Starting phenix.real_space_refine (version: dev) on Thu Dec 15 06:02:57 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uiw_26555/12_2022/7uiw_26555_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uiw_26555/12_2022/7uiw_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_26555/12_2022/7uiw_26555.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uiw_26555/12_2022/7uiw_26555.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uiw_26555/12_2022/7uiw_26555_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uiw_26555/12_2022/7uiw_26555_trim_updated.pdb" } resolution = 3.33 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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 Convert atoms to be neutral 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: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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: 26.36, per 1000 atoms: 0.35 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: 49.90 Conformation dependent library (CDL) restraints added in 5.1 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: 3.41 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: 26.29 Time building geometry restraints manager: 52.45 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: 29733 35.72 - 71.44: 396 71.44 - 107.15: 43 107.15 - 142.87: 8 142.87 - 178.59: 2 Dihedral angle restraints: 30182 sinusoidal: 14747 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 30179 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 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. 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: 0.330 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: 1.050 Extract box with map and model: 6.780 Check model and map are aligned: 0.840 Convert atoms to be neutral: 0.510 Process input model: 184.320 Find NCS groups from input model: 3.330 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 199.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 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 : 13.742 178.591 14529 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 % 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 *********************** 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 : 4.586 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 outliers start: 1 outliers final: 0 residues processed: 1306 average time/residue: 1.0767 time to fit residues: 2199.3178 Evaluate side-chains 1107 residues out of total 4045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1107 time to evaluate : 4.419 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.8651 ------------------------------------------------------------------------------- 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: 6.9990 chunk 201 optimal weight: 5.9990 chunk 123 optimal weight: 7.9990 chunk 244 optimal weight: 9.9990 chunk 193 optimal weight: 9.9990 chunk 374 optimal weight: 8.9990 chunk 144 optimal weight: 4.9990 chunk 227 optimal weight: 9.9990 chunk 278 optimal weight: 7.9990 chunk 434 optimal weight: 40.0000 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 659 HIS A 675 GLN A 688 ASN B 175 ASN B 209 ASN B 325 GLN B 558 HIS ** C 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 463 GLN C 660 GLN D 233 GLN D 528 HIS ** D 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 642 ASN ** D 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 583 ASN F 718 ASN H 41 ASN I 41 ASN ** I 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 159 GLN ** J 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 150 ASN L 41 ASN L 54 ASN L 156 HIS N 41 ASN N 122 HIS N 150 ASN ** N 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.051 38343 Z= 0.397 Angle : 0.643 11.618 51789 Z= 0.345 Chirality : 0.042 0.197 5951 Planarity : 0.005 0.070 6683 Dihedral : 8.088 179.371 5269 Min Nonbonded Distance : 1.690 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer Outliers : 1.46 % 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: -0.33 (0.11), residues: 4752 helix: 0.65 (0.10), residues: 2366 sheet: -1.62 (0.19), residues: 656 loop : -0.70 (0.14), residues: 1730 *********************** 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 1196 residues out of total 4045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 1137 time to evaluate : 4.541 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 outliers start: 59 outliers final: 49 residues processed: 1166 average time/residue: 1.0747 time to fit residues: 1977.1019 Evaluate side-chains 1090 residues out of total 4045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 1041 time to evaluate : 4.625 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 49 outliers final: 1 residues processed: 49 average time/residue: 0.7629 time to fit residues: 74.4878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 478 random chunks: chunk 241 optimal weight: 9.9990 chunk 134 optimal weight: 5.9990 chunk 361 optimal weight: 40.0000 chunk 295 optimal weight: 20.0000 chunk 119 optimal weight: 4.9990 chunk 434 optimal weight: 20.0000 chunk 469 optimal weight: 0.0030 chunk 387 optimal weight: 9.9990 chunk 431 optimal weight: 5.9990 chunk 148 optimal weight: 3.9990 chunk 348 optimal weight: 10.0000 overall best weight: 4.1998 ------------------------------------------------------------------------------- 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** C 233 GLN C 305 ASN C 325 GLN C 329 ASN C 368 HIS ** C 483 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 342 GLN ** E 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 718 ASN ** H 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 116 ASN ** J 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 41 ASN ** N 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 38343 Z= 0.246 Angle : 0.521 9.240 51789 Z= 0.274 Chirality : 0.039 0.163 5951 Planarity : 0.004 0.063 6683 Dihedral : 7.842 178.227 5269 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer Outliers : 0.77 % 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 (0.12), residues: 4752 helix: 0.79 (0.10), residues: 2374 sheet: -1.46 (0.18), residues: 711 loop : -0.64 (0.14), residues: 1667 *********************** 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 1110 residues out of total 4045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 1079 time to evaluate : 4.571 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 outliers start: 31 outliers final: 19 residues processed: 1087 average time/residue: 1.0698 time to fit residues: 1825.9970 Evaluate side-chains 1049 residues out of total 4045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 1030 time to evaluate : 4.526 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 19 outliers final: 1 residues processed: 19 average time/residue: 0.7603 time to fit residues: 31.7393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 478 random chunks: chunk 429 optimal weight: 40.0000 chunk 326 optimal weight: 30.0000 chunk 225 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 207 optimal weight: 4.9990 chunk 292 optimal weight: 5.9990 chunk 436 optimal weight: 30.0000 chunk 462 optimal weight: 20.0000 chunk 228 optimal weight: 8.9990 chunk 413 optimal weight: 8.9990 chunk 124 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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** B 276 GLN B 606 ASN C 177 ASN C 233 GLN C 329 ASN ** C 483 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** ** F 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 41 ASN K 46 GLN L 94 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.3833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.055 38343 Z= 0.335 Angle : 0.551 7.484 51789 Z= 0.293 Chirality : 0.040 0.173 5951 Planarity : 0.004 0.081 6683 Dihedral : 7.966 177.736 5269 Min Nonbonded Distance : 1.735 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer Outliers : 1.24 % 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: -0.32 (0.12), residues: 4752 helix: 0.63 (0.10), residues: 2388 sheet: -1.40 (0.18), residues: 709 loop : -0.72 (0.14), residues: 1655 *********************** 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 1124 residues out of total 4045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 1074 time to evaluate : 4.607 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 outliers start: 50 outliers final: 38 residues processed: 1089 average time/residue: 1.0590 time to fit residues: 1815.9441 Evaluate side-chains 1070 residues out of total 4045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 1032 time to evaluate : 4.448 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 3 residues processed: 38 average time/residue: 0.7003 time to fit residues: 54.9302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 478 random chunks: chunk 384 optimal weight: 20.0000 chunk 262 optimal weight: 10.0000 chunk 6 optimal weight: 30.0000 chunk 344 optimal weight: 20.0000 chunk 190 optimal weight: 0.9980 chunk 394 optimal weight: 4.9990 chunk 319 optimal weight: 5.9990 chunk 0 optimal weight: 40.0000 chunk 235 optimal weight: 4.9990 chunk 414 optimal weight: 30.0000 chunk 116 optimal weight: 0.7980 overall best weight: 3.5586 ------------------------------------------------------------------------------- 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 483 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 356 GLN ** D 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 642 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** ** J 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.4030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 38343 Z= 0.217 Angle : 0.500 6.938 51789 Z= 0.261 Chirality : 0.038 0.155 5951 Planarity : 0.004 0.070 6683 Dihedral : 7.821 178.317 5269 Min Nonbonded Distance : 1.763 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer Outliers : 0.77 % 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: -0.11 (0.12), residues: 4752 helix: 0.84 (0.10), residues: 2387 sheet: -1.33 (0.18), residues: 686 loop : -0.69 (0.14), residues: 1679 *********************** 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 1080 residues out of total 4045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 1049 time to evaluate : 4.605 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 outliers start: 31 outliers final: 21 residues processed: 1061 average time/residue: 1.0631 time to fit residues: 1772.9243 Evaluate side-chains 1054 residues out of total 4045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 1033 time to evaluate : 4.485 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 4 residues processed: 21 average time/residue: 0.7851 time to fit residues: 35.0896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 271 optimal weight: 3.9990 chunk 114 optimal weight: 6.9990 chunk 462 optimal weight: 10.0000 chunk 383 optimal weight: 10.0000 chunk 214 optimal weight: 6.9990 chunk 38 optimal weight: 10.0000 chunk 152 optimal weight: 7.9990 chunk 242 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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 171 ASN ** B 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 GLN C 483 HIS ** 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** ** H 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 46 GLN ** J 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.4363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.059 38343 Z= 0.345 Angle : 0.545 6.976 51789 Z= 0.288 Chirality : 0.040 0.177 5951 Planarity : 0.004 0.073 6683 Dihedral : 8.008 179.727 5269 Min Nonbonded Distance : 1.713 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer Outliers : 1.31 % 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: -0.26 (0.12), residues: 4752 helix: 0.68 (0.10), residues: 2395 sheet: -1.31 (0.19), residues: 680 loop : -0.75 (0.14), residues: 1677 *********************** 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 1121 residues out of total 4045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 1068 time to evaluate : 5.108 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 outliers start: 53 outliers final: 38 residues processed: 1092 average time/residue: 1.0498 time to fit residues: 1793.9422 Evaluate side-chains 1083 residues out of total 4045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 1045 time to evaluate : 4.535 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 5 residues processed: 38 average time/residue: 0.7036 time to fit residues: 54.7788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 263 optimal weight: 9.9990 chunk 337 optimal weight: 50.0000 chunk 261 optimal weight: 2.9990 chunk 389 optimal weight: 9.9990 chunk 258 optimal weight: 9.9990 chunk 460 optimal weight: 20.0000 chunk 288 optimal weight: 1.9990 chunk 280 optimal weight: 10.0000 chunk 212 optimal weight: 0.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 GLN D 356 GLN ** E 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 718 ASN H 34 GLN ** H 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.4527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 38343 Z= 0.260 Angle : 0.517 6.377 51789 Z= 0.271 Chirality : 0.039 0.155 5951 Planarity : 0.004 0.073 6683 Dihedral : 7.893 173.803 5269 Min Nonbonded Distance : 1.725 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer Outliers : 0.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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 (0.12), residues: 4752 helix: 0.76 (0.10), residues: 2400 sheet: -1.30 (0.18), residues: 699 loop : -0.71 (0.15), residues: 1653 *********************** 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 1084 residues out of total 4045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 1056 time to evaluate : 4.470 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 outliers start: 28 outliers final: 24 residues processed: 1063 average time/residue: 1.0587 time to fit residues: 1759.0614 Evaluate side-chains 1067 residues out of total 4045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 1043 time to evaluate : 4.424 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 5 residues processed: 24 average time/residue: 0.7261 time to fit residues: 37.2100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 478 random chunks: chunk 285 optimal weight: 8.9990 chunk 183 optimal weight: 3.9990 chunk 275 optimal weight: 5.9990 chunk 138 optimal weight: 7.9990 chunk 90 optimal weight: 4.9990 chunk 89 optimal weight: 0.7980 chunk 292 optimal weight: 2.9990 chunk 313 optimal weight: 20.0000 chunk 227 optimal weight: 9.9990 chunk 42 optimal weight: 6.9990 chunk 362 optimal weight: 10.0000 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 ASN ** B 579 GLN ** 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** ** J 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.4617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 38343 Z= 0.232 Angle : 0.510 6.520 51789 Z= 0.265 Chirality : 0.039 0.149 5951 Planarity : 0.004 0.073 6683 Dihedral : 7.803 173.208 5269 Min Nonbonded Distance : 1.738 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer Outliers : 0.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.12), residues: 4752 helix: 0.84 (0.10), residues: 2399 sheet: -1.20 (0.19), residues: 697 loop : -0.70 (0.15), residues: 1656 *********************** 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 1087 residues out of total 4045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 1063 time to evaluate : 4.528 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 outliers start: 24 outliers final: 16 residues processed: 1069 average time/residue: 1.0788 time to fit residues: 1807.3542 Evaluate side-chains 1057 residues out of total 4045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 1041 time to evaluate : 4.480 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 5 residues processed: 16 average time/residue: 0.7329 time to fit residues: 26.8734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 478 random chunks: chunk 419 optimal weight: 2.9990 chunk 441 optimal weight: 6.9990 chunk 402 optimal weight: 8.9990 chunk 429 optimal weight: 30.0000 chunk 258 optimal weight: 0.9990 chunk 187 optimal weight: 4.9990 chunk 337 optimal weight: 50.0000 chunk 131 optimal weight: 6.9990 chunk 387 optimal weight: 9.9990 chunk 406 optimal weight: 10.0000 chunk 427 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 GLN C 279 ASN D 730 GLN ** E 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 150 ASN ** M 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.4725 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= 0.234 Angle : 0.516 6.468 51789 Z= 0.269 Chirality : 0.039 0.152 5951 Planarity : 0.004 0.074 6683 Dihedral : 7.755 173.134 5269 Min Nonbonded Distance : 1.739 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer Outliers : 0.72 % 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: 0.86 (0.10), residues: 2399 sheet: -1.15 (0.19), residues: 685 loop : -0.72 (0.15), residues: 1668 *********************** 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 1077 residues out of total 4045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 1048 time to evaluate : 4.522 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 outliers start: 29 outliers final: 21 residues processed: 1058 average time/residue: 1.0858 time to fit residues: 1803.2771 Evaluate side-chains 1057 residues out of total 4045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 1036 time to evaluate : 4.471 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 5 residues processed: 21 average time/residue: 0.7812 time to fit residues: 34.6765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 478 random chunks: chunk 281 optimal weight: 8.9990 chunk 453 optimal weight: 40.0000 chunk 277 optimal weight: 2.9990 chunk 215 optimal weight: 7.9990 chunk 315 optimal weight: 20.0000 chunk 476 optimal weight: 9.9990 chunk 438 optimal weight: 1.9990 chunk 379 optimal weight: 2.9990 chunk 39 optimal weight: 0.0970 chunk 292 optimal weight: 5.9990 chunk 232 optimal weight: 0.8980 overall best weight: 1.7984 ------------------------------------------------------------------------------- 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 ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 156 HIS ** J 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.4755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 38343 Z= 0.167 Angle : 0.503 6.854 51789 Z= 0.259 Chirality : 0.038 0.147 5951 Planarity : 0.004 0.067 6683 Dihedral : 7.567 169.085 5269 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer Outliers : 0.27 % 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: 1.03 (0.11), residues: 2398 sheet: -1.05 (0.19), residues: 695 loop : -0.66 (0.15), residues: 1659 ********************** 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 1056 residues out of total 4045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 1045 time to evaluate : 4.526 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 outliers start: 11 outliers final: 7 residues processed: 1051 average time/residue: 1.0463 time to fit residues: 1729.5094 Evaluate side-chains 1033 residues out of total 4045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 1026 time to evaluate : 4.481 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 7 average time/residue: 0.7625 time to fit residues: 15.3667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 116 optimal weight: 1.9990 chunk 349 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 chunk 105 optimal weight: 2.9990 chunk 379 optimal weight: 20.0000 chunk 158 optimal weight: 7.9990 chunk 390 optimal weight: 7.9990 chunk 48 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 579 GLN ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 GLN C 279 ASN ** E 369 HIS ** 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 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.194380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.143888 restraints weight = 139296.374| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.17 r_work: 0.3154 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.4846 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= 0.233 Angle : 0.515 9.474 51789 Z= 0.267 Chirality : 0.039 0.148 5951 Planarity : 0.004 0.068 6683 Dihedral : 7.597 174.187 5269 Min Nonbonded Distance : 1.750 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer Outliers : 0.42 % 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: 0.12 (0.12), residues: 4752 helix: 1.02 (0.10), residues: 2399 sheet: -1.05 (0.19), residues: 695 loop : -0.67 (0.15), residues: 1658 =============================================================================== Job complete usr+sys time: 25122.59 seconds wall clock time: 431 minutes 49.89 seconds (25909.89 seconds total)