30) REVERT: J 78 ASP cc_start: 0.7020 (m-30) cc_final: 0.6704 (m-30) REVERT: L 149 MET cc_start: 0.6310 (mmp) cc_final: 0.6062 (mmp) REVERT: L 153 MET cc_start: 0.6123 (ttm) cc_final: 0.5769 (ttm) REVERT: M 60 TYR cc_start: 0.7314 (m-80) cc_final: 0.7092 (m-80) REVERT: M 92 MET cc_start: 0.6243 (mmt) cc_final: 0.5954 (mmt) REVERT: N 123 GLN cc_start: 0.8029 (pp30) cc_final: 0.7456 (pp30) outliers start: 86 outliers final: 71 residues processed: 1106 average time/residue: 1.0975 time to fit residues: 1892.6770 Evaluate side-chains 1100 residues out of total 4045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 1029 time to evaluate : 4.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 527 ARG Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 724 SER Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 620 ILE Chi-restraints excluded: chain B residue 656 ASP Chi-restraints excluded: chain B residue 679 SER Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain C residue 635 ILE Chi-restraints excluded: chain C residue 657 VAL Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 681 GLU Chi-restraints excluded: chain C residue 688 ASN Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 302 ASP Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain D residue 321 SER Chi-restraints excluded: chain D residue 464 ASP Chi-restraints excluded: chain D residue 531 SER Chi-restraints excluded: chain D residue 722 PHE Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 186 ASP Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 302 ASP Chi-restraints excluded: chain E residue 324 TYR Chi-restraints excluded: chain E residue 331 PHE Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 629 MET Chi-restraints excluded: chain F residue 327 PHE Chi-restraints excluded: chain F residue 561 LEU Chi-restraints excluded: chain F residue 612 THR Chi-restraints excluded: chain F residue 721 LEU Chi-restraints excluded: chain F residue 726 VAL Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 128 TYR Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 169 GLU Chi-restraints excluded: chain I residue 142 ILE Chi-restraints excluded: chain I residue 156 HIS Chi-restraints excluded: chain J residue 65 SER Chi-restraints excluded: chain J residue 88 SER Chi-restraints excluded: chain J residue 141 GLU Chi-restraints excluded: chain K residue 41 ASN Chi-restraints excluded: chain K residue 63 ILE Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 90 ILE Chi-restraints excluded: chain L residue 155 LEU Chi-restraints excluded: chain M residue 58 ASP Chi-restraints excluded: chain M residue 79 THR Chi-restraints excluded: chain M residue 82 PHE Chi-restraints excluded: chain M residue 120 MET Chi-restraints excluded: chain N residue 24 LEU Chi-restraints excluded: chain S residue 5 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 478 random chunks: chunk 384 optimal weight: 10.0000 chunk 262 optimal weight: 1.9990 chunk 6 optimal weight: 30.0000 chunk 344 optimal weight: 20.0000 chunk 190 optimal weight: 2.9990 chunk 394 optimal weight: 6.9990 chunk 319 optimal weight: 8.9990 chunk 0 optimal weight: 40.0000 chunk 235 optimal weight: 9.9990 chunk 414 optimal weight: 40.0000 chunk 116 optimal weight: 0.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 288 HIS C 233 GLN ** C 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.4209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 38343 Z= 0.259 Angle : 0.518 7.459 51789 Z= 0.272 Chirality : 0.039 0.155 5951 Planarity : 0.004 0.072 6683 Dihedral : 9.038 173.138 5368 Min Nonbonded Distance : 1.746 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.90 % Allowed : 15.75 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.12), residues: 4752 helix: 0.61 (0.10), residues: 2397 sheet: -1.34 (0.19), residues: 680 loop : -0.79 (0.14), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 649 HIS 0.016 0.001 HIS E 659 PHE 0.017 0.001 PHE B 172 TYR 0.010 0.001 TYR E 259 ARG 0.007 0.000 ARG I 15 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 324 is missing expected H atoms. Skipping. Evaluate side-chains 1131 residues out of total 4045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 1054 time to evaluate : 4.537 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 MET cc_start: 0.5179 (tmm) cc_final: 0.4928 (tmm) REVERT: C 432 ARG cc_start: 0.8504 (mtp85) cc_final: 0.8237 (ttt90) REVERT: C 458 MET cc_start: 0.6712 (mmt) cc_final: 0.6498 (mmt) REVERT: D 249 ASP cc_start: 0.7828 (t0) cc_final: 0.7376 (t70) REVERT: D 264 GLU cc_start: 0.7859 (mp0) cc_final: 0.7426 (mp0) REVERT: D 450 LYS cc_start: 0.8227 (OUTLIER) cc_final: 0.7588 (tttt) REVERT: D 564 ASP cc_start: 0.8781 (OUTLIER) cc_final: 0.8411 (m-30) REVERT: E 307 ILE cc_start: 0.9102 (pt) cc_final: 0.8646 (tt) REVERT: E 366 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7721 (mp0) REVERT: E 510 LYS cc_start: 0.8367 (mmmm) cc_final: 0.8159 (mmtm) REVERT: F 240 MET cc_start: 0.4440 (tpp) cc_final: 0.4180 (tpp) REVERT: F 488 VAL cc_start: 0.7047 (OUTLIER) cc_final: 0.6837 (p) REVERT: F 659 HIS cc_start: 0.6922 (m90) cc_final: 0.6636 (m90) REVERT: F 664 LYS cc_start: 0.8545 (pttt) cc_final: 0.8230 (ttpt) REVERT: H 5 MET cc_start: 0.7246 (mmt) cc_final: 0.6847 (mmt) REVERT: H 47 MET cc_start: 0.7954 (mtt) cc_final: 0.7734 (mtt) REVERT: J 78 ASP cc_start: 0.7010 (m-30) cc_final: 0.6689 (m-30) REVERT: K 128 TYR cc_start: 0.4994 (t80) cc_final: 0.4626 (t80) REVERT: L 153 MET cc_start: 0.6072 (ttm) cc_final: 0.5726 (ttm) REVERT: M 60 TYR cc_start: 0.7360 (m-80) cc_final: 0.7094 (m-80) REVERT: M 92 MET cc_start: 0.6269 (mmt) cc_final: 0.5909 (mmt) REVERT: M 156 HIS cc_start: 0.6521 (OUTLIER) cc_final: 0.6265 (m170) outliers start: 77 outliers final: 63 residues processed: 1087 average time/residue: 1.0826 time to fit residues: 1832.5561 Evaluate side-chains 1097 residues out of total 4045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 1029 time to evaluate : 4.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 724 SER Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 620 ILE Chi-restraints excluded: chain B residue 623 ASP Chi-restraints excluded: chain B residue 656 ASP Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 679 SER Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 286 GLU Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain C residue 657 VAL Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain D residue 321 SER Chi-restraints excluded: chain D residue 440 SER Chi-restraints excluded: chain D residue 450 LYS Chi-restraints excluded: chain D residue 509 SER Chi-restraints excluded: chain D residue 564 ASP Chi-restraints excluded: chain D residue 722 PHE Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 186 ASP Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 302 ASP Chi-restraints excluded: chain E residue 324 TYR Chi-restraints excluded: chain E residue 366 GLU Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 454 ASP Chi-restraints excluded: chain E residue 629 MET Chi-restraints excluded: chain F residue 311 LEU Chi-restraints excluded: chain F residue 327 PHE Chi-restraints excluded: chain F residue 488 VAL Chi-restraints excluded: chain F residue 563 LEU Chi-restraints excluded: chain F residue 612 THR Chi-restraints excluded: chain F residue 692 GLU Chi-restraints excluded: chain F residue 721 LEU Chi-restraints excluded: chain H residue 16 SER Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 41 ASN Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 51 GLU Chi-restraints excluded: chain H residue 128 TYR Chi-restraints excluded: chain I residue 142 ILE Chi-restraints excluded: chain I residue 156 HIS Chi-restraints excluded: chain J residue 65 SER Chi-restraints excluded: chain J residue 88 SER Chi-restraints excluded: chain J residue 141 GLU Chi-restraints excluded: chain J residue 151 GLU Chi-restraints excluded: chain K residue 41 ASN Chi-restraints excluded: chain K residue 63 ILE Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain L residue 16 SER Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain L residue 155 LEU Chi-restraints excluded: chain M residue 58 ASP Chi-restraints excluded: chain M residue 79 THR Chi-restraints excluded: chain M residue 120 MET Chi-restraints excluded: chain M residue 156 HIS Chi-restraints excluded: chain N residue 24 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 478 random chunks: chunk 155 optimal weight: 5.9990 chunk 416 optimal weight: 20.0000 chunk 91 optimal weight: 3.9990 chunk 271 optimal weight: 4.9990 chunk 114 optimal weight: 10.0000 chunk 462 optimal weight: 0.8980 chunk 383 optimal weight: 5.9990 chunk 214 optimal weight: 6.9990 chunk 38 optimal weight: 7.9990 chunk 152 optimal weight: 0.7980 chunk 242 optimal weight: 4.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 GLN ** C 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 356 GLN ** D 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 556 HIS ** F 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 718 ASN ** H 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 94 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.4336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 38343 Z= 0.212 Angle : 0.496 6.613 51789 Z= 0.259 Chirality : 0.038 0.152 5951 Planarity : 0.004 0.070 6683 Dihedral : 8.850 179.142 5368 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.05 % Allowed : 15.90 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.12), residues: 4752 helix: 0.83 (0.10), residues: 2392 sheet: -1.25 (0.19), residues: 690 loop : -0.70 (0.15), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 649 HIS 0.011 0.001 HIS E 659 PHE 0.017 0.001 PHE F 267 TYR 0.010 0.001 TYR C 388 ARG 0.006 0.000 ARG L 148 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 324 is missing expected H atoms. Skipping. Evaluate side-chains 1131 residues out of total 4045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 1048 time to evaluate : 4.487 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 MET cc_start: 0.5194 (tmm) cc_final: 0.4932 (tmm) REVERT: C 432 ARG cc_start: 0.8489 (mtp85) cc_final: 0.8251 (ttt90) REVERT: C 458 MET cc_start: 0.6732 (mmt) cc_final: 0.6486 (mmt) REVERT: C 627 ASP cc_start: 0.7495 (OUTLIER) cc_final: 0.7179 (m-30) REVERT: C 711 ASN cc_start: 0.8407 (m-40) cc_final: 0.8089 (m-40) REVERT: D 264 GLU cc_start: 0.7824 (mp0) cc_final: 0.7400 (mp0) REVERT: D 450 LYS cc_start: 0.8206 (OUTLIER) cc_final: 0.7574 (tttt) REVERT: E 307 ILE cc_start: 0.9113 (pt) cc_final: 0.8640 (tt) REVERT: E 366 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7634 (mp0) REVERT: F 240 MET cc_start: 0.4649 (tpp) cc_final: 0.4366 (tpp) REVERT: F 488 VAL cc_start: 0.6984 (OUTLIER) cc_final: 0.6776 (p) REVERT: F 659 HIS cc_start: 0.6919 (m90) cc_final: 0.6649 (m90) REVERT: F 664 LYS cc_start: 0.8530 (pttt) cc_final: 0.8203 (ttpt) REVERT: H 5 MET cc_start: 0.7238 (mmt) cc_final: 0.6783 (mmt) REVERT: H 47 MET cc_start: 0.7941 (mtt) cc_final: 0.7724 (mtt) REVERT: J 78 ASP cc_start: 0.6996 (m-30) cc_final: 0.6640 (m-30) REVERT: K 98 MET cc_start: 0.8174 (tpp) cc_final: 0.7876 (tpp) REVERT: K 128 TYR cc_start: 0.5073 (t80) cc_final: 0.4659 (t80) REVERT: L 149 MET cc_start: 0.6315 (mmp) cc_final: 0.5836 (mmp) REVERT: L 153 MET cc_start: 0.6061 (ttm) cc_final: 0.5731 (ttm) REVERT: M 60 TYR cc_start: 0.7375 (m-80) cc_final: 0.7095 (m-80) REVERT: M 92 MET cc_start: 0.6294 (mmt) cc_final: 0.5887 (mmt) REVERT: M 156 HIS cc_start: 0.6564 (OUTLIER) cc_final: 0.6336 (m170) outliers start: 83 outliers final: 69 residues processed: 1087 average time/residue: 1.1253 time to fit residues: 1915.6432 Evaluate side-chains 1115 residues out of total 4045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 1041 time to evaluate : 4.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 623 ASP Chi-restraints excluded: chain B residue 656 ASP Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 679 SER Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 286 GLU Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain C residue 635 ILE Chi-restraints excluded: chain C residue 657 VAL Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 302 ASP Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain D residue 321 SER Chi-restraints excluded: chain D residue 440 SER Chi-restraints excluded: chain D residue 450 LYS Chi-restraints excluded: chain D residue 531 SER Chi-restraints excluded: chain D residue 722 PHE Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 186 ASP Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 302 ASP Chi-restraints excluded: chain E residue 324 TYR Chi-restraints excluded: chain E residue 331 PHE Chi-restraints excluded: chain E residue 366 GLU Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 629 MET Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 242 ASP Chi-restraints excluded: chain F residue 311 LEU Chi-restraints excluded: chain F residue 327 PHE Chi-restraints excluded: chain F residue 488 VAL Chi-restraints excluded: chain F residue 563 LEU Chi-restraints excluded: chain F residue 612 THR Chi-restraints excluded: chain F residue 692 GLU Chi-restraints excluded: chain F residue 721 LEU Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 128 TYR Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 88 SER Chi-restraints excluded: chain I residue 141 GLU Chi-restraints excluded: chain I residue 142 ILE Chi-restraints excluded: chain I residue 156 HIS Chi-restraints excluded: chain J residue 86 ASP Chi-restraints excluded: chain J residue 88 SER Chi-restraints excluded: chain J residue 141 GLU Chi-restraints excluded: chain K residue 63 ILE Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain L residue 18 ASP Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain L residue 155 LEU Chi-restraints excluded: chain M residue 43 ILE Chi-restraints excluded: chain M residue 58 ASP Chi-restraints excluded: chain M residue 79 THR Chi-restraints excluded: chain M residue 120 MET Chi-restraints excluded: chain M residue 138 HIS Chi-restraints excluded: chain M residue 156 HIS Chi-restraints excluded: chain N residue 24 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 478 random chunks: chunk 445 optimal weight: 20.0000 chunk 52 optimal weight: 9.9990 chunk 263 optimal weight: 10.0000 chunk 337 optimal weight: 30.0000 chunk 261 optimal weight: 5.9990 chunk 389 optimal weight: 10.0000 chunk 258 optimal weight: 10.0000 chunk 460 optimal weight: 20.0000 chunk 288 optimal weight: 50.0000 chunk 280 optimal weight: 8.9990 chunk 212 optimal weight: 2.9990 overall best weight: 7.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 558 HIS ** A 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 GLN ** C 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 558 HIS C 642 ASN ** D 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 730 GLN ** E 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 718 ASN ** H 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 46 GLN J 150 ASN ** L 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.4652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 38343 Z= 0.405 Angle : 0.573 7.707 51789 Z= 0.305 Chirality : 0.041 0.213 5951 Planarity : 0.004 0.076 6683 Dihedral : 9.169 176.137 5368 Min Nonbonded Distance : 1.709 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.57 % Allowed : 16.09 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.12), residues: 4752 helix: 0.51 (0.10), residues: 2403 sheet: -1.31 (0.19), residues: 688 loop : -0.88 (0.15), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 689 HIS 0.010 0.001 HIS E 659 PHE 0.026 0.002 PHE E 263 TYR 0.015 0.001 TYR C 365 ARG 0.009 0.001 ARG H 111 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 324 is missing expected H atoms. Skipping. Evaluate side-chains 1163 residues out of total 4045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 1059 time to evaluate : 4.642 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 MET cc_start: 0.5295 (tmm) cc_final: 0.5007 (tmm) REVERT: C 432 ARG cc_start: 0.8534 (mtp85) cc_final: 0.8289 (ttt90) REVERT: C 458 MET cc_start: 0.6878 (mmt) cc_final: 0.6646 (mmt) REVERT: D 264 GLU cc_start: 0.7927 (mp0) cc_final: 0.7518 (mp0) REVERT: D 450 LYS cc_start: 0.8311 (OUTLIER) cc_final: 0.7662 (tttt) REVERT: D 564 ASP cc_start: 0.8862 (OUTLIER) cc_final: 0.8429 (m-30) REVERT: D 623 ASP cc_start: 0.7279 (OUTLIER) cc_final: 0.6974 (m-30) REVERT: E 307 ILE cc_start: 0.9168 (pt) cc_final: 0.8688 (tt) REVERT: E 366 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7731 (mp0) REVERT: F 240 MET cc_start: 0.4862 (tpp) cc_final: 0.4590 (tpp) REVERT: F 488 VAL cc_start: 0.7132 (OUTLIER) cc_final: 0.6916 (p) REVERT: F 659 HIS cc_start: 0.6907 (m90) cc_final: 0.6638 (m90) REVERT: H 5 MET cc_start: 0.7249 (mmt) cc_final: 0.7010 (mmt) REVERT: H 47 MET cc_start: 0.7982 (mtt) cc_final: 0.7780 (mtt) REVERT: H 74 MET cc_start: 0.7884 (mmp) cc_final: 0.7246 (mmp) REVERT: H 156 HIS cc_start: 0.7030 (OUTLIER) cc_final: 0.6532 (t-90) REVERT: J 78 ASP cc_start: 0.7095 (m-30) cc_final: 0.6737 (m-30) REVERT: K 128 TYR cc_start: 0.5071 (t80) cc_final: 0.4725 (t80) REVERT: L 49 PHE cc_start: 0.7130 (t80) cc_final: 0.6867 (t80) REVERT: L 149 MET cc_start: 0.6270 (mmp) cc_final: 0.5790 (mmp) REVERT: L 153 MET cc_start: 0.6038 (ttm) cc_final: 0.5696 (ttm) REVERT: M 60 TYR cc_start: 0.7398 (m-80) cc_final: 0.7120 (m-80) REVERT: M 92 MET cc_start: 0.6335 (mmt) cc_final: 0.5954 (mmt) outliers start: 104 outliers final: 83 residues processed: 1109 average time/residue: 1.0693 time to fit residues: 1836.1877 Evaluate side-chains 1124 residues out of total 4045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 1035 time to evaluate : 4.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 724 SER Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 276 GLN Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 509 SER Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 623 ASP Chi-restraints excluded: chain B residue 656 ASP Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 679 SER Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain C residue 635 ILE Chi-restraints excluded: chain C residue 657 VAL Chi-restraints excluded: chain C residue 688 ASN Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 302 ASP Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain D residue 321 SER Chi-restraints excluded: chain D residue 440 SER Chi-restraints excluded: chain D residue 450 LYS Chi-restraints excluded: chain D residue 464 ASP Chi-restraints excluded: chain D residue 509 SER Chi-restraints excluded: chain D residue 531 SER Chi-restraints excluded: chain D residue 564 ASP Chi-restraints excluded: chain D residue 623 ASP Chi-restraints excluded: chain D residue 722 PHE Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 186 ASP Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 302 ASP Chi-restraints excluded: chain E residue 324 TYR Chi-restraints excluded: chain E residue 331 PHE Chi-restraints excluded: chain E residue 366 GLU Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 629 MET Chi-restraints excluded: chain E residue 645 ASP Chi-restraints excluded: chain F residue 195 LEU Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 242 ASP Chi-restraints excluded: chain F residue 311 LEU Chi-restraints excluded: chain F residue 327 PHE Chi-restraints excluded: chain F residue 447 ASP Chi-restraints excluded: chain F residue 488 VAL Chi-restraints excluded: chain F residue 504 VAL Chi-restraints excluded: chain F residue 563 LEU Chi-restraints excluded: chain F residue 612 THR Chi-restraints excluded: chain F residue 692 GLU Chi-restraints excluded: chain F residue 721 LEU Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 156 HIS Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 88 SER Chi-restraints excluded: chain I residue 142 ILE Chi-restraints excluded: chain I residue 156 HIS Chi-restraints excluded: chain J residue 88 SER Chi-restraints excluded: chain J residue 141 GLU Chi-restraints excluded: chain K residue 41 ASN Chi-restraints excluded: chain K residue 63 ILE Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain L residue 14 GLU Chi-restraints excluded: chain L residue 16 SER Chi-restraints excluded: chain L residue 17 PHE Chi-restraints excluded: chain L residue 18 ASP Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain L residue 155 LEU Chi-restraints excluded: chain M residue 43 ILE Chi-restraints excluded: chain M residue 58 ASP Chi-restraints excluded: chain M residue 79 THR Chi-restraints excluded: chain M residue 120 MET Chi-restraints excluded: chain S residue 5 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 478 random chunks: chunk 285 optimal weight: 20.0000 chunk 183 optimal weight: 1.9990 chunk 275 optimal weight: 1.9990 chunk 138 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 292 optimal weight: 6.9990 chunk 313 optimal weight: 30.0000 chunk 227 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 362 optimal weight: 8.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 579 GLN ** A 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 ASN ** B 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.4709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 38343 Z= 0.188 Angle : 0.507 7.626 51789 Z= 0.264 Chirality : 0.038 0.155 5951 Planarity : 0.004 0.069 6683 Dihedral : 8.794 174.652 5368 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.00 % Allowed : 16.98 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.12), residues: 4752 helix: 0.79 (0.10), residues: 2406 sheet: -1.19 (0.19), residues: 687 loop : -0.73 (0.15), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 649 HIS 0.009 0.001 HIS E 659 PHE 0.022 0.001 PHE J 30 TYR 0.021 0.001 TYR A 695 ARG 0.009 0.000 ARG I 15 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 324 is missing expected H atoms. Skipping. Evaluate side-chains 1134 residues out of total 4045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 1053 time to evaluate : 4.533 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 MET cc_start: 0.5244 (tmm) cc_final: 0.4972 (tmm) REVERT: A 450 LYS cc_start: 0.7865 (ttpp) cc_final: 0.7640 (ttpp) REVERT: A 456 LEU cc_start: 0.9115 (mt) cc_final: 0.8907 (mp) REVERT: A 704 MET cc_start: 0.6700 (mmm) cc_final: 0.6338 (mmm) REVERT: C 432 ARG cc_start: 0.8485 (mtp85) cc_final: 0.8280 (ttt90) REVERT: C 458 MET cc_start: 0.6834 (mmt) cc_final: 0.6581 (mmt) REVERT: C 627 ASP cc_start: 0.7475 (OUTLIER) cc_final: 0.7179 (m-30) REVERT: D 450 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7574 (tttt) REVERT: E 307 ILE cc_start: 0.9147 (pt) cc_final: 0.8701 (tt) REVERT: E 366 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7584 (mp0) REVERT: F 488 VAL cc_start: 0.7028 (OUTLIER) cc_final: 0.6824 (p) REVERT: F 659 HIS cc_start: 0.6885 (m90) cc_final: 0.6639 (m90) REVERT: F 664 LYS cc_start: 0.8573 (pttp) cc_final: 0.8362 (ttpt) REVERT: H 74 MET cc_start: 0.7803 (mmp) cc_final: 0.7050 (mmp) REVERT: H 156 HIS cc_start: 0.6971 (OUTLIER) cc_final: 0.6521 (t-90) REVERT: J 78 ASP cc_start: 0.6836 (m-30) cc_final: 0.6593 (m-30) REVERT: K 128 TYR cc_start: 0.5046 (t80) cc_final: 0.4596 (t80) REVERT: L 49 PHE cc_start: 0.7005 (t80) cc_final: 0.6776 (t80) REVERT: L 149 MET cc_start: 0.6358 (mmp) cc_final: 0.5878 (mmp) REVERT: L 153 MET cc_start: 0.6057 (ttm) cc_final: 0.5711 (ttm) REVERT: M 60 TYR cc_start: 0.7391 (m-80) cc_final: 0.7087 (m-80) REVERT: M 92 MET cc_start: 0.6309 (mmt) cc_final: 0.5902 (mmt) outliers start: 81 outliers final: 68 residues processed: 1091 average time/residue: 1.0938 time to fit residues: 1861.2411 Evaluate side-chains 1114 residues out of total 4045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 1041 time to evaluate : 4.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 509 SER Chi-restraints excluded: chain B residue 623 ASP Chi-restraints excluded: chain B residue 656 ASP Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 679 SER Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 345 ASP Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain C residue 635 ILE Chi-restraints excluded: chain C residue 657 VAL Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 302 ASP Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain D residue 321 SER Chi-restraints excluded: chain D residue 440 SER Chi-restraints excluded: chain D residue 450 LYS Chi-restraints excluded: chain D residue 509 SER Chi-restraints excluded: chain D residue 531 SER Chi-restraints excluded: chain D residue 722 PHE Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 186 ASP Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 302 ASP Chi-restraints excluded: chain E residue 324 TYR Chi-restraints excluded: chain E residue 366 GLU Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 629 MET Chi-restraints excluded: chain F residue 195 LEU Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 242 ASP Chi-restraints excluded: chain F residue 311 LEU Chi-restraints excluded: chain F residue 327 PHE Chi-restraints excluded: chain F residue 488 VAL Chi-restraints excluded: chain F residue 504 VAL Chi-restraints excluded: chain F residue 612 THR Chi-restraints excluded: chain F residue 692 GLU Chi-restraints excluded: chain F residue 721 LEU Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 156 HIS Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 142 ILE Chi-restraints excluded: chain J residue 65 SER Chi-restraints excluded: chain J residue 88 SER Chi-restraints excluded: chain J residue 141 GLU Chi-restraints excluded: chain J residue 151 GLU Chi-restraints excluded: chain K residue 41 ASN Chi-restraints excluded: chain K residue 63 ILE Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain L residue 16 SER Chi-restraints excluded: chain L residue 17 PHE Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain L residue 155 LEU Chi-restraints excluded: chain M residue 43 ILE Chi-restraints excluded: chain M residue 58 ASP Chi-restraints excluded: chain M residue 79 THR Chi-restraints excluded: chain M residue 120 MET Chi-restraints excluded: chain N residue 24 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 478 random chunks: chunk 419 optimal weight: 9.9990 chunk 441 optimal weight: 20.0000 chunk 402 optimal weight: 6.9990 chunk 429 optimal weight: 20.0000 chunk 258 optimal weight: 3.9990 chunk 187 optimal weight: 6.9990 chunk 337 optimal weight: 30.0000 chunk 131 optimal weight: 8.9990 chunk 387 optimal weight: 4.9990 chunk 406 optimal weight: 10.0000 chunk 427 optimal weight: 3.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 528 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 579 GLN ** A 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 356 GLN ** D 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 730 GLN ** E 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.4850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 38343 Z= 0.305 Angle : 0.539 10.308 51789 Z= 0.282 Chirality : 0.039 0.167 5951 Planarity : 0.004 0.071 6683 Dihedral : 8.823 171.753 5368 Min Nonbonded Distance : 1.732 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.18 % Allowed : 17.18 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.12), residues: 4752 helix: 0.70 (0.10), residues: 2406 sheet: -1.20 (0.19), residues: 687 loop : -0.83 (0.15), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 689 HIS 0.008 0.001 HIS E 659 PHE 0.021 0.001 PHE F 267 TYR 0.019 0.001 TYR A 695 ARG 0.013 0.000 ARG I 15 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 324 is missing expected H atoms. Skipping. Evaluate side-chains 1138 residues out of total 4045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 1050 time to evaluate : 4.537 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 MET cc_start: 0.5296 (tmm) cc_final: 0.4999 (tmm) REVERT: A 704 MET cc_start: 0.6763 (mmm) cc_final: 0.6370 (mmm) REVERT: C 432 ARG cc_start: 0.8513 (mtp85) cc_final: 0.8300 (ttt90) REVERT: C 458 MET cc_start: 0.6874 (mmt) cc_final: 0.6632 (mmt) REVERT: C 675 GLN cc_start: 0.8040 (OUTLIER) cc_final: 0.7524 (tm-30) REVERT: D 264 GLU cc_start: 0.7909 (mp0) cc_final: 0.7466 (mp0) REVERT: D 410 ARG cc_start: 0.7545 (ttp-170) cc_final: 0.7278 (tmm-80) REVERT: D 450 LYS cc_start: 0.8272 (OUTLIER) cc_final: 0.7630 (tttt) REVERT: E 307 ILE cc_start: 0.9170 (pt) cc_final: 0.8728 (tt) REVERT: E 366 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7654 (mp0) REVERT: E 668 GLU cc_start: 0.4851 (OUTLIER) cc_final: 0.3792 (tm-30) REVERT: F 488 VAL cc_start: 0.7044 (OUTLIER) cc_final: 0.6810 (p) REVERT: F 659 HIS cc_start: 0.6918 (m90) cc_final: 0.6674 (m90) REVERT: H 74 MET cc_start: 0.7909 (mmp) cc_final: 0.7275 (mmp) REVERT: H 156 HIS cc_start: 0.7054 (OUTLIER) cc_final: 0.6543 (t-90) REVERT: I 140 ARG cc_start: 0.8149 (mmm-85) cc_final: 0.7927 (mtp-110) REVERT: I 156 HIS cc_start: 0.5515 (OUTLIER) cc_final: 0.5156 (t-90) REVERT: J 78 ASP cc_start: 0.6806 (m-30) cc_final: 0.6597 (m-30) REVERT: K 36 GLU cc_start: 0.6331 (mm-30) cc_final: 0.6010 (tm-30) REVERT: K 61 LEU cc_start: 0.8319 (tp) cc_final: 0.8114 (tp) REVERT: K 98 MET cc_start: 0.8086 (tpp) cc_final: 0.7865 (tpp) REVERT: K 128 TYR cc_start: 0.5166 (t80) cc_final: 0.4714 (t80) REVERT: L 20 TYR cc_start: 0.7194 (m-10) cc_final: 0.6959 (m-80) REVERT: L 149 MET cc_start: 0.6332 (mmp) cc_final: 0.5835 (mmp) REVERT: L 153 MET cc_start: 0.6076 (ttm) cc_final: 0.5727 (ttm) REVERT: M 60 TYR cc_start: 0.7447 (m-80) cc_final: 0.7120 (m-80) REVERT: M 92 MET cc_start: 0.6417 (mmt) cc_final: 0.6009 (mmt) REVERT: N 38 HIS cc_start: 0.7163 (OUTLIER) cc_final: 0.6909 (m-70) outliers start: 88 outliers final: 75 residues processed: 1090 average time/residue: 1.1024 time to fit residues: 1877.8735 Evaluate side-chains 1124 residues out of total 4045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 1041 time to evaluate : 4.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 509 SER Chi-restraints excluded: chain B residue 623 ASP Chi-restraints excluded: chain B residue 656 ASP Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 679 SER Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 345 ASP Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain C residue 635 ILE Chi-restraints excluded: chain C residue 657 VAL Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 688 ASN Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 302 ASP Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain D residue 321 SER Chi-restraints excluded: chain D residue 440 SER Chi-restraints excluded: chain D residue 450 LYS Chi-restraints excluded: chain D residue 509 SER Chi-restraints excluded: chain D residue 531 SER Chi-restraints excluded: chain D residue 722 PHE Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 186 ASP Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 302 ASP Chi-restraints excluded: chain E residue 324 TYR Chi-restraints excluded: chain E residue 366 GLU Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 629 MET Chi-restraints excluded: chain E residue 645 ASP Chi-restraints excluded: chain E residue 668 GLU Chi-restraints excluded: chain F residue 195 LEU Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 242 ASP Chi-restraints excluded: chain F residue 311 LEU Chi-restraints excluded: chain F residue 327 PHE Chi-restraints excluded: chain F residue 447 ASP Chi-restraints excluded: chain F residue 488 VAL Chi-restraints excluded: chain F residue 504 VAL Chi-restraints excluded: chain F residue 612 THR Chi-restraints excluded: chain F residue 692 GLU Chi-restraints excluded: chain F residue 721 LEU Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 108 LYS Chi-restraints excluded: chain H residue 128 TYR Chi-restraints excluded: chain H residue 156 HIS Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 88 SER Chi-restraints excluded: chain I residue 142 ILE Chi-restraints excluded: chain I residue 156 HIS Chi-restraints excluded: chain J residue 65 SER Chi-restraints excluded: chain J residue 88 SER Chi-restraints excluded: chain J residue 141 GLU Chi-restraints excluded: chain K residue 41 ASN Chi-restraints excluded: chain K residue 63 ILE Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain L residue 16 SER Chi-restraints excluded: chain L residue 17 PHE Chi-restraints excluded: chain L residue 18 ASP Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain L residue 155 LEU Chi-restraints excluded: chain M residue 43 ILE Chi-restraints excluded: chain M residue 58 ASP Chi-restraints excluded: chain M residue 79 THR Chi-restraints excluded: chain M residue 120 MET Chi-restraints excluded: chain N residue 5 MET Chi-restraints excluded: chain N residue 24 LEU Chi-restraints excluded: chain N residue 38 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 478 random chunks: chunk 281 optimal weight: 10.0000 chunk 453 optimal weight: 40.0000 chunk 277 optimal weight: 1.9990 chunk 215 optimal weight: 8.9990 chunk 315 optimal weight: 40.0000 chunk 476 optimal weight: 9.9990 chunk 438 optimal weight: 7.9990 chunk 379 optimal weight: 20.0000 chunk 39 optimal weight: 6.9990 chunk 292 optimal weight: 9.9990 chunk 232 optimal weight: 0.8980 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 528 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 579 GLN ** A 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 GLN C 305 ASN ** C 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 356 GLN ** D 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 730 GLN ** E 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 451 ASN ** H 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.4989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 38343 Z= 0.296 Angle : 0.541 9.449 51789 Z= 0.283 Chirality : 0.040 0.158 5951 Planarity : 0.004 0.073 6683 Dihedral : 8.813 166.655 5368 Min Nonbonded Distance : 1.725 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.32 % Allowed : 17.11 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.12), residues: 4752 helix: 0.65 (0.10), residues: 2412 sheet: -1.24 (0.19), residues: 687 loop : -0.84 (0.15), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 689 HIS 0.008 0.001 HIS E 659 PHE 0.023 0.002 PHE F 267 TYR 0.015 0.001 TYR A 695 ARG 0.015 0.000 ARG I 15 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9504 Ramachandran restraints generated. 4752 Oldfield, 0 Emsley, 4752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 324 is missing expected H atoms. Skipping. Evaluate side-chains 1152 residues out of total 4045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 1058 time to evaluate : 4.591 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 MET cc_start: 0.5283 (tmm) cc_final: 0.4996 (tmm) REVERT: A 704 MET cc_start: 0.6791 (mmm) cc_final: 0.6397 (mmm) REVERT: C 279 ASN cc_start: 0.7160 (p0) cc_final: 0.6804 (p0) REVERT: C 432 ARG cc_start: 0.8518 (mtp85) cc_final: 0.8305 (ttt90) REVERT: C 458 MET cc_start: 0.6882 (mmt) cc_final: 0.6632 (mmt) REVERT: C 627 ASP cc_start: 0.7580 (OUTLIER) cc_final: 0.7255 (m-30) REVERT: C 675 GLN cc_start: 0.8044 (OUTLIER) cc_final: 0.7534 (tm-30) REVERT: D 264 GLU cc_start: 0.7899 (mp0) cc_final: 0.7471 (mp0) REVERT: D 410 ARG cc_start: 0.7534 (ttp-170) cc_final: 0.7274 (tmm-80) REVERT: D 450 LYS cc_start: 0.8280 (OUTLIER) cc_final: 0.7631 (tttt) REVERT: E 307 ILE cc_start: 0.9172 (pt) cc_final: 0.8757 (tt) REVERT: E 366 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7631 (mp0) REVERT: E 668 GLU cc_start: 0.4788 (OUTLIER) cc_final: 0.3648 (tm-30) REVERT: F 488 VAL cc_start: 0.7049 (OUTLIER) cc_final: 0.6811 (p) REVERT: F 659 HIS cc_start: 0.6855 (m90) cc_final: 0.6637 (m90) REVERT: H 74 MET cc_start: 0.7923 (mmp) cc_final: 0.7324 (mmp) REVERT: H 156 HIS cc_start: 0.7064 (OUTLIER) cc_final: 0.6583 (t-90) REVERT: I 140 ARG cc_start: 0.8147 (mmm-85) cc_final: 0.7937 (mtp-110) REVERT: I 156 HIS cc_start: 0.5534 (OUTLIER) cc_final: 0.5188 (t-90) REVERT: J 78 ASP cc_start: 0.6831 (m-30) cc_final: 0.6603 (m-30) REVERT: K 36 GLU cc_start: 0.6355 (mm-30) cc_final: 0.6028 (tm-30) REVERT: K 61 LEU cc_start: 0.8316 (tp) cc_final: 0.8116 (tp) REVERT: K 98 MET cc_start: 0.8162 (tpp) cc_final: 0.7952 (tpp) REVERT: L 20 TYR cc_start: 0.7191 (m-10) cc_final: 0.6964 (m-80) REVERT: L 149 MET cc_start: 0.6246 (mmp) cc_final: 0.5771 (mmp) REVERT: L 153 MET cc_start: 0.6034 (ttm) cc_final: 0.5701 (ttm) REVERT: M 60 TYR cc_start: 0.7454 (m-80) cc_final: 0.7112 (m-80) REVERT: M 92 MET cc_start: 0.6434 (mmt) cc_final: 0.6023 (mmt) REVERT: N 38 HIS cc_start: 0.7176 (OUTLIER) cc_final: 0.6926 (m-70) outliers start: 94 outliers final: 77 residues processed: 1099 average time/residue: 1.0817 time to fit residues: 1844.4897 Evaluate side-chains 1131 residues out of total 4045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 1045 time to evaluate : 4.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 509 SER Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 623 ASP Chi-restraints excluded: chain B residue 656 ASP Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 679 SER Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain C residue 635 ILE Chi-restraints excluded: chain C residue 657 VAL Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 688 ASN Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain D residue 321 SER Chi-restraints excluded: chain D residue 440 SER Chi-restraints excluded: chain D residue 450 LYS Chi-restraints excluded: chain D residue 509 SER Chi-restraints excluded: chain D residue 531 SER Chi-restraints excluded: chain D residue 722 PHE Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 186 ASP Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 302 ASP Chi-restraints excluded: chain E residue 324 TYR Chi-restraints excluded: chain E residue 366 GLU Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 629 MET Chi-restraints excluded: chain E residue 645 ASP Chi-restraints excluded: chain E residue 668 GLU Chi-restraints excluded: chain F residue 195 LEU Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 242 ASP Chi-restraints excluded: chain F residue 311 LEU Chi-restraints excluded: chain F residue 327 PHE Chi-restraints excluded: chain F residue 447 ASP Chi-restraints excluded: chain F residue 488 VAL Chi-restraints excluded: chain F residue 504 VAL Chi-restraints excluded: chain F residue 612 THR Chi-restraints excluded: chain F residue 692 GLU Chi-restraints excluded: chain F residue 721 LEU Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 128 TYR Chi-restraints excluded: chain H residue 156 HIS Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 88 SER Chi-restraints excluded: chain I residue 142 ILE Chi-restraints excluded: chain I residue 156 HIS Chi-restraints excluded: chain J residue 65 SER Chi-restraints excluded: chain J residue 86 ASP Chi-restraints excluded: chain J residue 88 SER Chi-restraints excluded: chain J residue 141 GLU Chi-restraints excluded: chain K residue 41 ASN Chi-restraints excluded: chain K residue 63 ILE Chi-restraints excluded: chain K residue 133 THR Chi-restraints excluded: chain K residue 190 THR Chi-restraints excluded: chain L residue 16 SER Chi-restraints excluded: chain L residue 17 PHE Chi-restraints excluded: chain L residue 18 ASP Chi-restraints excluded: chain L residue 34 GLN Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain L residue 155 LEU Chi-restraints excluded: chain M residue 43 ILE Chi-restraints excluded: chain M residue 58 ASP Chi-restraints excluded: chain M residue 79 THR Chi-restraints excluded: chain M residue 120 MET Chi-restraints excluded: chain N residue 5 MET Chi-restraints excluded: chain N residue 24 LEU Chi-restraints excluded: chain N residue 38 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 478 random chunks: chunk 301 optimal weight: 50.0000 chunk 403 optimal weight: 3.9990 chunk 116 optimal weight: 0.4980 chunk 349 optimal weight: 10.0000 chunk 55 optimal weight: 9.9990 chunk 105 optimal weight: 2.9990 chunk 379 optimal weight: 8.9990 chunk 158 optimal weight: 5.9990 chunk 390 optimal weight: 20.0000 chunk 48 optimal weight: 5.9990 chunk 69 optimal weight: 7.9990 overall best weight: 3.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 528 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 579 GLN A 622 GLN ** B 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 718 ASN ** H 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 46 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.191523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.139997 restraints weight = 139761.565| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.23 r_work: 0.3155 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.5038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 38343 Z= 0.241 Angle : 0.525 9.284 51789 Z= 0.273 Chirality : 0.039 0.153 5951 Planarity : 0.004 0.070 6683 Dihedral : 8.688 160.504 5368 Min Nonbonded Distance : 1.740 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.15 % Allowed : 17.63 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.12), residues: 4752 helix: 0.74 (0.10), residues: 2412 sheet: -1.20 (0.19), residues: 686 loop : -0.80 (0.15), residues: 1654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 649 HIS 0.009 0.001 HIS C 288 PHE 0.024 0.001 PHE F 267 TYR 0.018 0.001 TYR N 128 ARG 0.008 0.000 ARG J 118 =============================================================================== Job complete usr+sys time: 26275.04 seconds wall clock time: 450 minutes 10.32 seconds (27010.32 seconds total)