Starting phenix.real_space_refine (version: dev) on Thu Dec 15 06:36:42 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uiv_26554/12_2022/7uiv_26554_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uiv_26554/12_2022/7uiv_26554.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uiv_26554/12_2022/7uiv_26554.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uiv_26554/12_2022/7uiv_26554.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uiv_26554/12_2022/7uiv_26554_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uiv_26554/12_2022/7uiv_26554_trim_updated.pdb" } resolution = 3.38 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 GLU 194": "OE1" <-> "OE2" Residue "A GLU 215": "OE1" <-> "OE2" Residue "A ASP 235": "OD1" <-> "OD2" Residue "A ASP 249": "OD1" <-> "OD2" Residue "A TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 262": "OD1" <-> "OD2" Residue "A PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 264": "OE1" <-> "OE2" Residue "A GLU 275": "OE1" <-> "OE2" Residue "A ASP 277": "OD1" <-> "OD2" Residue "A PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 302": "OD1" <-> "OD2" Residue "A GLU 332": "OE1" <-> "OE2" Residue "A ASP 334": "OD1" <-> "OD2" Residue "A GLU 352": "OE1" <-> "OE2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 370": "OD1" <-> "OD2" Residue "A ASP 396": "OD1" <-> "OD2" Residue "A ASP 403": "OD1" <-> "OD2" Residue "A GLU 438": "OE1" <-> "OE2" Residue "A ASP 445": "OD1" <-> "OD2" Residue "A ASP 454": "OD1" <-> "OD2" Residue "A GLU 484": "OE1" <-> "OE2" Residue "A PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 493": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 515": "OE1" <-> "OE2" Residue "A ASP 520": "OD1" <-> "OD2" Residue "A GLU 523": "OE1" <-> "OE2" Residue "A ASP 551": "OD1" <-> "OD2" Residue "A GLU 565": "OE1" <-> "OE2" Residue "A ASP 572": "OD1" <-> "OD2" Residue "A ASP 588": "OD1" <-> "OD2" Residue "A ASP 674": "OD1" <-> "OD2" Residue "A GLU 681": "OE1" <-> "OE2" Residue "A ASP 710": "OD1" <-> "OD2" Residue "A ASP 727": "OD1" <-> "OD2" Residue "A GLU 741": "OE1" <-> "OE2" Residue "B GLU 170": "OE1" <-> "OE2" Residue "B PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 235": "OD1" <-> "OD2" 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 PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 264": "OE1" <-> "OE2" Residue "B ASP 345": "OD1" <-> "OD2" Residue "B GLU 366": "OE1" <-> "OE2" Residue "B ASP 391": "OD1" <-> "OD2" Residue "B ASP 400": "OD1" <-> "OD2" Residue "B ASP 447": "OD1" <-> "OD2" Residue "B PHE 461": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 515": "OE1" <-> "OE2" Residue "B PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 567": "OE1" <-> "OE2" Residue "B GLU 630": "OE1" <-> "OE2" Residue "B PHE 640": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 674": "OD1" <-> "OD2" Residue "B GLU 681": "OE1" <-> "OE2" Residue "C ASP 186": "OD1" <-> "OD2" Residue "C ASP 277": "OD1" <-> "OD2" Residue "C GLU 326": "OE1" <-> "OE2" Residue "C PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 334": "OD1" <-> "OD2" Residue "C PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 370": "OD1" <-> "OD2" Residue "C GLU 438": "OE1" <-> "OE2" Residue "C PHE 461": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 515": "OE1" <-> "OE2" Residue "C PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 544": "OD1" <-> "OD2" Residue "C GLU 565": "OE1" <-> "OE2" Residue "C GLU 567": "OE1" <-> "OE2" Residue "C GLU 613": "OE1" <-> "OE2" Residue "C ASP 627": "OD1" <-> "OD2" Residue "C PHE 640": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 668": "OE1" <-> "OE2" Residue "C GLU 685": "OE1" <-> "OE2" Residue "D ASP 242": "OD1" <-> "OD2" Residue "D ASP 262": "OD1" <-> "OD2" Residue "D GLU 326": "OE1" <-> "OE2" Residue "D ASP 345": "OD1" <-> "OD2" Residue "D ASP 370": "OD1" <-> "OD2" Residue "D ASP 400": "OD1" <-> "OD2" Residue "D GLU 427": "OE1" <-> "OE2" Residue "D PHE 461": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 520": "OD1" <-> "OD2" Residue "D TYR 524": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 613": "OE1" <-> "OE2" Residue "D ASP 627": "OD1" <-> "OD2" Residue "D PHE 636": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 674": "OD1" <-> "OD2" Residue "D ASP 710": "OD1" <-> "OD2" Residue "E ASP 235": "OD1" <-> "OD2" Residue "E ASP 249": "OD1" <-> "OD2" Residue "E ASP 262": "OD1" <-> "OD2" Residue "E PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 326": "OE1" <-> "OE2" Residue "E ASP 345": "OD1" <-> "OD2" Residue "E ASP 370": "OD1" <-> "OD2" Residue "E GLU 383": "OE1" <-> "OE2" Residue "E ASP 400": "OD1" <-> "OD2" Residue "E ASP 425": "OD1" <-> "OD2" Residue "E GLU 427": "OE1" <-> "OE2" Residue "E GLU 438": "OE1" <-> "OE2" Residue "E ASP 445": "OD1" <-> "OD2" Residue "E ASP 464": "OD1" <-> "OD2" Residue "E PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 565": "OE1" <-> "OE2" Residue "E GLU 567": "OE1" <-> "OE2" Residue "E ASP 572": "OD1" <-> "OD2" Residue "E PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 595": "OD1" <-> "OD2" Residue "E ASP 627": "OD1" <-> "OD2" Residue "E GLU 631": "OE1" <-> "OE2" Residue "E PHE 636": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 656": "OD1" <-> "OD2" Residue "E ASP 663": "OD1" <-> "OD2" Residue "E GLU 668": "OE1" <-> "OE2" Residue "E ARG 702": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ASP 727": "OD1" <-> "OD2" Residue "E ASP 736": "OD1" <-> "OD2" 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 GLU 194": "OE1" <-> "OE2" Residue "F TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 249": "OD1" <-> "OD2" Residue "F ASP 262": "OD1" <-> "OD2" Residue "F GLU 264": "OE1" <-> "OE2" Residue "F ASP 285": "OD1" <-> "OD2" Residue "F GLU 326": "OE1" <-> "OE2" Residue "F ASP 334": "OD1" <-> "OD2" Residue "F ASP 370": "OD1" <-> "OD2" Residue "F GLU 383": "OE1" <-> "OE2" Residue "F ASP 400": "OD1" <-> "OD2" Residue "F ASP 403": "OD1" <-> "OD2" Residue "F GLU 404": "OE1" <-> "OE2" Residue "F GLU 427": "OE1" <-> "OE2" Residue "F ASP 445": "OD1" <-> "OD2" Residue "F GLU 484": "OE1" <-> "OE2" Residue "F PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 520": "OD1" <-> "OD2" Residue "F TYR 524": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 526": "OE1" <-> "OE2" Residue "F ASP 551": "OD1" <-> "OD2" Residue "F GLU 565": "OE1" <-> "OE2" Residue "F ASP 572": "OD1" <-> "OD2" Residue "F ASP 582": "OD1" <-> "OD2" Residue "F ASP 588": "OD1" <-> "OD2" Residue "F ASP 595": "OD1" <-> "OD2" Residue "F GLU 611": "OE1" <-> "OE2" Residue "F GLU 613": "OE1" <-> "OE2" Residue "F ASP 623": "OD1" <-> "OD2" Residue "F GLU 631": "OE1" <-> "OE2" Residue "F PHE 636": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 645": "OD1" <-> "OD2" Residue "F PHE 650": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 663": "OD1" <-> "OD2" Residue "F PHE 665": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 668": "OE1" <-> "OE2" Residue "F ASP 674": "OD1" <-> "OD2" Residue "F ASP 696": "OD1" <-> "OD2" Residue "F ASP 710": "OD1" <-> "OD2" Residue "F ASP 736": "OD1" <-> "OD2" Residue "S ASP 6": "OD1" <-> "OD2" Residue "S GLU 16": "OE1" <-> "OE2" Residue "H GLU 8": "OE1" <-> "OE2" Residue "H ARG 12": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ASP 37": "OD1" <-> "OD2" Residue "H GLU 51": "OE1" <-> "OE2" Residue "H GLU 56": "OE1" <-> "OE2" Residue "H ASP 78": "OD1" <-> "OD2" Residue "H PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 136": "OE1" <-> "OE2" Residue "H ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H GLU 151": "OE1" <-> "OE2" Residue "H GLU 162": "OE1" <-> "OE2" Residue "H GLU 165": "OE1" <-> "OE2" 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 GLU 181": "OE1" <-> "OE2" Residue "I GLU 8": "OE1" <-> "OE2" Residue "I ARG 12": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ASP 37": "OD1" <-> "OD2" Residue "I TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 ASP 134": "OD1" <-> "OD2" Residue "I ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I GLU 162": "OE1" <-> "OE2" Residue "I ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ASP 167": "OD1" <-> "OD2" Residue "I GLU 169": "OE1" <-> "OE2" Residue "I ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ASP 171": "OD1" <-> "OD2" Residue "I GLU 181": "OE1" <-> "OE2" Residue "I TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J ARG 12": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ASP 18": "OD1" <-> "OD2" Residue "J ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ASP 37": "OD1" <-> "OD2" Residue "J TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J ASP 134": "OD1" <-> "OD2" Residue "J GLU 136": "OE1" <-> "OE2" Residue "J ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J GLU 151": "OE1" <-> "OE2" Residue "J ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J GLU 169": "OE1" <-> "OE2" Residue "J ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J GLU 178": "OE1" <-> "OE2" Residue "J GLU 181": "OE1" <-> "OE2" Residue "J TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K GLU 8": "OE1" <-> "OE2" Residue "K ARG 12": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ASP 18": "OD1" <-> "OD2" 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 GLU 56": "OE1" <-> "OE2" Residue "K TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ASP 78": "OD1" <-> "OD2" Residue "K GLU 136": "OE1" <-> "OE2" Residue "K ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K GLU 151": "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 ASP 186": "OD1" <-> "OD2" Residue "L ARG 12": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ASP 18": "OD1" <-> "OD2" Residue "L ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ARG 118": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L GLU 136": "OE1" <-> "OE2" Residue "L ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L GLU 151": "OE1" <-> "OE2" Residue "L ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M GLU 8": "OE1" <-> "OE2" Residue "M ARG 12": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M GLU 14": "OE1" <-> "OE2" Residue "M PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M GLU 26": "OE1" <-> "OE2" Residue "M ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M GLU 51": "OE1" <-> "OE2" Residue "M ASP 78": "OD1" <-> "OD2" Residue "M PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M ASP 134": "OD1" <-> "OD2" Residue "M GLU 136": "OE1" <-> "OE2" Residue "M ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M GLU 151": "OE1" <-> "OE2" Residue "M GLU 165": "OE1" <-> "OE2" Residue "M ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ASP 167": "OD1" <-> "OD2" Residue "M GLU 169": "OE1" <-> "OE2" Residue "M ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M GLU 178": "OE1" <-> "OE2" Residue "M TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N GLU 8": "OE1" <-> "OE2" Residue "N ARG 12": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N GLU 14": "OE1" <-> "OE2" Residue "N TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N GLU 56": "OE1" <-> "OE2" Residue "N TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N ASP 78": "OD1" <-> "OD2" Residue "N PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N GLU 136": "OE1" <-> "OE2" Residue "N ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N GLU 162": "OE1" <-> "OE2" Residue "N GLU 165": "OE1" <-> "OE2" Residue "N ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ASP 167": "OD1" <-> "OD2" Residue "N GLU 169": "OE1" <-> "OE2" Residue "N ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 76152 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 8908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 561, 8908 Classifications: {'peptide': 561} Link IDs: {'PTRANS': 18, 'TRANS': 542} Chain breaks: 2 Chain: "B" 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: "C" Number of atoms: 9191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 9191 Classifications: {'peptide': 583} Link IDs: {'PTRANS': 18, 'TRANS': 564} 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: 9133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 9133 Classifications: {'peptide': 579} Link IDs: {'PTRANS': 18, 'TRANS': 560} Chain: "F" Number of atoms: 9006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 567, 9006 Classifications: {'peptide': 567} Link IDs: {'PTRANS': 18, 'TRANS': 548} Chain breaks: 1 Chain: "S" Number of atoms: 294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 294 Classifications: {'peptide': 18} Link IDs: {'PTRANS': 2, 'TRANS': 15} Chain breaks: 1 Chain: "H" Number of atoms: 3002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 3002 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 7, 'TRANS': 183} Chain: "I" Number of atoms: 3002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 3002 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 7, 'TRANS': 183} Chain: "J" Number of atoms: 3002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 3002 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 7, 'TRANS': 183} Chain: "K" Number of atoms: 3002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 3002 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 7, 'TRANS': 183} Chain: "L" Number of atoms: 3002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 3002 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 7, 'TRANS': 183} Chain: "M" Number of atoms: 3002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 3002 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 7, 'TRANS': 183} 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: "A" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'AGS': 1} 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: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 2, 'ADP': 1, 'AGS': 1} 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} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 27.09, per 1000 atoms: 0.36 Number of scatterers: 76152 At special positions: 0 Unit cell: (152.25, 149.64, 163.56, 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 169 16.00 P 29 15.00 Mg 7 11.99 O 7206 8.00 N 6708 7.00 C 23781 6.00 H 38252 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: 53.46 Conformation dependent library (CDL) restraints added in 5.5 seconds 9538 Ramachandran restraints generated. 4769 Oldfield, 0 Emsley, 4769 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8892 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 224 helices and 46 sheets defined 49.2% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.13 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: 3.539A pdb=" N ALA A 228 " --> pdb=" O ALA A 224 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 254 No H-bonds generated for 'chain 'A' and resid 251 through 254' Processing helix chain 'A' and resid 262 through 274 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 301 through 312 removed outlier: 3.542A 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 331 removed outlier: 3.614A pdb=" N ASN A 329 " --> pdb=" O GLN A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 340 Processing helix chain 'A' and resid 351 through 369 removed outlier: 3.523A pdb=" N GLN A 356 " --> pdb=" O GLU A 352 " (cutoff:3.500A) Proline residue: A 363 - end of helix Processing helix chain 'A' and resid 375 through 388 Processing helix chain 'A' and resid 394 through 411 Processing helix chain 'A' and resid 423 through 434 removed outlier: 3.604A pdb=" N SER A 428 " --> pdb=" O ALA A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 459 removed outlier: 3.674A pdb=" N GLY A 453 " --> pdb=" O LEU A 449 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N ASP A 454 " --> pdb=" O LYS A 450 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG A 455 " --> pdb=" O ASN A 451 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU A 456 " --> pdb=" O LEU A 452 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N LYS A 457 " --> pdb=" O GLY A 453 " (cutoff:3.500A) removed outlier: 3.606A 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: 3.706A pdb=" N THR A 505 " --> pdb=" O LYS A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 533 Processing helix chain 'A' and resid 549 through 555 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 Processing helix chain 'A' and resid 607 through 609 No H-bonds generated for 'chain 'A' and resid 607 through 609' Processing helix chain 'A' and resid 630 through 635 Processing helix chain 'A' and resid 638 through 643 Processing helix chain 'A' and resid 655 through 676 removed outlier: 3.578A pdb=" N GLN A 660 " --> pdb=" O ASP A 656 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP A 663 " --> pdb=" O HIS A 659 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLN A 675 " --> pdb=" O VAL A 671 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LYS A 676 " --> pdb=" O GLN A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 684 through 693 removed outlier: 3.520A pdb=" N ASN A 688 " --> pdb=" O GLN A 684 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 711 removed outlier: 3.801A pdb=" N ARG A 706 " --> pdb=" O ARG A 702 " (cutoff:3.500A) 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: 3.838A pdb=" N ALA B 228 " --> pdb=" O ALA B 224 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TRP B 229 " --> pdb=" O GLU B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 241 No H-bonds generated for 'chain 'B' and resid 238 through 241' Processing helix chain 'B' and resid 250 through 254 Processing helix chain 'B' and resid 262 through 277 Processing helix chain 'B' and resid 289 through 291 No H-bonds generated for 'chain 'B' and resid 289 through 291' 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 Proline residue: B 363 - end of helix Processing helix chain 'B' and resid 375 through 388 Processing helix chain 'B' and resid 394 through 412 removed outlier: 3.613A pdb=" N VAL B 401 " --> pdb=" O LYS B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 434 Processing helix chain 'B' and resid 443 through 450 removed outlier: 3.575A 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 528 through 534 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: 3.623A pdb=" N GLN B 579 " --> pdb=" O ASN B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 610 through 613 No H-bonds generated for 'chain 'B' and resid 610 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 676 removed outlier: 3.724A pdb=" N LYS B 676 " --> pdb=" O GLN B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 684 through 694 Processing helix chain 'B' and resid 702 through 711 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: 3.573A pdb=" N ALA C 224 " --> pdb=" O LYS C 220 " (cutoff:3.500A) removed outlier: 4.123A 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 253 No H-bonds generated for 'chain 'C' and resid 250 through 253' Processing helix chain 'C' and resid 262 through 277 Processing helix chain 'C' and resid 287 through 292 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: 3.601A 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 removed outlier: 3.540A pdb=" N HIS C 368 " --> pdb=" O LYS C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 388 Processing helix chain 'C' and resid 394 through 411 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 501 through 512 removed outlier: 3.538A pdb=" N THR C 505 " --> pdb=" O LYS C 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 528 through 534 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 576 Processing helix chain 'C' and resid 578 through 582 Processing helix chain 'C' and resid 609 through 613 Processing helix chain 'C' and resid 625 through 635 removed outlier: 3.961A pdb=" N MET C 629 " --> pdb=" O SER C 625 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU C 630 " --> pdb=" O THR C 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 638 through 643 Processing helix chain 'C' and resid 655 through 676 removed outlier: 3.533A pdb=" N GLN C 660 " --> pdb=" O ASP C 656 " (cutoff:3.500A) removed outlier: 3.984A 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: 3.713A pdb=" N ARG C 706 " --> pdb=" O ARG C 702 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 721 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 182 removed outlier: 3.502A pdb=" N VAL D 182 " --> pdb=" O GLN D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 202 Processing helix chain 'D' and resid 220 through 233 removed outlier: 4.167A pdb=" N ALA D 228 " --> pdb=" O ALA D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 254 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: 3.673A pdb=" N ARG D 340 " --> pdb=" O ALA D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 369 removed outlier: 3.928A 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 412 Processing helix chain 'D' and resid 423 through 432 Processing helix chain 'D' and resid 440 through 442 No H-bonds generated for 'chain 'D' and resid 440 through 442' Processing helix chain 'D' and resid 446 through 459 removed outlier: 4.353A pdb=" N GLY D 453 " --> pdb=" O LEU D 449 " (cutoff:3.500A) removed outlier: 4.681A 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 501 through 512 removed outlier: 3.976A pdb=" N THR D 505 " --> pdb=" O LYS D 501 " (cutoff:3.500A) Processing helix chain 'D' and resid 527 through 534 Processing helix chain 'D' and resid 548 through 555 Processing helix chain 'D' and resid 571 through 583 removed outlier: 3.661A pdb=" N GLN D 579 " --> pdb=" O ILE D 576 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ASN D 583 " --> pdb=" O VAL D 580 " (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 643 Processing helix chain 'D' and resid 655 through 676 removed outlier: 3.645A pdb=" N LYS D 676 " --> pdb=" O GLN D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 684 through 693 Processing helix chain 'D' and resid 702 through 711 removed outlier: 3.510A pdb=" N ARG D 706 " --> pdb=" O ARG D 702 " (cutoff:3.500A) Processing helix chain 'D' and resid 713 through 721 removed outlier: 3.578A pdb=" N ASN D 718 " --> pdb=" O LYS D 714 " (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 removed outlier: 3.568A pdb=" N VAL E 182 " --> pdb=" O GLN E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 192 through 202 Processing helix chain 'E' and resid 220 through 232 removed outlier: 3.818A pdb=" N ALA E 224 " --> pdb=" O LYS E 220 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA E 228 " --> pdb=" O ALA E 224 " (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 287 through 293 removed outlier: 3.513A pdb=" N ILE E 291 " --> pdb=" O HIS E 288 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA E 293 " --> pdb=" O ILE E 290 " (cutoff:3.500A) 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: 3.697A pdb=" N ARG E 340 " --> pdb=" O ALA E 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 369 Proline residue: E 363 - end of helix Processing helix chain 'E' and resid 375 through 388 removed outlier: 3.531A pdb=" N VAL E 382 " --> pdb=" O VAL E 378 " (cutoff:3.500A) Processing helix chain 'E' and resid 394 through 412 removed outlier: 3.505A pdb=" N GLY E 406 " --> pdb=" O ILE E 402 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA E 407 " --> pdb=" O ASP E 403 " (cutoff:3.500A) Processing helix chain 'E' and resid 423 through 434 Processing helix chain 'E' and resid 446 through 450 Processing helix chain 'E' and resid 452 through 458 removed outlier: 3.602A pdb=" N MET E 458 " --> pdb=" O ASP E 454 " (cutoff:3.500A) Processing helix chain 'E' and resid 464 through 478 Processing helix chain 'E' and resid 501 through 512 removed outlier: 3.901A pdb=" N THR E 505 " --> pdb=" O LYS E 501 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS E 510 " --> pdb=" O VAL E 506 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA E 511 " --> pdb=" O GLN E 507 " (cutoff:3.500A) Processing helix chain 'E' and resid 527 through 534 removed outlier: 3.510A pdb=" N ILE E 534 " --> pdb=" O SER E 531 " (cutoff:3.500A) Processing helix chain 'E' and resid 548 through 555 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 583 removed outlier: 3.875A pdb=" N GLN E 579 " --> pdb=" O ASN E 575 " (cutoff:3.500A) Processing helix chain 'E' and resid 608 through 613 removed outlier: 3.519A pdb=" N THR E 612 " --> pdb=" O GLY E 608 " (cutoff:3.500A) Processing helix chain 'E' and resid 627 through 635 Processing helix chain 'E' and resid 638 through 643 removed outlier: 3.546A pdb=" N ARG E 643 " --> pdb=" O GLU E 639 " (cutoff:3.500A) Processing helix chain 'E' and resid 655 through 676 Processing helix chain 'E' and resid 684 through 694 Processing helix chain 'E' and resid 702 through 711 removed outlier: 3.688A pdb=" N ALA E 705 " --> pdb=" O ARG E 702 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL E 707 " --> pdb=" O MET E 704 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE E 708 " --> pdb=" O ALA E 705 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP E 710 " --> pdb=" O VAL E 707 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASN E 711 " --> pdb=" O ILE E 708 " (cutoff:3.500A) Processing helix chain 'E' and resid 713 through 721 removed outlier: 3.540A pdb=" N ASN E 718 " --> pdb=" O LYS E 714 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU E 719 " --> pdb=" O PRO E 715 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 182 Processing helix chain 'F' and resid 192 through 202 Processing helix chain 'F' and resid 220 through 233 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 254 Processing helix chain 'F' and resid 262 through 276 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 306 through 313 Processing helix chain 'F' and resid 324 through 329 Processing helix chain 'F' and resid 335 through 340 Processing helix chain 'F' and resid 351 through 369 Proline residue: F 363 - end of helix Processing helix chain 'F' and resid 375 through 388 removed outlier: 3.575A pdb=" N GLU F 383 " --> pdb=" O ARG F 379 " (cutoff:3.500A) Processing helix chain 'F' and resid 394 through 411 removed outlier: 3.607A pdb=" N ALA F 398 " --> pdb=" O LEU F 394 " (cutoff:3.500A) Processing helix chain 'F' and resid 413 through 415 No H-bonds generated for 'chain 'F' and resid 413 through 415' Processing helix chain 'F' and resid 423 through 434 removed outlier: 4.166A pdb=" N ARG F 432 " --> pdb=" O SER F 428 " (cutoff:3.500A) removed outlier: 4.090A 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 447 through 459 removed outlier: 3.509A pdb=" N ASP F 454 " --> pdb=" O LYS F 450 " (cutoff:3.500A) Processing helix chain 'F' and resid 464 through 479 removed outlier: 3.532A pdb=" N MET F 476 " --> pdb=" O GLU F 472 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ALA F 477 " --> pdb=" O ALA F 473 " (cutoff:3.500A) Processing helix chain 'F' and resid 501 through 512 Processing helix chain 'F' and resid 521 through 523 No H-bonds generated for 'chain 'F' and resid 521 through 523' Processing helix chain 'F' and resid 527 through 533 removed outlier: 3.740A pdb=" N ARG F 532 " --> pdb=" O HIS F 528 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N LEU F 533 " --> pdb=" O THR F 529 " (cutoff:3.500A) Processing helix chain 'F' and resid 548 through 555 removed outlier: 3.543A pdb=" N VAL F 553 " --> pdb=" O LEU F 549 " (cutoff:3.500A) Processing helix chain 'F' and resid 571 through 583 removed outlier: 3.834A pdb=" N ILE F 576 " --> pdb=" O ASP F 572 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU F 577 " --> pdb=" O VAL F 573 " (cutoff:3.500A) Processing helix chain 'F' and resid 608 through 613 Processing helix chain 'F' and resid 628 through 635 Processing helix chain 'F' and resid 638 through 643 Processing helix chain 'F' and resid 655 through 676 removed outlier: 3.624A pdb=" N GLN F 675 " --> pdb=" O VAL F 671 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LYS F 676 " --> pdb=" O GLN F 672 " (cutoff:3.500A) Processing helix chain 'F' and resid 684 through 694 removed outlier: 3.834A pdb=" N LYS F 693 " --> pdb=" O TRP F 689 " (cutoff:3.500A) Processing helix chain 'F' and resid 702 through 721 removed outlier: 3.556A pdb=" N ARG F 706 " --> pdb=" O ARG F 702 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS F 714 " --> pdb=" O ASP F 710 " (cutoff:3.500A) Proline residue: F 715 - end of helix removed outlier: 3.697A pdb=" N ASN F 718 " --> pdb=" O LYS F 714 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU F 719 " --> pdb=" O PRO F 715 " (cutoff:3.500A) Processing helix chain 'F' and resid 724 through 726 No H-bonds generated for 'chain 'F' and resid 724 through 726' Processing helix chain 'H' and resid 19 through 26 removed outlier: 3.734A pdb=" N GLU H 26 " --> pdb=" O ARG H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 53 Processing helix chain 'H' and resid 70 through 82 removed outlier: 3.679A pdb=" N SER H 75 " --> pdb=" O THR H 71 " (cutoff:3.500A) removed outlier: 3.602A 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 Processing helix chain 'H' and resid 161 through 168 Processing helix chain 'H' and resid 176 through 182 removed outlier: 3.664A pdb=" N VAL H 180 " --> pdb=" O ALA H 176 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU H 181 " --> pdb=" O PRO H 177 " (cutoff:3.500A) Processing helix chain 'I' and resid 19 through 26 removed outlier: 3.548A 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: 3.585A pdb=" N SER I 75 " --> pdb=" O THR I 71 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE I 76 " --> pdb=" O ALA I 72 " (cutoff:3.500A) Processing helix chain 'I' and resid 97 through 104 Processing helix chain 'I' and resid 132 through 157 Processing helix chain 'I' and resid 161 through 169 Processing helix chain 'I' and resid 176 through 182 Processing helix chain 'J' and resid 19 through 26 removed outlier: 3.660A pdb=" N GLU J 26 " --> pdb=" O ARG J 22 " (cutoff:3.500A) Processing helix chain 'J' and resid 37 through 53 Processing helix chain 'J' and resid 70 through 82 removed outlier: 3.765A pdb=" N SER J 75 " --> pdb=" O THR J 71 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE J 76 " --> pdb=" O ALA J 72 " (cutoff:3.500A) Processing helix chain 'J' and resid 100 through 105 Processing helix chain 'J' and resid 132 through 157 Processing helix chain 'J' and resid 161 through 169 Processing helix chain 'J' and resid 176 through 182 Processing helix chain 'K' and resid 19 through 26 removed outlier: 3.612A pdb=" N GLU K 26 " --> pdb=" O ARG K 22 " (cutoff:3.500A) Processing helix chain 'K' and resid 37 through 53 Processing helix chain 'K' and resid 70 through 82 Processing helix chain 'K' and resid 100 through 104 Processing helix chain 'K' and resid 132 through 157 Processing helix chain 'K' and resid 161 through 169 Processing helix chain 'K' and resid 176 through 182 removed outlier: 3.752A pdb=" N VAL K 180 " --> pdb=" O ALA K 176 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU K 181 " --> pdb=" O PRO K 177 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 26 removed outlier: 3.736A pdb=" N GLU L 26 " --> pdb=" O ARG L 22 " (cutoff:3.500A) Processing helix chain 'L' and resid 37 through 53 Processing helix chain 'L' and resid 70 through 82 removed outlier: 3.736A pdb=" N SER L 75 " --> pdb=" O THR L 71 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE L 76 " --> pdb=" O ALA L 72 " (cutoff:3.500A) Processing helix chain 'L' and resid 97 through 105 Processing helix chain 'L' and resid 132 through 157 Processing helix chain 'L' and resid 161 through 168 removed outlier: 3.561A pdb=" N ARG L 166 " --> pdb=" O GLU L 162 " (cutoff:3.500A) Processing helix chain 'L' and resid 176 through 182 removed outlier: 3.544A pdb=" N VAL L 180 " --> pdb=" O ALA L 176 " (cutoff:3.500A) Processing helix chain 'M' and resid 19 through 26 Processing helix chain 'M' and resid 37 through 53 removed outlier: 3.560A pdb=" N LEU M 42 " --> pdb=" O HIS M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 70 through 82 removed outlier: 3.551A pdb=" N SER M 75 " --> pdb=" O THR M 71 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE M 76 " --> pdb=" O ALA M 72 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE M 82 " --> pdb=" O ASP M 78 " (cutoff:3.500A) Processing helix chain 'M' and resid 97 through 105 Processing helix chain 'M' and resid 132 through 157 Processing helix chain 'M' and resid 161 through 168 Processing helix chain 'M' and resid 176 through 181 Processing helix chain 'N' and resid 19 through 26 removed outlier: 3.767A pdb=" N GLU N 26 " --> pdb=" O ARG N 22 " (cutoff:3.500A) Processing helix chain 'N' and resid 37 through 53 Processing helix chain 'N' and resid 70 through 82 removed outlier: 3.698A pdb=" N SER N 75 " --> pdb=" O THR N 71 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE N 76 " --> pdb=" O ALA N 72 " (cutoff:3.500A) Processing helix chain 'N' and resid 97 through 105 Processing helix chain 'N' and resid 132 through 157 Processing helix chain 'N' and resid 161 through 169 Processing helix chain 'N' and resid 176 through 182 removed outlier: 3.775A pdb=" N GLU N 181 " --> pdb=" O PRO N 177 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 341 through 343 removed outlier: 7.118A pdb=" N ASN A 209 " --> pdb=" O GLN A 342 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N VAL A 318 " --> pdb=" O PRO A 210 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N LEU A 212 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N GLY A 320 " --> pdb=" O LEU A 212 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N GLY A 214 " --> pdb=" O GLY A 320 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N THR A 322 " --> pdb=" O GLY A 214 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER A 321 " --> pdb=" O ILE A 284 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 647 through 650 removed outlier: 7.336A pdb=" N ILE A 648 " --> pdb=" O SER A 490 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N LEU A 492 " --> pdb=" O ILE A 648 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N PHE A 650 " --> pdb=" O LEU A 492 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ALA A 494 " --> pdb=" O PHE A 650 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N LEU A 601 " --> pdb=" O PHE A 491 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N PHE A 493 " --> pdb=" O LEU A 601 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N MET A 603 " --> pdb=" O PHE A 493 " (cutoff:3.500A) removed outlier: 8.617A pdb=" N GLY A 495 " --> pdb=" O MET A 603 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N THR A 605 " --> pdb=" O GLY A 495 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N THR A 604 " --> pdb=" O LEU A 563 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N GLU A 515 " --> pdb=" O VAL A 560 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N LEU A 562 " --> pdb=" O GLU A 515 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N LEU A 517 " --> pdb=" O LEU A 562 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N ASP A 564 " --> pdb=" O LEU A 517 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N PHE A 519 " --> pdb=" O ASP A 564 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 679 through 682 removed outlier: 3.700A pdb=" N GLU A 741 " --> pdb=" O ASP A 736 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 173 through 175 removed outlier: 6.263A pdb=" N ILE B 281 " --> pdb=" O TYR B 246 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N LEU B 248 " --> pdb=" O ILE B 281 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N PHE B 283 " --> pdb=" O LEU B 248 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER B 321 " --> pdb=" O ILE B 284 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 646 through 650 removed outlier: 3.709A pdb=" N ASN B 646 " --> pdb=" O SER B 490 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLY B 495 " --> pdb=" O THR B 605 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 585 through 587 removed outlier: 3.590A pdb=" N LEU B 586 " --> pdb=" O ALA B 594 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 679 through 682 Processing sheet with id= H, first strand: chain 'C' and resid 173 through 175 removed outlier: 4.788A pdb=" N ASP C 285 " --> pdb=" O LEU C 248 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER C 321 " --> pdb=" O ILE C 284 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N THR C 322 " --> pdb=" O LEU C 212 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 646 through 650 removed outlier: 3.699A pdb=" N ASN C 646 " --> pdb=" O SER C 490 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU C 492 " --> pdb=" O ASN C 646 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA C 494 " --> pdb=" O ILE C 648 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LEU C 601 " --> pdb=" O PHE C 491 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N PHE C 493 " --> pdb=" O LEU C 601 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N MET C 603 " --> pdb=" O PHE C 493 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N GLY C 495 " --> pdb=" O MET C 603 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N THR C 605 " --> pdb=" O GLY C 495 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR C 604 " --> pdb=" O LEU C 563 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N GLU C 515 " --> pdb=" O VAL C 560 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N LEU C 562 " --> pdb=" O GLU C 515 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LEU C 517 " --> pdb=" O LEU C 562 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ASP C 564 " --> pdb=" O LEU C 517 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N PHE C 519 " --> pdb=" O ASP C 564 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 585 through 587 Processing sheet with id= K, first strand: chain 'C' and resid 680 through 682 removed outlier: 6.802A pdb=" N VAL C 731 " --> pdb=" O GLU C 681 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU C 741 " --> pdb=" O ASP C 736 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 173 through 175 removed outlier: 4.947A pdb=" N ASP D 285 " --> pdb=" O LEU D 248 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ARG D 317 " --> pdb=" O LEU D 282 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ILE D 284 " --> pdb=" O ARG D 317 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ILE D 319 " --> pdb=" O ILE D 284 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N GLN D 342 " --> pdb=" O LEU D 211 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N VAL D 213 " --> pdb=" O GLN D 342 " (cutoff:3.500A) removed outlier: 5.729A 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 removed outlier: 3.827A pdb=" N ASN D 646 " --> pdb=" O SER D 490 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU D 492 " --> pdb=" O ASN D 646 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 585 through 587 removed outlier: 3.718A pdb=" N LEU D 586 " --> pdb=" O ALA D 594 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 679 through 682 Processing sheet with id= P, first strand: chain 'E' and resid 173 through 175 removed outlier: 6.664A pdb=" N ILE E 281 " --> pdb=" O TYR E 246 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N LEU E 248 " --> pdb=" O ILE E 281 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N PHE E 283 " --> pdb=" O LEU E 248 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER E 321 " --> pdb=" O ILE E 284 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N GLN E 342 " --> pdb=" O LEU E 211 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VAL E 213 " --> pdb=" O GLN E 342 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N ILE E 344 " --> pdb=" O VAL E 213 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 646 through 650 removed outlier: 6.669A pdb=" N LEU E 601 " --> pdb=" O PHE E 491 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N PHE E 493 " --> pdb=" O LEU E 601 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N MET E 603 " --> pdb=" O PHE E 493 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N GLY E 495 " --> pdb=" O MET E 603 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N THR E 605 " --> pdb=" O GLY E 495 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL E 600 " --> pdb=" O ALA E 559 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU E 561 " --> pdb=" O VAL E 600 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N GLU E 515 " --> pdb=" O VAL E 560 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N LEU E 562 " --> pdb=" O GLU E 515 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU E 517 " --> pdb=" O LEU E 562 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N ASP E 564 " --> pdb=" O LEU E 517 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N PHE E 519 " --> pdb=" O ASP E 564 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 585 through 587 Processing sheet with id= S, first strand: chain 'E' and resid 679 through 682 removed outlier: 3.782A pdb=" N GLU E 681 " --> pdb=" O VAL E 731 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'F' and resid 173 through 175 removed outlier: 3.674A pdb=" N THR F 174 " --> pdb=" O SER F 247 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'F' and resid 209 through 211 Processing sheet with id= V, first strand: chain 'F' and resid 516 through 518 removed outlier: 5.370A pdb=" N VAL F 560 " --> pdb=" O LEU F 517 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'F' and resid 585 through 587 Processing sheet with id= X, first strand: chain 'F' and resid 679 through 682 removed outlier: 3.610A pdb=" N GLU F 681 " --> pdb=" O VAL F 731 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLN F 730 " --> pdb=" O GLN F 747 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN F 747 " --> pdb=" O GLN F 730 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU F 741 " --> pdb=" O ASP F 736 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'H' and resid 5 through 9 Processing sheet with id= Z, first strand: chain 'H' and resid 28 through 32 removed outlier: 6.088A pdb=" N TYR H 60 " --> pdb=" O ILE H 29 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N LEU H 31 " --> pdb=" O TYR H 60 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N TYR H 62 " --> pdb=" O LEU H 31 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'H' and resid 118 through 121 removed outlier: 3.528A pdb=" N ILE H 121 " --> pdb=" O ARG H 172 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'I' and resid 5 through 8 Processing sheet with id= AC, first strand: chain 'I' and resid 28 through 32 removed outlier: 6.483A pdb=" N TYR I 60 " --> pdb=" O ILE I 29 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N LEU I 31 " --> pdb=" O TYR I 60 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N TYR I 62 " --> pdb=" O LEU I 31 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'I' and resid 118 through 121 Processing sheet with id= AE, first strand: chain 'J' and resid 5 through 9 Processing sheet with id= AF, first strand: chain 'J' and resid 28 through 32 removed outlier: 6.638A pdb=" N TYR J 60 " --> pdb=" O ILE J 29 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N LEU J 31 " --> pdb=" O TYR J 60 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N TYR J 62 " --> pdb=" O LEU J 31 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'J' and resid 118 through 121 Processing sheet with id= AH, first strand: chain 'K' and resid 5 through 8 removed outlier: 3.505A pdb=" N ARG K 15 " --> pdb=" O GLU K 8 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'K' and resid 28 through 32 removed outlier: 6.524A pdb=" N TYR K 60 " --> pdb=" O ILE K 29 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N LEU K 31 " --> pdb=" O TYR K 60 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N TYR K 62 " --> pdb=" O LEU K 31 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'K' and resid 118 through 121 Processing sheet with id= AK, first strand: chain 'L' and resid 5 through 8 removed outlier: 3.514A pdb=" N ARG L 15 " --> pdb=" O GLU L 8 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'L' and resid 28 through 32 removed outlier: 6.560A pdb=" N TYR L 60 " --> pdb=" O ILE L 29 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N LEU L 31 " --> pdb=" O TYR L 60 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N TYR L 62 " --> pdb=" O LEU L 31 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'L' and resid 112 through 114 removed outlier: 6.850A pdb=" N SER L 187 " --> pdb=" O CYS L 113 " (cutoff:3.500A) No H-bonds generated for sheet with id= AM Processing sheet with id= AN, first strand: chain 'L' and resid 118 through 121 Processing sheet with id= AO, first strand: chain 'M' and resid 5 through 9 Processing sheet with id= AP, first strand: chain 'M' and resid 28 through 31 removed outlier: 6.333A pdb=" N TYR M 60 " --> pdb=" O ILE M 29 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N LEU M 31 " --> pdb=" O TYR M 60 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N TYR M 62 " --> pdb=" O LEU M 31 " (cutoff:3.500A) No H-bonds generated for sheet with id= AP Processing sheet with id= AQ, first strand: chain 'M' and resid 119 through 121 Processing sheet with id= AR, first strand: chain 'N' and resid 5 through 9 removed outlier: 3.648A pdb=" N ARG N 15 " --> pdb=" O GLU N 8 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'N' and resid 28 through 31 removed outlier: 6.353A pdb=" N TYR N 60 " --> pdb=" O ILE N 29 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N LEU N 31 " --> pdb=" O TYR N 60 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N TYR N 62 " --> pdb=" O LEU N 31 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'N' and resid 119 through 121 removed outlier: 3.552A pdb=" N ARG N 172 " --> pdb=" O ILE N 121 " (cutoff:3.500A) 1576 hydrogen bonds defined for protein. 4566 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 29.80 Time building geometry restraints manager: 56.11 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: 38226 1.06 - 1.28: 6521 1.28 - 1.50: 15435 1.50 - 1.73: 16240 1.73 - 1.95: 305 Bond restraints: 76727 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 2.96e+01 bond pdb=" C4 ADP F 801 " pdb=" C5 ADP F 801 " ideal model delta sigma weight residual 1.490 1.382 0.108 2.00e-02 2.50e+03 2.94e+01 bond pdb=" C4 ADP D 802 " pdb=" C5 ADP D 802 " ideal model delta sigma weight residual 1.490 1.383 0.107 2.00e-02 2.50e+03 2.86e+01 bond pdb=" C4 ADP A 801 " pdb=" C5 ADP A 801 " ideal model delta sigma weight residual 1.490 1.383 0.107 2.00e-02 2.50e+03 2.85e+01 bond pdb=" C5 ADP A 801 " pdb=" C6 ADP A 801 " ideal model delta sigma weight residual 1.490 1.407 0.083 2.00e-02 2.50e+03 1.71e+01 ... (remaining 76722 not shown) Histogram of bond angle deviations from ideal: 84.75 - 94.61: 3 94.61 - 104.46: 573 104.46 - 114.32: 96166 114.32 - 124.17: 37620 124.17 - 134.03: 4720 Bond angle restraints: 139082 Sorted by residual: angle pdb=" CB LEU F 517 " pdb=" CG LEU F 517 " pdb=" HG LEU F 517 " ideal model delta sigma weight residual 109.00 85.25 23.75 3.00e+00 1.11e-01 6.27e+01 angle pdb=" CD2 LEU F 517 " pdb=" CG LEU F 517 " pdb=" HG LEU F 517 " ideal model delta sigma weight residual 108.00 84.75 23.25 3.00e+00 1.11e-01 6.00e+01 angle pdb=" CD1 LEU F 517 " pdb=" CG LEU F 517 " pdb=" HG LEU F 517 " ideal model delta sigma weight residual 108.00 85.08 22.92 3.00e+00 1.11e-01 5.84e+01 angle pdb=" PA AGS B 801 " pdb=" O3A AGS B 801 " pdb=" PB AGS B 801 " ideal model delta sigma weight residual 119.76 133.62 -13.86 3.00e+00 1.11e-01 2.13e+01 angle pdb=" PB AGS E 802 " pdb=" O3B AGS E 802 " pdb=" PG AGS E 802 " ideal model delta sigma weight residual 120.12 133.82 -13.70 3.00e+00 1.11e-01 2.09e+01 ... (remaining 139077 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.24: 29580 32.24 - 64.48: 628 64.48 - 96.72: 64 96.72 - 128.96: 10 128.96 - 161.20: 7 Dihedral angle restraints: 30289 sinusoidal: 14817 harmonic: 15472 Sorted by residual: dihedral pdb=" O1B ADP F 801 " pdb=" O3A ADP F 801 " pdb=" PB ADP F 801 " pdb=" PA ADP F 801 " ideal model delta sinusoidal sigma weight residual 300.00 165.91 134.09 1 2.00e+01 2.50e-03 4.07e+01 dihedral pdb=" C5' ADP A 801 " pdb=" O5' ADP A 801 " pdb=" PA ADP A 801 " pdb=" O2A ADP A 801 " ideal model delta sinusoidal sigma weight residual -60.00 72.14 -132.14 1 2.00e+01 2.50e-03 4.01e+01 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 -60.00 68.95 -128.96 1 2.00e+01 2.50e-03 3.91e+01 ... (remaining 30286 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.353: 5969 0.353 - 0.705: 0 0.705 - 1.058: 0 1.058 - 1.410: 0 1.410 - 1.763: 1 Chirality restraints: 5970 Sorted by residual: chirality pdb=" CG LEU F 517 " pdb=" CB LEU F 517 " pdb=" CD1 LEU F 517 " pdb=" CD2 LEU F 517 " both_signs ideal model delta sigma weight residual False -2.59 -0.83 -1.76 2.00e-01 2.50e+01 7.77e+01 chirality pdb=" C3' ADP A 801 " pdb=" C2' ADP A 801 " pdb=" C4' ADP A 801 " pdb=" O3' ADP A 801 " both_signs ideal model delta sigma weight residual False -2.51 -2.71 0.20 2.00e-01 2.50e+01 9.91e-01 chirality pdb=" CA MET D 412 " pdb=" N MET D 412 " pdb=" C MET D 412 " pdb=" CB MET D 412 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.39e-01 ... (remaining 5967 not shown) Planarity restraints: 11332 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG B 702 " 0.050 5.00e-02 4.00e+02 7.55e-02 9.11e+00 pdb=" N PRO B 703 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO B 703 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 703 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS F 308 " 0.047 5.00e-02 4.00e+02 7.09e-02 8.03e+00 pdb=" N PRO F 309 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO F 309 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO F 309 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU F 394 " 0.047 5.00e-02 4.00e+02 7.00e-02 7.84e+00 pdb=" N PRO F 395 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO F 395 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO F 395 " 0.039 5.00e-02 4.00e+02 ... (remaining 11329 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.25: 7910 2.25 - 2.83: 175702 2.83 - 3.42: 202875 3.42 - 4.01: 280135 4.01 - 4.60: 429695 Nonbonded interactions: 1096317 Sorted by model distance: nonbonded pdb=" O ALA M 96 " pdb=" H ALA M 100 " model vdw 1.657 1.850 nonbonded pdb=" O ALA H 96 " pdb=" H ALA H 100 " model vdw 1.686 1.850 nonbonded pdb=" O SER F 531 " pdb=" H GLY F 535 " model vdw 1.687 1.850 nonbonded pdb=" OE1 GLU C 567 " pdb=" H GLU C 567 " model vdw 1.700 1.850 nonbonded pdb=" O ALA N 96 " pdb=" H ALA N 100 " model vdw 1.701 1.850 ... (remaining 1096312 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 173 through 220 or (resid 221 and (name N or name CA or na \ me C or name O or name CB or name OG1 or name CG2 or name H or name HA or name H \ B or name HG21 or name HG22 or name HG23)) or resid 222 through 291 or resid 305 \ through 501 or (resid 502 and (name N or name CA or name C or name O or name CB \ or name OG1 or name CG2 or name H or name HA or name HB or name HG21 or name HG \ 22 or name HG23)) or resid 503 through 747)) selection = (chain 'B' and ((resid 173 and (name N or name CA or name C or name O or name CB \ or name OG1 or name CG2 or name HA or name HB or name HG1 or name HG21 or name \ HG22 or name HG23)) or resid 174 through 220 or (resid 221 and (name N or name C \ A or name C or name O or name CB or name OG1 or name CG2 or name H or name HA or \ name HB or name HG21 or name HG22 or name HG23)) or resid 222 through 291 or re \ sid 305 through 431 or (resid 432 and (name N or name CA or name C or name O or \ name CB or name CG or name CD or name NE or name CZ or name NH1 or name NH2 or n \ ame H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or \ name HD3 or name HE or name HH11 or name HH21)) or resid 433 through 454 or (res \ id 455 and (name N or name CA or name C or name O or name CB or name CG or name \ CD or name NE or name CZ or name NH1 or name NH2 or name H or name HA or name HB \ 2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE or name \ HH11 or name HH12 or name HH22)) or resid 456 through 501 or (resid 502 and (na \ me N or name CA or name C or name O or name CB or name OG1 or name CG2 or name H \ or name HA or name HB or name HG21 or name HG22 or name HG23)) or resid 503 thr \ ough 539 or resid 548 through 747)) selection = (chain 'C' and ((resid 173 and (name N or name CA or name C or name O or name CB \ or name OG1 or name CG2 or name HA or name HB or name HG1 or name HG21 or name \ HG22 or name HG23)) or resid 174 through 291 or resid 305 through 431 or (resid \ 432 and (name N or name CA or name C or name O or name CB or name CG or name CD \ or name NE or name CZ or name NH1 or name NH2 or name H or name HA or name HB2 o \ r name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE or name HH \ 11 or name HH21)) or resid 433 through 454 or (resid 455 and (name N or name CA \ or name C or name O or name CB or name CG or name CD or name NE or name CZ or na \ me NH1 or name NH2 or name H or name HA or name HB2 or name HB3 or name HG2 or n \ ame HG3 or name HD2 or name HD3 or name HE or name HH11 or name HH12 or name HH2 \ 2)) or resid 456 through 539 or resid 548 through 747)) selection = (chain 'D' and ((resid 173 and (name N or name CA or name C or name O or name CB \ or name OG1 or name CG2 or name HA or name HB or name HG1 or name HG21 or name \ HG22 or name HG23)) or resid 174 through 220 or (resid 221 and (name N or name C \ A or name C or name O or name CB or name OG1 or name CG2 or name H or name HA or \ name HB or name HG21 or name HG22 or name HG23)) or resid 222 through 291 or re \ sid 305 through 431 or (resid 432 and (name N or name CA or name C or name O or \ name CB or name CG or name CD or name NE or name CZ or name NH1 or name NH2 or n \ ame H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or \ name HD3 or name HE or name HH11 or name HH21)) or resid 433 through 454 or (res \ id 455 and (name N or name CA or name C or name O or name CB or name CG or name \ CD or name NE or name CZ or name NH1 or name NH2 or name H or name HA or name HB \ 2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE or name \ HH11 or name HH12 or name HH22)) or resid 456 through 501 or (resid 502 and (na \ me N or name CA or name C or name O or name CB or name OG1 or name CG2 or name H \ or name HA or name HB or name HG21 or name HG22 or name HG23)) or resid 503 thr \ ough 539 or resid 548 through 747)) selection = (chain 'E' and ((resid 173 and (name N or name CA or name C or name O or name CB \ or name OG1 or name CG2 or name HA or name HB or name HG1 or name HG21 or name \ HG22 or name HG23)) or resid 174 through 220 or (resid 221 and (name N or name C \ A or name C or name O or name CB or name OG1 or name CG2 or name H or name HA or \ name HB or name HG21 or name HG22 or name HG23)) or resid 222 through 291 or re \ sid 305 through 431 or (resid 432 and (name N or name CA or name C or name O or \ name CB or name CG or name CD or name NE or name CZ or name NH1 or name NH2 or n \ ame H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or \ name HD3 or name HE or name HH11 or name HH21)) or resid 433 through 454 or (res \ id 455 and (name N or name CA or name C or name O or name CB or name CG or name \ CD or name NE or name CZ or name NH1 or name NH2 or name H or name HA or name HB \ 2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE or name \ HH11 or name HH12 or name HH22)) or resid 456 through 501 or (resid 502 and (na \ me N or name CA or name C or name O or name CB or name OG1 or name CG2 or name H \ or name HA or name HB or name HG21 or name HG22 or name HG23)) or resid 503 thr \ ough 539 or resid 548 through 747)) selection = (chain 'F' and ((resid 173 and (name N or name CA or name C or name O or name CB \ or name OG1 or name CG2 or name HA or name HB or name HG1 or name HG21 or name \ HG22 or name HG23)) or resid 174 through 220 or (resid 221 and (name N or name C \ A or name C or name O or name CB or name OG1 or name CG2 or name H or name HA or \ name HB or name HG21 or name HG22 or name HG23)) or resid 222 through 431 or (r \ esid 432 and (name N or name CA or name C or name O or name CB or name CG or nam \ e CD or name NE or name CZ or name NH1 or name NH2 or name H or name HA or name \ HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE or na \ me HH11 or name HH21)) or resid 433 through 454 or (resid 455 and (name N or nam \ e CA or name C or name O or name CB or name CG or name CD or name NE or name CZ \ or name NH1 or name NH2 or name H or name HA or name HB2 or name HB3 or name HG2 \ or name HG3 or name HD2 or name HD3 or name HE or name HH11 or name HH12 or nam \ e HH22)) or resid 456 through 501 or (resid 502 and (name N or name CA or name C \ or name O or name CB or name OG1 or name CG2 or name H or name HA or name HB or \ name HG21 or name HG22 or name HG23)) or resid 503 through 539 or resid 548 thr \ ough 747)) } 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' and resid 2 through 191) selection = chain 'N' } 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 169 5.16 5 C 23781 2.51 5 N 6708 2.21 5 O 7206 1.98 5 H 38252 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: 0.350 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: 1.100 Extract box with map and model: 7.160 Check model and map are aligned: 0.860 Convert atoms to be neutral: 0.510 Process input model: 199.210 Find NCS groups from input model: 3.960 Set up NCS constraints: 0.260 Set refine NCS operators: 0.000 Set scattering table: 0.040 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 216.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 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 38475 Z= 0.295 Angle : 0.808 13.862 51976 Z= 0.412 Chirality : 0.048 1.763 5970 Planarity : 0.004 0.075 6704 Dihedral : 14.777 161.196 14598 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.11), residues: 4769 helix: 1.62 (0.09), residues: 2395 sheet: -0.06 (0.18), residues: 726 loop : -0.22 (0.14), residues: 1648 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9538 Ramachandran restraints generated. 4769 Oldfield, 0 Emsley, 4769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9538 Ramachandran restraints generated. 4769 Oldfield, 0 Emsley, 4769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Evaluate side-chains 1436 residues out of total 4058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1436 time to evaluate : 4.737 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 outliers start: 0 outliers final: 0 residues processed: 1436 average time/residue: 1.0972 time to fit residues: 2433.3997 Evaluate side-chains 1173 residues out of total 4058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1173 time to evaluate : 4.696 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.1534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 477 random chunks: chunk 402 optimal weight: 10.0000 chunk 361 optimal weight: 10.0000 chunk 200 optimal weight: 6.9990 chunk 123 optimal weight: 10.0000 chunk 243 optimal weight: 10.0000 chunk 193 optimal weight: 6.9990 chunk 373 optimal weight: 7.9990 chunk 144 optimal weight: 5.9990 chunk 227 optimal weight: 10.0000 chunk 278 optimal weight: 10.0000 chunk 433 optimal weight: 20.0000 overall best weight: 7.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 583 ASN B 209 ASN ** B 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 178 GLN C 329 ASN C 422 ASN C 606 ASN C 621 HIS C 624 ASN ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 390 ASN D 589 ASN D 660 GLN D 740 ASN ** E 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 558 HIS E 642 ASN ** F 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 558 HIS F 583 ASN F 590 ASN F 670 GLN H 46 GLN I 41 ASN I 122 HIS J 116 ASN J 129 GLN K 41 ASN L 41 ASN ** M 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 138 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.087 38475 Z= 0.417 Angle : 0.650 10.368 51976 Z= 0.346 Chirality : 0.048 1.708 5970 Planarity : 0.004 0.072 6704 Dihedral : 8.831 164.430 5301 Min Nonbonded Distance : 1.652 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer Outliers : 1.48 % 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: 0.77 (0.11), residues: 4769 helix: 1.30 (0.10), residues: 2457 sheet: -0.14 (0.18), residues: 790 loop : -0.27 (0.14), residues: 1522 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9538 Ramachandran restraints generated. 4769 Oldfield, 0 Emsley, 4769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9538 Ramachandran restraints generated. 4769 Oldfield, 0 Emsley, 4769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Evaluate side-chains 1331 residues out of total 4058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 1271 time to evaluate : 4.676 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 outliers start: 60 outliers final: 49 residues processed: 1291 average time/residue: 1.1132 time to fit residues: 2229.8532 Evaluate side-chains 1246 residues out of total 4058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 1197 time to evaluate : 4.657 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 49 outliers final: 1 residues processed: 49 average time/residue: 0.7057 time to fit residues: 70.8124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 477 random chunks: chunk 240 optimal weight: 7.9990 chunk 134 optimal weight: 10.0000 chunk 360 optimal weight: 20.0000 chunk 294 optimal weight: 20.0000 chunk 119 optimal weight: 3.9990 chunk 433 optimal weight: 8.9990 chunk 468 optimal weight: 6.9990 chunk 386 optimal weight: 2.9990 chunk 430 optimal weight: 10.0000 chunk 147 optimal weight: 3.9990 chunk 348 optimal weight: 0.7980 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 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 709 GLN B 369 HIS ** B 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 642 ASN C 178 GLN ** C 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 ASN ** C 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 390 ASN ** E 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 558 HIS ** F 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 116 ASN I 122 HIS J 34 GLN M 64 ASN ** N 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 38475 Z= 0.232 Angle : 0.540 10.343 51976 Z= 0.278 Chirality : 0.045 1.708 5970 Planarity : 0.004 0.051 6704 Dihedral : 8.720 165.879 5301 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer Outliers : 0.86 % 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: 0.86 (0.12), residues: 4769 helix: 1.40 (0.10), residues: 2460 sheet: -0.18 (0.18), residues: 790 loop : -0.24 (0.15), residues: 1519 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9538 Ramachandran restraints generated. 4769 Oldfield, 0 Emsley, 4769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9538 Ramachandran restraints generated. 4769 Oldfield, 0 Emsley, 4769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Evaluate side-chains 1251 residues out of total 4058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 1216 time to evaluate : 4.866 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 outliers start: 35 outliers final: 19 residues processed: 1223 average time/residue: 1.0979 time to fit residues: 2086.6787 Evaluate side-chains 1192 residues out of total 4058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 1173 time to evaluate : 4.713 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.7018 time to fit residues: 31.0077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 477 random chunks: chunk 428 optimal weight: 1.9990 chunk 326 optimal weight: 30.0000 chunk 225 optimal weight: 9.9990 chunk 48 optimal weight: 2.9990 chunk 207 optimal weight: 10.0000 chunk 291 optimal weight: 20.0000 chunk 435 optimal weight: 20.0000 chunk 461 optimal weight: 10.0000 chunk 227 optimal weight: 20.0000 chunk 412 optimal weight: 7.9990 chunk 124 optimal weight: 7.9990 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 652 HIS ** B 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 178 GLN ** C 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 ASN ** C 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 390 ASN ** D 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 558 HIS E 575 ASN ** F 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 670 GLN I 116 ASN I 122 HIS J 159 GLN ** L 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 64 ASN M 138 HIS ** N 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.3725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.053 38475 Z= 0.342 Angle : 0.575 10.192 51976 Z= 0.296 Chirality : 0.046 1.706 5970 Planarity : 0.004 0.054 6704 Dihedral : 8.866 170.108 5301 Min Nonbonded Distance : 1.716 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer Outliers : 1.11 % 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: 0.63 (0.12), residues: 4769 helix: 1.21 (0.10), residues: 2472 sheet: -0.29 (0.18), residues: 801 loop : -0.35 (0.15), residues: 1496 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9538 Ramachandran restraints generated. 4769 Oldfield, 0 Emsley, 4769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9538 Ramachandran restraints generated. 4769 Oldfield, 0 Emsley, 4769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Evaluate side-chains 1257 residues out of total 4058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 1212 time to evaluate : 4.850 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 outliers start: 45 outliers final: 31 residues processed: 1223 average time/residue: 1.0928 time to fit residues: 2080.0778 Evaluate side-chains 1198 residues out of total 4058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 1167 time to evaluate : 4.697 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 31 outliers final: 1 residues processed: 31 average time/residue: 0.6866 time to fit residues: 45.8809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 477 random chunks: chunk 383 optimal weight: 1.9990 chunk 261 optimal weight: 10.0000 chunk 6 optimal weight: 0.9980 chunk 343 optimal weight: 30.0000 chunk 190 optimal weight: 6.9990 chunk 393 optimal weight: 3.9990 chunk 318 optimal weight: 9.9990 chunk 0 optimal weight: 50.0000 chunk 235 optimal weight: 7.9990 chunk 413 optimal weight: 10.0000 chunk 116 optimal weight: 6.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 GLN ** B 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 ASN B 583 ASN ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 ASN ** C 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 718 ASN ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 390 ASN D 642 ASN ** E 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 558 HIS ** F 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 709 GLN I 122 HIS M 64 ASN M 138 HIS ** N 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.3963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 38475 Z= 0.236 Angle : 0.533 10.324 51976 Z= 0.272 Chirality : 0.045 1.709 5970 Planarity : 0.003 0.058 6704 Dihedral : 8.798 168.979 5301 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer Outliers : 0.89 % 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: 0.67 (0.12), residues: 4769 helix: 1.28 (0.10), residues: 2475 sheet: -0.38 (0.18), residues: 781 loop : -0.34 (0.15), residues: 1513 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9538 Ramachandran restraints generated. 4769 Oldfield, 0 Emsley, 4769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9538 Ramachandran restraints generated. 4769 Oldfield, 0 Emsley, 4769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Evaluate side-chains 1229 residues out of total 4058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 1193 time to evaluate : 4.833 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: 36 outliers final: 23 residues processed: 1203 average time/residue: 1.0803 time to fit residues: 2025.2345 Evaluate side-chains 1186 residues out of total 4058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 1163 time to evaluate : 4.655 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 23 outliers final: 1 residues processed: 23 average time/residue: 0.7052 time to fit residues: 36.1006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 477 random chunks: chunk 155 optimal weight: 5.9990 chunk 415 optimal weight: 6.9990 chunk 91 optimal weight: 9.9990 chunk 270 optimal weight: 2.9990 chunk 113 optimal weight: 10.0000 chunk 461 optimal weight: 9.9990 chunk 383 optimal weight: 7.9990 chunk 213 optimal weight: 5.9990 chunk 38 optimal weight: 20.0000 chunk 152 optimal weight: 3.9990 chunk 242 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 200 GLN ** B 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 583 ASN C 178 GLN ** C 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 ASN ** C 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 652 HIS ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 558 HIS ** F 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 122 HIS M 138 HIS ** N 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.4187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 38475 Z= 0.291 Angle : 0.549 10.084 51976 Z= 0.282 Chirality : 0.045 1.704 5970 Planarity : 0.004 0.085 6704 Dihedral : 8.861 167.998 5301 Min Nonbonded Distance : 1.740 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer Outliers : 0.86 % 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: 0.60 (0.12), residues: 4769 helix: 1.24 (0.10), residues: 2479 sheet: -0.46 (0.18), residues: 752 loop : -0.39 (0.15), residues: 1538 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9538 Ramachandran restraints generated. 4769 Oldfield, 0 Emsley, 4769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9538 Ramachandran restraints generated. 4769 Oldfield, 0 Emsley, 4769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Evaluate side-chains 1225 residues out of total 4058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 1190 time to evaluate : 4.698 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: 35 outliers final: 25 residues processed: 1200 average time/residue: 1.0698 time to fit residues: 1998.8167 Evaluate side-chains 1183 residues out of total 4058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 1158 time to evaluate : 4.637 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 25 outliers final: 1 residues processed: 25 average time/residue: 0.6650 time to fit residues: 37.1534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 477 random chunks: chunk 444 optimal weight: 10.0000 chunk 52 optimal weight: 0.9980 chunk 262 optimal weight: 9.9990 chunk 337 optimal weight: 40.0000 chunk 261 optimal weight: 9.9990 chunk 388 optimal weight: 3.9990 chunk 257 optimal weight: 20.0000 chunk 459 optimal weight: 0.9980 chunk 287 optimal weight: 20.0000 chunk 280 optimal weight: 10.0000 chunk 212 optimal weight: 5.9990 overall best weight: 4.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 GLN ** B 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 583 ASN ** C 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 ASN ** C 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 390 ASN E 329 ASN ** E 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 558 HIS ** F 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 122 HIS M 54 ASN M 138 HIS ** N 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.4353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 38475 Z= 0.250 Angle : 0.536 10.171 51976 Z= 0.274 Chirality : 0.045 1.702 5970 Planarity : 0.004 0.107 6704 Dihedral : 8.867 166.919 5301 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer Outliers : 0.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.12), residues: 4769 helix: 1.32 (0.10), residues: 2458 sheet: -0.55 (0.18), residues: 760 loop : -0.35 (0.15), residues: 1551 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9538 Ramachandran restraints generated. 4769 Oldfield, 0 Emsley, 4769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9538 Ramachandran restraints generated. 4769 Oldfield, 0 Emsley, 4769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Evaluate side-chains 1197 residues out of total 4058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 1177 time to evaluate : 4.873 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: 20 outliers final: 17 residues processed: 1183 average time/residue: 1.0681 time to fit residues: 1965.6608 Evaluate side-chains 1173 residues out of total 4058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 1156 time to evaluate : 4.730 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 17 outliers final: 1 residues processed: 17 average time/residue: 0.7161 time to fit residues: 28.3434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 477 random chunks: chunk 284 optimal weight: 30.0000 chunk 183 optimal weight: 4.9990 chunk 274 optimal weight: 10.0000 chunk 138 optimal weight: 0.5980 chunk 90 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 292 optimal weight: 9.9990 chunk 313 optimal weight: 1.9990 chunk 227 optimal weight: 20.0000 chunk 42 optimal weight: 30.0000 chunk 361 optimal weight: 0.7980 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 233 GLN B 583 ASN ** C 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 329 ASN C 422 ASN ** C 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 390 ASN D 558 HIS E 558 HIS ** F 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 122 HIS ** L 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.4418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 38475 Z= 0.175 Angle : 0.520 10.310 51976 Z= 0.263 Chirality : 0.044 1.700 5970 Planarity : 0.003 0.063 6704 Dihedral : 8.712 170.056 5301 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % 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: 0.80 (0.12), residues: 4769 helix: 1.45 (0.10), residues: 2464 sheet: -0.48 (0.18), residues: 770 loop : -0.29 (0.15), residues: 1535 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9538 Ramachandran restraints generated. 4769 Oldfield, 0 Emsley, 4769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9538 Ramachandran restraints generated. 4769 Oldfield, 0 Emsley, 4769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Evaluate side-chains 1198 residues out of total 4058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 1187 time to evaluate : 5.119 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 outliers start: 11 outliers final: 7 residues processed: 1192 average time/residue: 1.0761 time to fit residues: 1999.0359 Evaluate side-chains 1169 residues out of total 4058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 1162 time to evaluate : 4.755 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 7 average time/residue: 0.6680 time to fit residues: 14.8189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 477 random chunks: chunk 418 optimal weight: 1.9990 chunk 440 optimal weight: 8.9990 chunk 401 optimal weight: 0.9980 chunk 428 optimal weight: 5.9990 chunk 257 optimal weight: 9.9990 chunk 186 optimal weight: 2.9990 chunk 336 optimal weight: 3.9990 chunk 131 optimal weight: 7.9990 chunk 387 optimal weight: 0.6980 chunk 405 optimal weight: 4.9990 chunk 426 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 583 ASN ** C 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 ASN C 451 ASN ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 390 ASN E 558 HIS ** F 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 740 ASN I 122 HIS M 54 ASN ** N 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.4481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.054 38475 Z= 0.163 Angle : 0.514 10.275 51976 Z= 0.258 Chirality : 0.044 1.702 5970 Planarity : 0.004 0.103 6704 Dihedral : 8.584 170.736 5301 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % 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: 0.92 (0.12), residues: 4769 helix: 1.55 (0.10), residues: 2466 sheet: -0.44 (0.18), residues: 770 loop : -0.23 (0.15), residues: 1533 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9538 Ramachandran restraints generated. 4769 Oldfield, 0 Emsley, 4769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9538 Ramachandran restraints generated. 4769 Oldfield, 0 Emsley, 4769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Evaluate side-chains 1188 residues out of total 4058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 1177 time to evaluate : 4.705 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 outliers start: 11 outliers final: 8 residues processed: 1180 average time/residue: 1.0749 time to fit residues: 1979.5394 Evaluate side-chains 1163 residues out of total 4058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 1155 time to evaluate : 4.695 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 2 residues processed: 8 average time/residue: 0.6617 time to fit residues: 15.9676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 477 random chunks: chunk 281 optimal weight: 6.9990 chunk 453 optimal weight: 20.0000 chunk 276 optimal weight: 5.9990 chunk 214 optimal weight: 9.9990 chunk 314 optimal weight: 1.9990 chunk 475 optimal weight: 9.9990 chunk 437 optimal weight: 0.0470 chunk 378 optimal weight: 20.0000 chunk 39 optimal weight: 9.9990 chunk 292 optimal weight: 9.9990 chunk 232 optimal weight: 10.0000 overall best weight: 5.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 583 ASN ** C 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 ASN C 652 HIS D 390 ASN E 558 HIS ** F 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 122 HIS ** N 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.4633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 38475 Z= 0.280 Angle : 0.554 10.328 51976 Z= 0.283 Chirality : 0.045 1.710 5970 Planarity : 0.004 0.088 6704 Dihedral : 8.793 172.677 5301 Min Nonbonded Distance : 1.706 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer Outliers : 0.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.12), residues: 4769 helix: 1.44 (0.10), residues: 2467 sheet: -0.48 (0.18), residues: 761 loop : -0.32 (0.15), residues: 1541 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9538 Ramachandran restraints generated. 4769 Oldfield, 0 Emsley, 4769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9538 Ramachandran restraints generated. 4769 Oldfield, 0 Emsley, 4769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Evaluate side-chains 1173 residues out of total 4058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 1164 time to evaluate : 5.393 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 outliers start: 9 outliers final: 7 residues processed: 1168 average time/residue: 1.0795 time to fit residues: 1969.3872 Evaluate side-chains 1161 residues out of total 4058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 1154 time to evaluate : 4.740 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 7 average time/residue: 0.6896 time to fit residues: 15.0034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 477 random chunks: chunk 300 optimal weight: 20.0000 chunk 403 optimal weight: 4.9990 chunk 115 optimal weight: 0.8980 chunk 348 optimal weight: 0.7980 chunk 55 optimal weight: 20.0000 chunk 105 optimal weight: 4.9990 chunk 379 optimal weight: 20.0000 chunk 158 optimal weight: 0.0000 chunk 389 optimal weight: 9.9990 chunk 47 optimal weight: 10.0000 chunk 69 optimal weight: 20.0000 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 583 ASN ** C 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 ASN D 390 ASN ** F 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 122 HIS M 54 ASN ** N 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.178541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.132210 restraints weight = 142225.043| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.51 r_work: 0.3070 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.4672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 38475 Z= 0.179 Angle : 0.525 10.301 51976 Z= 0.266 Chirality : 0.044 1.706 5970 Planarity : 0.003 0.070 6704 Dihedral : 8.676 173.518 5301 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer Outliers : 0.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.12), residues: 4769 helix: 1.50 (0.10), residues: 2476 sheet: -0.45 (0.18), residues: 759 loop : -0.25 (0.15), residues: 1534 =============================================================================== Job complete usr+sys time: 27338.68 seconds wall clock time: 469 minutes 18.11 seconds (28158.11 seconds total)