Starting phenix.real_space_refine (version: dev) on Thu Dec 15 06:44:31 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uiy_26557/12_2022/7uiy_26557_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uiy_26557/12_2022/7uiy_26557.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uiy_26557/12_2022/7uiy_26557.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uiy_26557/12_2022/7uiy_26557.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uiy_26557/12_2022/7uiy_26557_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uiy_26557/12_2022/7uiy_26557_trim_updated.pdb" } resolution = 3.22 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ASP 186": "OD1" <-> "OD2" Residue "A GLU 194": "OE1" <-> "OE2" Residue "A GLU 215": "OE1" <-> "OE2" Residue "A GLU 225": "OE1" <-> "OE2" Residue "A TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 249": "OD1" <-> "OD2" Residue "A TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 264": "OE1" <-> "OE2" Residue "A PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 285": "OD1" <-> "OD2" Residue "A PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 334": "OD1" <-> "OD2" Residue "A PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 345": "OD1" <-> "OD2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 366": "OE1" <-> "OE2" Residue "A ASP 370": "OD1" <-> "OD2" Residue "A GLU 404": "OE1" <-> "OE2" Residue "A GLU 427": "OE1" <-> "OE2" Residue "A ASP 445": "OD1" <-> "OD2" Residue "A ASP 447": "OD1" <-> "OD2" Residue "A GLU 484": "OE1" <-> "OE2" Residue "A GLU 503": "OE1" <-> "OE2" Residue "A GLU 515": "OE1" <-> "OE2" Residue "A ARG 527": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 540": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 565": "OE1" <-> "OE2" Residue "A ASP 572": "OD1" <-> "OD2" Residue "A PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 627": "OD1" <-> "OD2" Residue "A GLU 630": "OE1" <-> "OE2" Residue "A GLU 631": "OE1" <-> "OE2" Residue "A GLU 639": "OE1" <-> "OE2" Residue "A PHE 650": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 710": "OD1" <-> "OD2" Residue "A PHE 746": "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 PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 302": "OD1" <-> "OD2" Residue "B TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 373": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 388": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 403": "OD1" <-> "OD2" Residue "B PHE 461": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 515": "OE1" <-> "OE2" Residue "B PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 524": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 565": "OE1" <-> "OE2" Residue "B PHE 636": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 650": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 665": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 736": "OD1" <-> "OD2" Residue "C GLU 194": "OE1" <-> "OE2" Residue "C GLU 238": "OE1" <-> "OE2" Residue "C TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 334": "OD1" <-> "OD2" Residue "C ASP 345": "OD1" <-> "OD2" Residue "C GLU 352": "OE1" <-> "OE2" Residue "C GLU 383": "OE1" <-> "OE2" Residue "C TYR 388": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 565": "OE1" <-> "OE2" Residue "C PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 636": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 665": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 746": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 264": "OE1" <-> "OE2" Residue "D ASP 277": "OD1" <-> "OD2" Residue "D GLU 326": "OE1" <-> "OE2" Residue "D PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 373": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 383": "OE1" <-> "OE2" Residue "D TYR 388": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 391": "OD1" <-> "OD2" Residue "D GLU 427": "OE1" <-> "OE2" Residue "D PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 611": "OE1" <-> "OE2" Residue "D GLU 613": "OE1" <-> "OE2" Residue "D PHE 636": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 668": "OE1" <-> "OE2" Residue "D ASP 674": "OD1" <-> "OD2" Residue "D GLU 741": "OE1" <-> "OE2" Residue "E PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 242": "OD1" <-> "OD2" Residue "E ARG 260": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 353": "OE1" <-> "OE2" Residue "E TYR 373": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 388": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 396": "OD1" <-> "OD2" Residue "E ASP 454": "OD1" <-> "OD2" Residue "E PHE 461": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 503": "OE1" <-> "OE2" Residue "E GLU 526": "OE1" <-> "OE2" Residue "E ASP 544": "OD1" <-> "OD2" Residue "E ASP 551": "OD1" <-> "OD2" Residue "E PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 627": "OD1" <-> "OD2" Residue "E PHE 636": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 650": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 665": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 668": "OE1" <-> "OE2" Residue "E GLU 681": "OE1" <-> "OE2" Residue "E GLU 692": "OE1" <-> "OE2" Residue "E ASP 727": "OD1" <-> "OD2" Residue "E ASP 736": "OD1" <-> "OD2" Residue "E GLU 738": "OE1" <-> "OE2" Residue "F GLU 275": "OE1" <-> "OE2" Residue "F GLU 352": "OE1" <-> "OE2" Residue "F GLU 383": "OE1" <-> "OE2" Residue "F TYR 388": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 396": "OD1" <-> "OD2" Residue "F ASP 400": "OD1" <-> "OD2" Residue "F ASP 425": "OD1" <-> "OD2" Residue "F GLU 438": "OE1" <-> "OE2" Residue "F ASP 447": "OD1" <-> "OD2" Residue "F PHE 461": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 464": "OD1" <-> "OD2" Residue "F GLU 468": "OE1" <-> "OE2" Residue "F GLU 472": "OE1" <-> "OE2" Residue "F GLU 484": "OE1" <-> "OE2" Residue "F PHE 493": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 520": "OD1" <-> "OD2" Residue "F GLU 523": "OE1" <-> "OE2" Residue "F TYR 524": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 526": "OE1" <-> "OE2" Residue "F ASP 564": "OD1" <-> "OD2" Residue "F GLU 567": "OE1" <-> "OE2" Residue "F GLU 631": "OE1" <-> "OE2" Residue "F PHE 636": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 639": "OE1" <-> "OE2" Residue "F PHE 640": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 651": "OD1" <-> "OD2" Residue "F ASP 656": "OD1" <-> "OD2" Residue "F GLU 668": "OE1" <-> "OE2" Residue "F GLU 692": "OE1" <-> "OE2" Residue "F ASP 696": "OD1" <-> "OD2" Residue "F ASP 710": "OD1" <-> "OD2" Residue "F PHE 746": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ARG 12": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H GLU 14": "OE1" <-> "OE2" Residue "H ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 37": "OD1" <-> "OD2" Residue "H GLU 51": "OE1" <-> "OE2" Residue "H TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 78": "OD1" <-> "OD2" Residue "H PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ARG 118": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ASP 134": "OD1" <-> "OD2" Residue "H GLU 141": "OE1" <-> "OE2" Residue "H ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H GLU 169": "OE1" <-> "OE2" Residue "H ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I ASP 37": "OD1" <-> "OD2" Residue "I PHE 82": "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 ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J ARG 12": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J GLU 36": "OE1" <-> "OE2" Residue "J PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J GLU 141": "OE1" <-> "OE2" Residue "J ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J 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 "K ARG 12": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ASP 78": "OD1" <-> "OD2" Residue "K PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K GLU 165": "OE1" <-> "OE2" Residue "K ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 12": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ASP 58": "OD1" <-> "OD2" Residue "L TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 77": "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 GLU 136": "OE1" <-> "OE2" Residue "L ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L GLU 169": "OE1" <-> "OE2" Residue "L ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L GLU 181": "OE1" <-> "OE2" Residue "L TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M ARG 12": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M GLU 26": "OE1" <-> "OE2" Residue "M ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M GLU 51": "OE1" <-> "OE2" Residue "M ASP 78": "OD1" <-> "OD2" Residue "M PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M ASP 134": "OD1" <-> "OD2" Residue "M ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M GLU 162": "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 "N ARG 12": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N GLU 169": "OE1" <-> "OE2" Residue "N ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ASP 186": "OD1" <-> "OD2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 76262 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 9101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 9101 Classifications: {'peptide': 577} Link IDs: {'PTRANS': 18, 'TRANS': 558} Chain: "B" Number of atoms: 9138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 580, 9138 Classifications: {'peptide': 580} Link IDs: {'PTRANS': 18, 'TRANS': 561} Chain: "C" Number of atoms: 9154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 581, 9154 Classifications: {'peptide': 581} Link IDs: {'PTRANS': 18, 'TRANS': 562} Chain: "D" Number of atoms: 9144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 580, 9144 Classifications: {'peptide': 580} Link IDs: {'PTRANS': 18, 'TRANS': 561} Chain: "E" Number of atoms: 9137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 580, 9137 Classifications: {'peptide': 580} Link IDs: {'PTRANS': 18, 'TRANS': 561} Chain: "F" Number of atoms: 9087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 575, 9087 Classifications: {'peptide': 575} Link IDs: {'PTRANS': 18, 'TRANS': 556} Chain breaks: 1 Chain: "S" Number of atoms: 178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 178 Classifications: {'peptide': 11} Link IDs: {'PTRANS': 2, 'TRANS': 8} 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: 2978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 2978 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 7, 'TRANS': 182} Chain: "N" Number of atoms: 2978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 2978 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 7, 'TRANS': 182} Chain: "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: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'AGS': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" 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: "E" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 27.17, per 1000 atoms: 0.36 Number of scatterers: 76262 At special positions: 0 Unit cell: (150.51, 155.73, 166.17, 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 31 15.00 Mg 5 11.99 O 7230 8.00 N 6720 7.00 C 23824 6.00 H 38283 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: 53.02 Conformation dependent library (CDL) restraints added in 5.5 seconds 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8904 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 220 helices and 44 sheets defined 47.9% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.60 Creating SS restraints... Processing helix chain 'A' and resid 176 through 182 removed outlier: 3.831A pdb=" N ARG A 181 " --> pdb=" O ASN A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 203 Processing helix chain 'A' and resid 220 through 233 removed outlier: 3.573A pdb=" N ALA A 224 " --> pdb=" O THR A 221 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLU A 225 " --> pdb=" O ALA A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 256 removed outlier: 3.610A pdb=" N LEU A 254 " --> pdb=" O ILE A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 274 removed outlier: 3.677A pdb=" N GLN A 273 " --> pdb=" O ALA A 269 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU A 274 " --> pdb=" O LEU A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 290 Processing helix chain 'A' and resid 303 through 306 No H-bonds generated for 'chain 'A' and resid 303 through 306' Processing helix chain 'A' and resid 308 through 313 Processing helix chain 'A' and resid 324 through 333 removed outlier: 3.760A pdb=" N SER A 328 " --> pdb=" O TYR A 324 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASN A 329 " --> pdb=" O GLN A 325 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE A 330 " --> pdb=" O GLU A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 340 Processing helix chain 'A' and resid 351 through 369 removed outlier: 3.717A pdb=" N GLY A 360 " --> pdb=" O GLN A 356 " (cutoff:3.500A) Proline residue: A 363 - end of helix Processing helix chain 'A' and resid 375 through 388 removed outlier: 3.626A pdb=" N VAL A 382 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU A 383 " --> pdb=" O ARG A 379 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL A 386 " --> pdb=" O VAL A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 411 removed outlier: 3.612A pdb=" N ARG A 410 " --> pdb=" O GLY A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 434 removed outlier: 4.329A pdb=" N VAL A 429 " --> pdb=" O ASP A 425 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N VAL A 430 " --> pdb=" O ILE A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 442 No H-bonds generated for 'chain 'A' and resid 440 through 442' Processing helix chain 'A' and resid 446 through 450 Processing helix chain 'A' and resid 452 through 459 removed outlier: 3.688A 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: 3.591A pdb=" N THR A 505 " --> pdb=" O LYS A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 534 removed outlier: 3.728A pdb=" N SER A 531 " --> pdb=" O ARG A 527 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N ARG A 532 " --> pdb=" O HIS A 528 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU A 533 " --> pdb=" O THR A 529 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE A 534 " --> pdb=" O VAL A 530 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 527 through 534' Processing helix chain 'A' and resid 548 through 555 removed outlier: 3.623A pdb=" N ALA A 552 " --> pdb=" O LEU A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 583 removed outlier: 3.504A pdb=" N ASN A 575 " --> pdb=" O PRO A 571 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE A 576 " --> pdb=" O ASP A 572 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLN A 579 " --> pdb=" O ASN A 575 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL A 580 " --> pdb=" O ILE A 576 " (cutoff:3.500A) 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 631 through 635 Processing helix chain 'A' and resid 638 through 643 removed outlier: 3.512A pdb=" N ARG A 643 " --> pdb=" O GLU A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 676 removed outlier: 3.959A pdb=" N HIS A 659 " --> pdb=" O THR A 655 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLN A 660 " --> pdb=" O ASP A 656 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL A 667 " --> pdb=" O ASP A 663 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS A 676 " --> pdb=" O GLN A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 684 through 693 removed outlier: 3.547A pdb=" N ASN A 688 " --> pdb=" O GLN A 684 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 699 No H-bonds generated for 'chain 'A' and resid 697 through 699' Processing helix chain 'A' and resid 702 through 711 Processing helix chain 'A' and resid 713 through 722 Processing helix chain 'A' and resid 724 through 726 No H-bonds generated for 'chain 'A' and resid 724 through 726' Processing helix chain 'B' and resid 176 through 182 removed outlier: 3.713A pdb=" N VAL B 182 " --> pdb=" O GLN B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 203 Processing helix chain 'B' and resid 220 through 233 removed outlier: 3.747A pdb=" N ALA B 228 " --> pdb=" O ALA B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 240 No H-bonds generated for 'chain 'B' and resid 238 through 240' Processing helix chain 'B' and resid 250 through 253 No H-bonds generated for 'chain 'B' and resid 250 through 253' Processing helix chain 'B' and resid 262 through 277 removed outlier: 3.597A pdb=" N ASP B 277 " --> pdb=" O GLN B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 292 Processing helix chain 'B' and resid 303 through 313 Proline residue: B 309 - end of helix Processing helix chain 'B' and resid 331 through 333 No H-bonds generated for 'chain 'B' and resid 331 through 333' Processing helix chain 'B' and resid 335 through 340 removed outlier: 3.842A pdb=" N ARG B 340 " --> pdb=" O ALA B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 369 removed outlier: 3.524A pdb=" N GLN B 356 " --> pdb=" O GLU B 352 " (cutoff:3.500A) Proline residue: B 363 - end of helix Processing helix chain 'B' and resid 375 through 388 removed outlier: 3.774A pdb=" N ARG B 379 " --> pdb=" O ALA B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 410 Processing helix chain 'B' and resid 426 through 434 Processing helix chain 'B' and resid 443 through 452 Processing helix chain 'B' and resid 454 through 457 No H-bonds generated for 'chain 'B' and resid 454 through 457' Processing helix chain 'B' and resid 464 through 479 Processing helix chain 'B' and resid 503 through 512 Processing helix chain 'B' and resid 521 through 523 No H-bonds generated for 'chain 'B' and resid 521 through 523' Processing helix chain 'B' and resid 527 through 534 removed outlier: 3.519A pdb=" N ARG B 532 " --> pdb=" O HIS B 528 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU B 533 " --> pdb=" O THR B 529 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ILE B 534 " --> pdb=" O VAL B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 555 Processing helix chain 'B' and resid 571 through 583 removed outlier: 3.718A pdb=" N LEU B 578 " --> pdb=" O ASN B 575 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N MET B 581 " --> pdb=" O LEU B 578 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASP B 582 " --> pdb=" O GLN B 579 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASN B 583 " --> pdb=" O VAL B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 613 Processing helix chain 'B' and resid 625 through 635 Processing helix chain 'B' and resid 638 through 642 Processing helix chain 'B' and resid 655 through 676 removed outlier: 3.532A pdb=" N ASP B 663 " --> pdb=" O HIS B 659 " (cutoff:3.500A) removed outlier: 3.854A 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 removed outlier: 3.626A pdb=" N ARG B 706 " --> pdb=" O ARG B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 721 Processing helix chain 'C' and resid 176 through 182 removed outlier: 3.511A pdb=" N VAL C 182 " --> pdb=" O GLN C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 202 Processing helix chain 'C' and resid 220 through 233 removed outlier: 3.628A pdb=" N ALA C 224 " --> pdb=" O LYS C 220 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA C 228 " --> pdb=" O ALA C 224 " (cutoff:3.500A) 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 290 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 331 through 333 No H-bonds generated for 'chain 'C' and resid 331 through 333' Processing helix chain 'C' and resid 335 through 340 removed outlier: 3.552A pdb=" N ARG C 340 " --> pdb=" O ALA C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 369 removed outlier: 3.721A pdb=" N GLN C 356 " --> pdb=" O GLU C 352 " (cutoff:3.500A) Proline residue: C 363 - end of helix Processing helix chain 'C' and resid 375 through 388 removed outlier: 3.580A pdb=" N ARG C 379 " --> pdb=" O ALA C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 397 No H-bonds generated for 'chain 'C' and resid 394 through 397' Processing helix chain 'C' and resid 399 through 411 removed outlier: 3.667A pdb=" N ALA C 409 " --> pdb=" O ALA C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 423 through 434 Processing helix chain 'C' and resid 443 through 450 Processing helix chain 'C' and resid 452 through 458 Processing helix chain 'C' and resid 464 through 479 Processing helix chain 'C' and resid 501 through 512 removed outlier: 3.926A pdb=" N THR C 505 " --> pdb=" O LYS C 501 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS C 510 " --> pdb=" O VAL C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 523 No H-bonds generated for 'chain 'C' and resid 521 through 523' Processing helix chain 'C' and resid 528 through 530 No H-bonds generated for 'chain 'C' and resid 528 through 530' 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 582 removed outlier: 3.509A pdb=" N LEU C 578 " --> pdb=" O ASN C 575 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLN C 579 " --> pdb=" O ILE C 576 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N MET C 581 " --> pdb=" O LEU C 578 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASP C 582 " --> pdb=" O GLN C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 609 through 613 Processing helix chain 'C' and resid 625 through 635 Processing helix chain 'C' and resid 638 through 643 Processing helix chain 'C' and resid 655 through 676 removed outlier: 3.593A pdb=" N HIS C 659 " --> pdb=" O THR C 655 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLN C 660 " --> pdb=" O ASP C 656 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLN C 675 " --> pdb=" O VAL C 671 " (cutoff:3.500A) removed outlier: 3.805A 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 722 removed outlier: 4.338A pdb=" N LYS C 714 " --> pdb=" O ASP C 710 " (cutoff:3.500A) Proline residue: C 715 - end of helix Processing helix chain 'D' and resid 176 through 182 removed outlier: 3.548A pdb=" N ARG D 181 " --> pdb=" O ASN D 177 " (cutoff:3.500A) removed outlier: 3.512A 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: 3.539A pdb=" N ALA D 224 " --> pdb=" O LYS D 220 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA D 228 " --> pdb=" O ALA D 224 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL D 232 " --> pdb=" O ALA D 228 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN D 233 " --> pdb=" O TRP D 229 " (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 291 removed outlier: 3.839A pdb=" N ILE D 291 " --> pdb=" O HIS D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 312 Proline residue: D 309 - end of helix removed outlier: 3.546A pdb=" N SER D 312 " --> pdb=" O LYS D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 329 Processing helix chain 'D' and resid 335 through 340 removed outlier: 3.526A pdb=" N ARG D 340 " --> pdb=" O ALA D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 369 removed outlier: 3.655A 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 removed outlier: 3.658A pdb=" N ILE D 399 " --> pdb=" O PRO D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 434 Processing helix chain 'D' and resid 446 through 450 Processing helix chain 'D' and resid 452 through 459 Processing helix chain 'D' and resid 464 through 479 Processing helix chain 'D' and resid 504 through 512 Processing helix chain 'D' and resid 528 through 532 Processing helix chain 'D' and resid 548 through 555 Processing helix chain 'D' and resid 571 through 583 removed outlier: 3.522A pdb=" N ASN D 575 " --> pdb=" O ASP D 572 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU D 578 " --> pdb=" O ASN D 575 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLN D 579 " --> pdb=" O ILE D 576 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N MET D 581 " --> pdb=" O LEU D 578 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ASP D 582 " --> pdb=" O GLN D 579 " (cutoff:3.500A) removed outlier: 4.240A 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: 3.795A pdb=" N GLN D 660 " --> pdb=" O ASP D 656 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYS D 676 " --> pdb=" O GLN D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 684 through 694 Processing helix chain 'D' and resid 702 through 721 removed outlier: 3.845A pdb=" N ARG D 706 " --> pdb=" O ARG D 702 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LYS D 714 " --> pdb=" O ASP D 710 " (cutoff:3.500A) Proline residue: D 715 - end of helix 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: 3.655A 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: 3.941A pdb=" N ALA E 224 " --> pdb=" O LYS E 220 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA E 228 " --> pdb=" O ALA E 224 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 253 No H-bonds generated for 'chain 'E' and resid 250 through 253' Processing helix chain 'E' and resid 262 through 276 Processing helix chain 'E' and resid 287 through 289 No H-bonds generated for 'chain 'E' and resid 287 through 289' Processing helix chain 'E' and resid 303 through 312 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: 3.751A pdb=" N ARG E 340 " --> pdb=" O ALA E 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 353 through 369 Proline residue: E 363 - end of helix Processing helix chain 'E' and resid 375 through 388 removed outlier: 3.504A pdb=" N LYS E 387 " --> pdb=" O GLU E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 394 through 411 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 459 Processing helix chain 'E' and resid 464 through 479 Processing helix chain 'E' and resid 501 through 512 removed outlier: 3.867A pdb=" N THR E 505 " --> pdb=" O LYS E 501 " (cutoff:3.500A) Processing helix chain 'E' and resid 527 through 529 No H-bonds generated for 'chain 'E' and resid 527 through 529' Processing helix chain 'E' and resid 548 through 555 removed outlier: 3.865A pdb=" N ALA E 552 " --> pdb=" O LEU E 548 " (cutoff:3.500A) Processing helix chain 'E' and resid 571 through 583 removed outlier: 4.075A pdb=" N GLN E 579 " --> pdb=" O ASN E 575 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL E 580 " --> pdb=" O ILE E 576 " (cutoff:3.500A) Processing helix chain 'E' and resid 607 through 613 removed outlier: 4.283A pdb=" N GLU E 611 " --> pdb=" O ALA E 607 " (cutoff:3.500A) Processing helix chain 'E' and resid 627 through 635 Processing helix chain 'E' and resid 638 through 643 Processing helix chain 'E' and resid 655 through 676 removed outlier: 3.873A pdb=" N GLN E 660 " --> pdb=" O ASP E 656 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN E 675 " --> pdb=" O VAL E 671 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS E 676 " --> pdb=" O GLN E 672 " (cutoff:3.500A) Processing helix chain 'E' and resid 684 through 694 removed outlier: 3.662A pdb=" N ASN E 688 " --> pdb=" O GLN E 684 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TRP E 689 " --> pdb=" O GLU E 685 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS E 693 " --> pdb=" O TRP E 689 " (cutoff:3.500A) Processing helix chain 'E' and resid 702 through 711 removed outlier: 3.683A pdb=" N ALA E 705 " --> pdb=" O ARG E 702 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE E 708 " --> pdb=" O ALA E 705 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASP E 710 " --> pdb=" O VAL E 707 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASN E 711 " --> pdb=" O ILE E 708 " (cutoff:3.500A) Processing helix chain 'E' and resid 713 through 721 Processing helix chain 'F' and resid 176 through 182 removed outlier: 3.547A pdb=" N ARG F 181 " --> pdb=" O ASN F 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 192 through 202 Processing helix chain 'F' and resid 220 through 233 removed outlier: 3.786A pdb=" N ALA F 224 " --> pdb=" O LYS F 220 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA F 228 " --> pdb=" O ALA F 224 " (cutoff:3.500A) Processing helix chain 'F' and resid 238 through 241 No H-bonds generated for 'chain 'F' and resid 238 through 241' Processing helix chain 'F' and resid 250 through 253 No H-bonds generated for 'chain 'F' and resid 250 through 253' Processing helix chain 'F' and resid 262 through 276 Processing helix chain 'F' and resid 287 through 290 No H-bonds generated for 'chain 'F' and resid 287 through 290' Processing helix chain 'F' and resid 306 through 313 removed outlier: 3.773A pdb=" N LEU F 310 " --> pdb=" O LEU F 306 " (cutoff:3.500A) 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 removed outlier: 3.650A pdb=" N HIS F 369 " --> pdb=" O TYR F 365 " (cutoff:3.500A) Processing helix chain 'F' and resid 375 through 388 removed outlier: 3.596A pdb=" N LYS F 387 " --> pdb=" O GLU F 383 " (cutoff:3.500A) Processing helix chain 'F' and resid 394 through 411 Processing helix chain 'F' and resid 423 through 434 removed outlier: 3.502A pdb=" N ILE F 433 " --> pdb=" O VAL F 429 " (cutoff:3.500A) Processing helix chain 'F' and resid 438 through 441 No H-bonds generated for 'chain 'F' and resid 438 through 441' Processing helix chain 'F' and resid 445 through 450 Processing helix chain 'F' and resid 452 through 459 removed outlier: 3.824A pdb=" N LEU F 459 " --> pdb=" O ARG F 455 " (cutoff:3.500A) Processing helix chain 'F' and resid 464 through 479 removed outlier: 3.517A pdb=" N ALA F 479 " --> pdb=" O LYS F 475 " (cutoff:3.500A) Processing helix chain 'F' and resid 503 through 512 Processing helix chain 'F' and resid 527 through 533 Processing helix chain 'F' and resid 550 through 555 Processing helix chain 'F' and resid 571 through 583 removed outlier: 3.562A pdb=" N ASN F 575 " --> pdb=" O PRO F 571 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN F 579 " --> pdb=" O ASN F 575 " (cutoff:3.500A) Processing helix chain 'F' and resid 607 through 613 removed outlier: 3.699A pdb=" N THR F 612 " --> pdb=" O GLY F 608 " (cutoff:3.500A) Processing helix chain 'F' and resid 628 through 635 removed outlier: 3.547A pdb=" N ILE F 635 " --> pdb=" O GLU F 631 " (cutoff:3.500A) Processing helix chain 'F' and resid 655 through 676 removed outlier: 3.735A pdb=" N ASP F 663 " --> pdb=" O HIS F 659 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL F 667 " --> pdb=" O ASP F 663 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLU F 668 " --> pdb=" O LYS F 664 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU F 669 " --> pdb=" O PHE F 665 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN F 675 " --> pdb=" O VAL F 671 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS F 676 " --> pdb=" O GLN F 672 " (cutoff:3.500A) Processing helix chain 'F' and resid 684 through 694 removed outlier: 3.681A pdb=" N GLU F 692 " --> pdb=" O ASN F 688 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS F 693 " --> pdb=" O TRP F 689 " (cutoff:3.500A) Processing helix chain 'F' and resid 702 through 721 removed outlier: 4.115A pdb=" N ARG F 706 " --> pdb=" O ARG F 702 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS F 714 " --> pdb=" O ASP F 710 " (cutoff:3.500A) Proline residue: F 715 - end of helix 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: 3.747A pdb=" N GLU H 26 " --> pdb=" O ARG H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 53 removed outlier: 3.522A pdb=" N ALA H 52 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU H 53 " --> pdb=" O PHE H 49 " (cutoff:3.500A) Processing helix chain 'H' and resid 70 through 82 removed outlier: 3.853A pdb=" N SER H 75 " --> pdb=" O THR H 71 " (cutoff:3.500A) removed outlier: 3.791A 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 169 Processing helix chain 'H' and resid 176 through 182 removed outlier: 3.565A pdb=" N VAL H 180 " --> pdb=" O ALA H 176 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU H 181 " --> pdb=" O PRO H 177 " (cutoff:3.500A) Processing helix chain 'I' and resid 19 through 25 Processing helix chain 'I' and resid 37 through 53 Processing helix chain 'I' and resid 70 through 82 removed outlier: 3.586A pdb=" N SER I 75 " --> pdb=" O THR I 71 " (cutoff:3.500A) removed outlier: 3.695A 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 removed outlier: 3.574A pdb=" N GLU I 141 " --> pdb=" O ILE I 137 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE I 142 " --> pdb=" O HIS I 138 " (cutoff:3.500A) Processing helix chain 'I' and resid 161 through 168 Processing helix chain 'I' and resid 176 through 182 removed outlier: 3.666A pdb=" N GLU I 181 " --> pdb=" O PRO I 177 " (cutoff:3.500A) Processing helix chain 'J' and resid 19 through 26 removed outlier: 3.504A 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: 3.773A pdb=" N SER J 75 " --> pdb=" O THR J 71 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ILE J 76 " --> pdb=" O ALA J 72 " (cutoff:3.500A) Processing helix chain 'J' and resid 100 through 103 No H-bonds generated for 'chain 'J' and resid 100 through 103' Processing helix chain 'J' and resid 132 through 157 Processing helix chain 'J' and resid 161 through 168 Processing helix chain 'J' and resid 176 through 182 removed outlier: 3.643A pdb=" N VAL J 180 " --> pdb=" O ALA J 176 " (cutoff:3.500A) Processing helix chain 'K' and resid 19 through 25 Processing helix chain 'K' and resid 37 through 53 Processing helix chain 'K' and resid 70 through 82 removed outlier: 3.649A pdb=" N ILE K 76 " --> pdb=" O ALA K 72 " (cutoff:3.500A) Processing helix chain 'K' and resid 100 through 104 Processing helix chain 'K' and resid 132 through 157 Processing helix chain 'K' and resid 161 through 168 Processing helix chain 'K' and resid 176 through 182 removed outlier: 3.642A pdb=" N VAL K 180 " --> pdb=" O ALA K 176 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU K 181 " --> pdb=" O PRO K 177 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 26 removed outlier: 3.702A 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: 3.658A pdb=" N SER L 75 " --> pdb=" O THR L 71 " (cutoff:3.500A) removed outlier: 3.783A 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 Processing helix chain 'L' and resid 176 through 182 Processing helix chain 'M' and resid 19 through 26 removed outlier: 3.591A pdb=" N GLU M 26 " --> pdb=" O ARG M 22 " (cutoff:3.500A) Processing helix chain 'M' and resid 37 through 53 Processing helix chain 'M' and resid 70 through 82 Processing helix chain 'M' and resid 97 through 103 Processing helix chain 'M' and resid 132 through 157 removed outlier: 3.529A pdb=" N GLU M 141 " --> pdb=" O ILE M 137 " (cutoff:3.500A) Processing helix chain 'M' and resid 161 through 168 Processing helix chain 'M' and resid 176 through 182 Processing helix chain 'N' and resid 19 through 26 removed outlier: 3.543A 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: 3.552A pdb=" N SER N 75 " --> pdb=" O THR N 71 " (cutoff:3.500A) removed outlier: 3.670A 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 removed outlier: 3.574A pdb=" N ILE N 142 " --> pdb=" O HIS N 138 " (cutoff:3.500A) Processing helix chain 'N' and resid 161 through 168 Processing helix chain 'N' and resid 176 through 182 removed outlier: 3.602A pdb=" N GLU N 181 " --> pdb=" O PRO N 177 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 173 through 175 removed outlier: 6.871A pdb=" N ILE A 281 " --> pdb=" O TYR A 246 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N LEU A 248 " --> pdb=" O ILE A 281 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N PHE A 283 " --> pdb=" O LEU A 248 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 341 through 345 removed outlier: 6.674A pdb=" N ASN A 209 " --> pdb=" O GLN A 342 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N ILE A 344 " --> pdb=" O ASN A 209 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N LEU A 211 " --> pdb=" O ILE A 344 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N GLY A 320 " --> pdb=" O LEU A 212 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N GLY A 214 " --> pdb=" O GLY A 320 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N THR A 322 " --> pdb=" O GLY A 214 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 490 through 493 removed outlier: 6.625A pdb=" N LEU A 601 " --> pdb=" O PHE A 491 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N PHE A 493 " --> pdb=" O LEU A 601 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N MET A 603 " --> pdb=" O PHE A 493 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 585 through 587 Processing sheet with id= E, first strand: chain 'A' and resid 679 through 682 removed outlier: 3.784A pdb=" N GLU A 741 " --> pdb=" O ASP A 736 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 173 through 175 removed outlier: 6.521A pdb=" N ILE B 281 " --> pdb=" O TYR B 246 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N LEU B 248 " --> pdb=" O ILE B 281 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N PHE B 283 " --> pdb=" O LEU B 248 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER B 321 " --> pdb=" O ILE B 284 " (cutoff:3.500A) removed outlier: 8.481A pdb=" N THR B 322 " --> pdb=" O PRO B 210 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N LEU B 212 " --> pdb=" O THR B 322 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N GLN B 342 " --> pdb=" O LEU B 211 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N VAL B 213 " --> pdb=" O GLN B 342 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N ILE B 344 " --> pdb=" O VAL B 213 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 646 through 650 removed outlier: 3.551A pdb=" N ASN B 646 " --> pdb=" O SER B 490 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N LEU B 601 " --> pdb=" O PHE B 491 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N PHE B 493 " --> pdb=" O LEU B 601 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N MET B 603 " --> pdb=" O PHE B 493 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N GLY B 495 " --> pdb=" O MET B 603 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N GLU B 515 " --> pdb=" O VAL B 560 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N LEU B 562 " --> pdb=" O GLU B 515 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N LEU B 517 " --> pdb=" O LEU B 562 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N ASP B 564 " --> pdb=" O LEU B 517 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 585 through 587 removed outlier: 3.584A pdb=" N LEU B 586 " --> pdb=" O ALA B 594 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA B 594 " --> pdb=" O LEU B 586 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'B' and resid 680 through 682 removed outlier: 6.575A pdb=" N VAL B 731 " --> pdb=" O GLU B 681 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU B 741 " --> pdb=" O ASP B 736 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 173 through 175 removed outlier: 4.874A pdb=" N ASP C 285 " --> pdb=" O LEU C 248 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ARG C 317 " --> pdb=" O LEU C 282 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N ILE C 284 " --> pdb=" O ARG C 317 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ILE C 319 " --> pdb=" O ILE C 284 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N GLN C 342 " --> pdb=" O LEU C 211 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N VAL C 213 " --> pdb=" O GLN C 342 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N ILE C 344 " --> pdb=" O VAL C 213 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 646 through 649 removed outlier: 3.858A pdb=" N ASN C 646 " --> pdb=" O SER C 490 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU C 492 " --> pdb=" O ASN C 646 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LEU C 601 " --> pdb=" O PHE C 491 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N PHE C 493 " --> pdb=" O LEU C 601 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N MET C 603 " --> pdb=" O PHE C 493 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N GLU C 515 " --> pdb=" O VAL C 560 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N LEU C 562 " --> pdb=" O GLU C 515 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LEU C 517 " --> pdb=" O LEU C 562 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N ASP C 564 " --> pdb=" O LEU C 517 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N PHE C 519 " --> pdb=" O ASP C 564 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 679 through 682 removed outlier: 3.501A pdb=" N GLU C 741 " --> pdb=" O ASP C 736 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 173 through 175 Processing sheet with id= N, first strand: chain 'D' and resid 341 through 345 removed outlier: 6.956A pdb=" N ASN D 209 " --> pdb=" O GLN D 342 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N ILE D 344 " --> pdb=" O ASN D 209 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N LEU D 211 " --> pdb=" O ILE D 344 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N GLY D 320 " --> pdb=" O LEU D 212 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'D' and resid 646 through 649 removed outlier: 3.581A pdb=" N ASN D 646 " --> pdb=" O SER D 490 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU D 492 " --> pdb=" O ASN D 646 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 585 through 587 Processing sheet with id= Q, first strand: chain 'D' and resid 680 through 682 removed outlier: 6.622A pdb=" N VAL D 731 " --> pdb=" O GLU D 681 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 173 through 175 removed outlier: 3.556A pdb=" N THR E 174 " --> pdb=" O SER E 247 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ILE E 281 " --> pdb=" O TYR E 246 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N LEU E 248 " --> pdb=" O ILE E 281 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N PHE E 283 " --> pdb=" O LEU E 248 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ARG E 317 " --> pdb=" O LEU E 282 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N ILE E 284 " --> pdb=" O ARG E 317 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ILE E 319 " --> pdb=" O ILE E 284 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 646 through 650 removed outlier: 3.735A pdb=" N ASN E 646 " --> pdb=" O SER E 490 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU E 492 " --> pdb=" O ASN E 646 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LEU E 601 " --> pdb=" O PHE E 491 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N PHE E 493 " --> pdb=" O LEU E 601 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N MET E 603 " --> pdb=" O PHE E 493 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N GLY E 495 " --> pdb=" O MET E 603 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N THR E 605 " --> pdb=" O GLY E 495 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N GLU E 515 " --> pdb=" O VAL E 560 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N LEU E 562 " --> pdb=" O GLU E 515 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU E 517 " --> pdb=" O LEU E 562 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N ASP E 564 " --> pdb=" O LEU E 517 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N PHE E 519 " --> pdb=" O ASP E 564 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 585 through 587 Processing sheet with id= U, first strand: chain 'F' and resid 211 through 213 removed outlier: 7.754A pdb=" N LEU F 212 " --> pdb=" O VAL F 318 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N GLY F 320 " --> pdb=" O LEU F 212 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ARG F 317 " --> pdb=" O SER F 280 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N THR F 244 " --> pdb=" O ILE F 281 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N PHE F 283 " --> pdb=" O THR F 244 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N TYR F 246 " --> pdb=" O PHE F 283 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'F' and resid 493 through 495 removed outlier: 6.769A pdb=" N ILE F 648 " --> pdb=" O ALA F 494 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'F' and resid 517 through 520 removed outlier: 3.614A pdb=" N LEU F 517 " --> pdb=" O VAL F 560 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL F 600 " --> pdb=" O LEU F 561 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N LEU F 563 " --> pdb=" O VAL F 600 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL F 602 " --> pdb=" O LEU F 563 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'F' and resid 731 through 735 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: 6.277A pdb=" N TYR H 60 " --> pdb=" O ILE H 29 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N LEU H 31 " --> pdb=" O TYR H 60 " (cutoff:3.500A) removed outlier: 5.956A 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 Processing sheet with id= AB, first strand: chain 'I' and resid 6 through 9 Processing sheet with id= AC, first strand: chain 'I' and resid 28 through 32 removed outlier: 6.456A pdb=" N TYR I 60 " --> pdb=" O ILE I 29 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N LEU I 31 " --> pdb=" O TYR I 60 " (cutoff:3.500A) removed outlier: 6.116A 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 8 Processing sheet with id= AF, first strand: chain 'J' and resid 28 through 32 removed outlier: 6.422A pdb=" N TYR J 60 " --> pdb=" O ILE J 29 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N LEU J 31 " --> pdb=" O TYR J 60 " (cutoff:3.500A) removed outlier: 6.387A 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 Processing sheet with id= AI, first strand: chain 'K' and resid 28 through 32 removed outlier: 6.620A pdb=" N TYR K 60 " --> pdb=" O ILE K 29 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N LEU K 31 " --> pdb=" O TYR K 60 " (cutoff:3.500A) removed outlier: 6.040A 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 removed outlier: 3.539A pdb=" N ILE K 121 " --> pdb=" O ARG K 172 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG K 172 " --> pdb=" O ILE K 121 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'L' and resid 5 through 9 Processing sheet with id= AL, first strand: chain 'L' and resid 28 through 32 removed outlier: 6.722A pdb=" N TYR L 60 " --> pdb=" O ILE L 29 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N LEU L 31 " --> pdb=" O TYR L 60 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N TYR L 62 " --> pdb=" O LEU L 31 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'L' and resid 118 through 121 Processing sheet with id= AN, first strand: chain 'M' and resid 5 through 9 Processing sheet with id= AO, first strand: chain 'M' and resid 28 through 32 removed outlier: 6.565A pdb=" N TYR M 60 " --> pdb=" O ILE M 29 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N LEU M 31 " --> pdb=" O TYR M 60 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N TYR M 62 " --> pdb=" O LEU M 31 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'M' and resid 119 through 121 Processing sheet with id= AQ, first strand: chain 'N' and resid 5 through 8 Processing sheet with id= AR, first strand: chain 'N' and resid 28 through 32 removed outlier: 6.322A pdb=" N TYR N 60 " --> pdb=" O ILE N 29 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N LEU N 31 " --> pdb=" O TYR N 60 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N TYR N 62 " --> pdb=" O LEU N 31 " (cutoff:3.500A) 1453 hydrogen bonds defined for protein. 4215 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: 29.88 Time building geometry restraints manager: 55.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.06: 38257 1.06 - 1.28: 6534 1.28 - 1.50: 15829 1.50 - 1.73: 15920 1.73 - 1.95: 305 Bond restraints: 76845 Sorted by residual: bond pdb=" C4 ADP D 802 " pdb=" C5 ADP D 802 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.03e+01 bond pdb=" C4 ADP E 802 " pdb=" C5 ADP E 802 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.00e+01 bond pdb=" C4 ADP A 801 " pdb=" C5 ADP A 801 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.99e+01 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 802 " pdb=" C5 ADP F 802 " ideal model delta sigma weight residual 1.490 1.382 0.108 2.00e-02 2.50e+03 2.94e+01 ... (remaining 76840 not shown) Histogram of bond angle deviations from ideal: 98.68 - 106.17: 1207 106.17 - 113.66: 93560 113.66 - 121.15: 28578 121.15 - 128.64: 15624 128.64 - 136.14: 310 Bond angle restraints: 139279 Sorted by residual: angle pdb=" PA AGS C 801 " pdb=" O3A AGS C 801 " pdb=" PB AGS C 801 " ideal model delta sigma weight residual 119.76 136.14 -16.38 3.00e+00 1.11e-01 2.98e+01 angle pdb=" PB AGS D 801 " pdb=" O3B AGS D 801 " pdb=" PG AGS D 801 " ideal model delta sigma weight residual 120.12 132.85 -12.73 3.00e+00 1.11e-01 1.80e+01 angle pdb=" N LEU C 394 " pdb=" CA LEU C 394 " pdb=" C LEU C 394 " ideal model delta sigma weight residual 113.16 119.17 -6.01 1.42e+00 4.96e-01 1.79e+01 angle pdb=" PA AGS D 801 " pdb=" O3A AGS D 801 " pdb=" PB AGS D 801 " ideal model delta sigma weight residual 119.76 132.13 -12.37 3.00e+00 1.11e-01 1.70e+01 angle pdb=" PB AGS C 802 " pdb=" O3B AGS C 802 " pdb=" PG AGS C 802 " ideal model delta sigma weight residual 120.12 132.32 -12.20 3.00e+00 1.11e-01 1.65e+01 ... (remaining 139274 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.99: 29454 28.99 - 57.98: 770 57.98 - 86.97: 70 86.97 - 115.96: 15 115.96 - 144.95: 18 Dihedral angle restraints: 30327 sinusoidal: 14822 harmonic: 15505 Sorted by residual: dihedral pdb=" C5' ADP E 801 " pdb=" O5' ADP E 801 " pdb=" PA ADP E 801 " pdb=" O2A ADP E 801 " ideal model delta sinusoidal sigma weight residual -60.00 84.96 -144.95 1 2.00e+01 2.50e-03 4.36e+01 dihedral pdb=" C5' ADP D 802 " pdb=" O5' ADP D 802 " pdb=" PA ADP D 802 " pdb=" O2A ADP D 802 " ideal model delta sinusoidal sigma weight residual -60.00 82.83 -142.83 1 2.00e+01 2.50e-03 4.31e+01 dihedral pdb=" C5' ADP F 802 " pdb=" O5' ADP F 802 " pdb=" PA ADP F 802 " pdb=" O2A ADP F 802 " ideal model delta sinusoidal sigma weight residual 300.00 160.87 139.14 1 2.00e+01 2.50e-03 4.22e+01 ... (remaining 30324 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 4619 0.050 - 0.101: 1110 0.101 - 0.151: 231 0.151 - 0.201: 15 0.201 - 0.252: 4 Chirality restraints: 5979 Sorted by residual: chirality pdb=" CA PHE M 82 " pdb=" N PHE M 82 " pdb=" C PHE M 82 " pdb=" CB PHE M 82 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" C3' ADP E 801 " pdb=" C2' ADP E 801 " pdb=" C4' ADP E 801 " pdb=" O3' ADP E 801 " both_signs ideal model delta sigma weight residual False -2.51 -2.73 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA ILE F 436 " pdb=" N ILE F 436 " pdb=" C ILE F 436 " pdb=" CB ILE F 436 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 5976 not shown) Planarity restraints: 11367 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN E 545 " -0.128 2.00e-02 2.50e+03 4.32e-01 2.80e+03 pdb=" CD GLN E 545 " 0.012 2.00e-02 2.50e+03 pdb=" OE1 GLN E 545 " 0.123 2.00e-02 2.50e+03 pdb=" NE2 GLN E 545 " 0.001 2.00e-02 2.50e+03 pdb="HE21 GLN E 545 " -0.743 2.00e-02 2.50e+03 pdb="HE22 GLN E 545 " 0.734 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP E 544 " -0.017 2.00e-02 2.50e+03 3.15e-02 9.90e+00 pdb=" N GLN E 545 " 0.054 2.00e-02 2.50e+03 pdb=" CA GLN E 545 " -0.014 2.00e-02 2.50e+03 pdb=" H GLN E 545 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 362 " -0.050 5.00e-02 4.00e+02 7.57e-02 9.16e+00 pdb=" N PRO A 363 " 0.131 5.00e-02 4.00e+02 pdb=" CA PRO A 363 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 363 " -0.042 5.00e-02 4.00e+02 ... (remaining 11364 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.23: 7029 2.23 - 2.82: 173377 2.82 - 3.42: 201282 3.42 - 4.01: 279156 4.01 - 4.60: 431605 Nonbonded interactions: 1092449 Sorted by model distance: nonbonded pdb=" O ALA H 96 " pdb=" H ALA H 100 " model vdw 1.639 1.850 nonbonded pdb=" O ALA M 96 " pdb=" H ALA M 100 " model vdw 1.645 1.850 nonbonded pdb=" O ALA N 96 " pdb=" H ALA N 100 " model vdw 1.671 1.850 nonbonded pdb=" O ALA I 96 " pdb=" H ALA I 100 " model vdw 1.672 1.850 nonbonded pdb=" OE1 GLU C 567 " pdb=" H GLU C 567 " model vdw 1.674 1.850 ... (remaining 1092444 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 172 through 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 296 or (resid 30 \ 1 and (name N or name CA or name C or name O or name CB or name CG1 or name CG2 \ or name HA or name HB or name HG11 or name HG12 or name HG13 or name HG21 or nam \ e HG22 or name HG23)) or resid 302 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 542 or \ (resid 543 and (name N or name CA or name C or name O or name CB or name CG or n \ ame CD1 or name CD2 or name CE1 or name CE2 or name CZ or name H or name HA )) o \ r resid 544 through 748)) selection = (chain 'B' and ((resid 172 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name H \ A or name HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name HE2 or nam \ e HZ )) or resid 173 through 296 or (resid 301 and (name N or name CA or name C \ or name O or name CB or name CG1 or name CG2 or name HA or name HB or name HG11 \ or name HG12 or name HG13 or name HG21 or name HG22 or name HG23)) or resid 302 \ through 542 or (resid 543 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name H \ or name HA )) or resid 544 through 748)) selection = (chain 'C' and ((resid 172 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name H \ A or name HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name HE2 or nam \ e HZ )) or resid 173 through 220 or (resid 221 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 222 through 296 or (resid 301 and \ (name N or name CA or name C or name O or name CB or name CG1 or name CG2 or na \ me HA or name HB or name HG11 or name HG12 or name HG13 or name HG21 or name HG2 \ 2 or name HG23)) or resid 302 through 501 or (resid 502 and (name N or name CA o \ r name C or name O or name CB or name OG1 or name CG2 or name H or name HA or na \ me HB or name HG21 or name HG22 or name HG23)) or resid 503 through 542 or (resi \ d 543 and (name N or name CA or name C or name O or name CB or name CG or name C \ D1 or name CD2 or name CE1 or name CE2 or name CZ or name H or name HA )) or res \ id 544 through 748)) selection = (chain 'D' and ((resid 172 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name H \ A or name HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name HE2 or nam \ e HZ )) or resid 173 through 220 or (resid 221 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 222 through 296 or (resid 301 and \ (name N or name CA or name C or name O or name CB or name CG1 or name CG2 or na \ me HA or name HB or name HG11 or name HG12 or name HG13 or name HG21 or name HG2 \ 2 or name HG23)) or resid 302 through 501 or (resid 502 and (name N or name CA o \ r name C or name O or name CB or name OG1 or name CG2 or name H or name HA or na \ me HB or name HG21 or name HG22 or name HG23)) or resid 503 through 542 or (resi \ d 543 and (name N or name CA or name C or name O or name CB or name CG or name C \ D1 or name CD2 or name CE1 or name CE2 or name CZ or name H or name HA )) or res \ id 544 through 748)) selection = (chain 'E' and ((resid 172 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name H \ A or name HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name HE2 or nam \ e HZ )) or resid 173 through 220 or (resid 221 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 222 through 296 or (resid 301 and \ (name N or name CA or name C or name O or name CB or name CG1 or name CG2 or na \ me HA or name HB or name HG11 or name HG12 or name HG13 or name HG21 or name HG2 \ 2 or name HG23)) or resid 302 through 501 or (resid 502 and (name N or name CA o \ r name C or name O or name CB or name OG1 or name CG2 or name H or name HA or na \ me HB or name HG21 or name HG22 or name HG23)) or resid 503 through 748)) selection = (chain 'F' and ((resid 172 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name H \ A or name HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name HE2 or nam \ e HZ )) or resid 173 through 220 or (resid 221 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 222 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 na \ me H or name HA or name HB or name HG21 or name HG22 or name HG23)) or resid 503 \ through 542 or (resid 543 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name H \ or name HA )) or resid 544 through 748)) } ncs_group { reference = (chain 'H' and resid 2 through 191) selection = (chain 'I' and resid 2 through 191) selection = (chain 'J' and resid 2 through 191) selection = (chain 'K' and resid 2 through 191) selection = (chain 'L' and resid 2 through 191) selection = chain 'M' selection = chain 'N' } 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 31 5.49 5 Mg 5 5.21 5 S 169 5.16 5 C 23824 2.51 5 N 6720 2.21 5 O 7230 1.98 5 H 38283 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: 0.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 1.070 Extract box with map and model: 7.380 Check model and map are aligned: 0.850 Convert atoms to be neutral: 0.490 Process input model: 196.540 Find NCS groups from input model: 3.610 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Set scattering table: 0.030 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:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 213.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 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 : 0.006 0.110 38562 Z= 0.384 Angle : 0.855 16.376 52104 Z= 0.440 Chirality : 0.045 0.252 5979 Planarity : 0.005 0.076 6722 Dihedral : 14.262 144.954 14616 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % 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: -0.25 (0.11), residues: 4789 helix: 0.45 (0.10), residues: 2331 sheet: -0.34 (0.19), residues: 666 loop : -0.78 (0.13), residues: 1792 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 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 1263 residues out of total 4057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1263 time to evaluate : 4.662 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 outliers start: 0 outliers final: 0 residues processed: 1263 average time/residue: 1.0844 time to fit residues: 2157.2033 Evaluate side-chains 1046 residues out of total 4057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1046 time to evaluate : 4.612 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.9582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 405 optimal weight: 7.9990 chunk 363 optimal weight: 10.0000 chunk 201 optimal weight: 5.9990 chunk 124 optimal weight: 8.9990 chunk 245 optimal weight: 5.9990 chunk 194 optimal weight: 2.9990 chunk 376 optimal weight: 7.9990 chunk 145 optimal weight: 5.9990 chunk 228 optimal weight: 10.0000 chunk 280 optimal weight: 6.9990 chunk 435 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 483 HIS B 209 ASN B 528 HIS B 642 ASN C 325 GLN C 622 GLN C 642 ASN D 356 GLN D 598 ASN D 659 HIS E 273 GLN E 507 GLN E 740 ASN F 709 GLN I 41 ASN J 41 ASN K 41 ASN L 116 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.064 38562 Z= 0.337 Angle : 0.615 9.610 52104 Z= 0.323 Chirality : 0.041 0.172 5979 Planarity : 0.004 0.051 6722 Dihedral : 9.335 156.825 5329 Min Nonbonded Distance : 1.710 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer Outliers : 1.53 % 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: 0.29 (0.11), residues: 4789 helix: 0.92 (0.10), residues: 2377 sheet: -0.15 (0.19), residues: 694 loop : -0.54 (0.14), residues: 1718 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 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 1235 residues out of total 4057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 1173 time to evaluate : 5.011 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 outliers start: 62 outliers final: 42 residues processed: 1195 average time/residue: 1.0325 time to fit residues: 1934.9577 Evaluate side-chains 1150 residues out of total 4057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 1108 time to evaluate : 4.606 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 0 residues processed: 42 average time/residue: 0.7249 time to fit residues: 61.6308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 242 optimal weight: 1.9990 chunk 135 optimal weight: 8.9990 chunk 362 optimal weight: 9.9990 chunk 296 optimal weight: 9.9990 chunk 120 optimal weight: 3.9990 chunk 436 optimal weight: 6.9990 chunk 471 optimal weight: 9.9990 chunk 388 optimal weight: 0.9990 chunk 433 optimal weight: 9.9990 chunk 148 optimal weight: 3.9990 chunk 350 optimal weight: 10.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 483 HIS A 528 HIS C 422 ASN D 485 HIS D 606 ASN D 659 HIS E 273 GLN E 288 HIS F 177 ASN F 393 HIS F 659 HIS J 150 ASN K 191 HIS N 116 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 38562 Z= 0.233 Angle : 0.531 9.085 52104 Z= 0.271 Chirality : 0.039 0.160 5979 Planarity : 0.003 0.040 6722 Dihedral : 9.231 157.000 5329 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer Outliers : 0.57 % 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: 0.44 (0.12), residues: 4789 helix: 1.07 (0.10), residues: 2378 sheet: -0.13 (0.18), residues: 738 loop : -0.51 (0.14), residues: 1673 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 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 1160 residues out of total 4057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 1137 time to evaluate : 4.620 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 outliers start: 23 outliers final: 14 residues processed: 1142 average time/residue: 1.0366 time to fit residues: 1862.7160 Evaluate side-chains 1114 residues out of total 4057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 1100 time to evaluate : 4.617 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.7258 time to fit residues: 24.4754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 431 optimal weight: 8.9990 chunk 328 optimal weight: 50.0000 chunk 226 optimal weight: 7.9990 chunk 48 optimal weight: 20.0000 chunk 208 optimal weight: 10.0000 chunk 293 optimal weight: 9.9990 chunk 438 optimal weight: 10.0000 chunk 463 optimal weight: 0.7980 chunk 228 optimal weight: 9.9990 chunk 415 optimal weight: 0.9990 chunk 125 optimal weight: 8.9990 overall best weight: 5.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 507 GLN A 747 GLN C 342 GLN C 422 ASN C 528 HIS C 622 GLN C 711 ASN D 356 GLN D 606 ASN D 718 ASN F 659 HIS H 41 ASN I 41 ASN K 191 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.063 38562 Z= 0.331 Angle : 0.573 7.609 52104 Z= 0.294 Chirality : 0.040 0.152 5979 Planarity : 0.004 0.072 6722 Dihedral : 9.325 177.113 5329 Min Nonbonded Distance : 1.703 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer Outliers : 1.06 % 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: 0.23 (0.12), residues: 4789 helix: 0.93 (0.10), residues: 2404 sheet: -0.34 (0.18), residues: 730 loop : -0.63 (0.15), residues: 1655 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 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 1200 residues out of total 4057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 1157 time to evaluate : 4.615 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 outliers start: 43 outliers final: 29 residues processed: 1168 average time/residue: 1.0326 time to fit residues: 1885.7968 Evaluate side-chains 1137 residues out of total 4057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 1108 time to evaluate : 4.646 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.7166 time to fit residues: 44.1402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 386 optimal weight: 9.9990 chunk 263 optimal weight: 9.9990 chunk 6 optimal weight: 20.0000 chunk 345 optimal weight: 30.0000 chunk 191 optimal weight: 3.9990 chunk 395 optimal weight: 7.9990 chunk 320 optimal weight: 50.0000 chunk 0 optimal weight: 20.0000 chunk 236 optimal weight: 5.9990 chunk 416 optimal weight: 5.9990 chunk 117 optimal weight: 6.9990 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 305 ASN ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 483 HIS C 325 GLN C 422 ASN C 622 GLN D 451 ASN D 606 ASN D 659 HIS F 369 HIS H 41 ASN I 41 ASN K 191 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.059 38562 Z= 0.336 Angle : 0.562 9.230 52104 Z= 0.289 Chirality : 0.041 0.162 5979 Planarity : 0.004 0.071 6722 Dihedral : 9.408 178.702 5329 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % 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: 0.17 (0.12), residues: 4789 helix: 0.89 (0.10), residues: 2424 sheet: -0.42 (0.18), residues: 743 loop : -0.65 (0.15), residues: 1622 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 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 1184 residues out of total 4057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 1139 time to evaluate : 5.167 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 outliers start: 45 outliers final: 27 residues processed: 1154 average time/residue: 1.0477 time to fit residues: 1887.4514 Evaluate side-chains 1126 residues out of total 4057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 1099 time to evaluate : 4.678 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 27 outliers final: 1 residues processed: 27 average time/residue: 0.7046 time to fit residues: 41.1326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 156 optimal weight: 5.9990 chunk 417 optimal weight: 0.9990 chunk 91 optimal weight: 5.9990 chunk 272 optimal weight: 10.0000 chunk 114 optimal weight: 10.0000 chunk 464 optimal weight: 10.0000 chunk 385 optimal weight: 4.9990 chunk 215 optimal weight: 9.9990 chunk 38 optimal weight: 30.0000 chunk 153 optimal weight: 0.8980 chunk 243 optimal weight: 7.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 356 GLN C 622 GLN C 718 ASN D 329 ASN D 606 ASN H 41 ASN K 191 HIS L 159 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.3424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 38562 Z= 0.236 Angle : 0.527 7.127 52104 Z= 0.268 Chirality : 0.039 0.161 5979 Planarity : 0.004 0.052 6722 Dihedral : 9.199 178.813 5329 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer Outliers : 0.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.12), residues: 4789 helix: 1.04 (0.11), residues: 2426 sheet: -0.38 (0.18), residues: 741 loop : -0.60 (0.15), residues: 1622 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 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 1142 residues out of total 4057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 1121 time to evaluate : 4.736 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 outliers start: 21 outliers final: 14 residues processed: 1127 average time/residue: 1.0503 time to fit residues: 1850.2613 Evaluate side-chains 1108 residues out of total 4057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 1094 time to evaluate : 4.768 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 14 outliers final: 1 residues processed: 14 average time/residue: 0.8043 time to fit residues: 25.4768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 447 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 264 optimal weight: 2.9990 chunk 339 optimal weight: 30.0000 chunk 262 optimal weight: 10.0000 chunk 390 optimal weight: 4.9990 chunk 259 optimal weight: 10.0000 chunk 462 optimal weight: 10.0000 chunk 289 optimal weight: 0.2980 chunk 282 optimal weight: 20.0000 chunk 213 optimal weight: 0.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN A 483 HIS C 622 GLN C 684 GLN C 718 ASN D 606 ASN I 81 GLN I 131 GLN K 191 HIS L 159 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 38562 Z= 0.182 Angle : 0.506 7.656 52104 Z= 0.256 Chirality : 0.039 0.156 5979 Planarity : 0.003 0.043 6722 Dihedral : 9.023 179.282 5329 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer Outliers : 0.44 % 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: 0.51 (0.12), residues: 4789 helix: 1.20 (0.11), residues: 2426 sheet: -0.32 (0.18), residues: 744 loop : -0.54 (0.15), residues: 1619 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 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 1127 residues out of total 4057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 1109 time to evaluate : 4.713 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 outliers start: 18 outliers final: 10 residues processed: 1115 average time/residue: 1.0503 time to fit residues: 1829.2843 Evaluate side-chains 1096 residues out of total 4057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 1086 time to evaluate : 4.638 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 10 outliers final: 1 residues processed: 10 average time/residue: 0.6732 time to fit residues: 18.6353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 286 optimal weight: 8.9990 chunk 184 optimal weight: 4.9990 chunk 276 optimal weight: 8.9990 chunk 139 optimal weight: 3.9990 chunk 90 optimal weight: 7.9990 chunk 89 optimal weight: 4.9990 chunk 294 optimal weight: 10.0000 chunk 315 optimal weight: 9.9990 chunk 228 optimal weight: 20.0000 chunk 43 optimal weight: 20.0000 chunk 363 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 575 ASN D 606 ASN I 81 GLN I 131 GLN I 156 HIS K 191 HIS L 159 GLN N 129 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.3754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.064 38562 Z= 0.352 Angle : 0.568 7.670 52104 Z= 0.292 Chirality : 0.041 0.157 5979 Planarity : 0.004 0.062 6722 Dihedral : 9.203 176.989 5329 Min Nonbonded Distance : 1.695 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer Outliers : 0.79 % 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: 0.23 (0.12), residues: 4789 helix: 0.94 (0.10), residues: 2441 sheet: -0.38 (0.18), residues: 742 loop : -0.65 (0.15), residues: 1606 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 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 1147 residues out of total 4057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 1115 time to evaluate : 4.796 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 outliers start: 32 outliers final: 24 residues processed: 1124 average time/residue: 1.0655 time to fit residues: 1868.0435 Evaluate side-chains 1122 residues out of total 4057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 1098 time to evaluate : 4.650 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.6882 time to fit residues: 36.7730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 420 optimal weight: 2.9990 chunk 443 optimal weight: 10.0000 chunk 404 optimal weight: 0.9990 chunk 431 optimal weight: 4.9990 chunk 259 optimal weight: 9.9990 chunk 187 optimal weight: 0.0370 chunk 338 optimal weight: 40.0000 chunk 132 optimal weight: 4.9990 chunk 389 optimal weight: 4.9990 chunk 407 optimal weight: 0.0970 chunk 429 optimal weight: 2.9990 overall best weight: 1.4262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 ASN A 483 HIS A 507 GLN C 718 ASN D 606 ASN K 191 HIS L 159 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.3801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.050 38562 Z= 0.155 Angle : 0.510 7.856 52104 Z= 0.257 Chirality : 0.039 0.158 5979 Planarity : 0.003 0.053 6722 Dihedral : 8.940 179.878 5329 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer Outliers : 0.20 % 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: 0.50 (0.12), residues: 4789 helix: 1.17 (0.11), residues: 2437 sheet: -0.31 (0.18), residues: 740 loop : -0.52 (0.15), residues: 1612 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 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 1134 residues out of total 4057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 1126 time to evaluate : 4.867 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 outliers start: 8 outliers final: 4 residues processed: 1127 average time/residue: 1.0676 time to fit residues: 1885.9458 Evaluate side-chains 1111 residues out of total 4057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1107 time to evaluate : 4.670 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.9162 time to fit residues: 12.1204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 283 optimal weight: 1.9990 chunk 455 optimal weight: 20.0000 chunk 278 optimal weight: 7.9990 chunk 216 optimal weight: 10.0000 chunk 316 optimal weight: 20.0000 chunk 478 optimal weight: 8.9990 chunk 440 optimal weight: 8.9990 chunk 380 optimal weight: 9.9990 chunk 39 optimal weight: 10.0000 chunk 294 optimal weight: 9.9990 chunk 233 optimal weight: 7.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 606 ASN K 191 HIS L 159 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.3964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.063 38562 Z= 0.403 Angle : 0.587 8.135 52104 Z= 0.302 Chirality : 0.042 0.167 5979 Planarity : 0.004 0.055 6722 Dihedral : 9.168 176.781 5329 Min Nonbonded Distance : 1.692 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.36 % Favored : 96.62 % Rotamer Outliers : 0.37 % 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: 0.24 (0.12), residues: 4789 helix: 0.95 (0.11), residues: 2435 sheet: -0.36 (0.18), residues: 731 loop : -0.65 (0.15), residues: 1623 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 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 1128 residues out of total 4057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 1113 time to evaluate : 5.631 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 outliers start: 15 outliers final: 11 residues processed: 1115 average time/residue: 1.0627 time to fit residues: 1846.6361 Evaluate side-chains 1119 residues out of total 4057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 1108 time to evaluate : 4.701 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.6900 time to fit residues: 20.0307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 302 optimal weight: 5.9990 chunk 405 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 351 optimal weight: 1.9990 chunk 56 optimal weight: 7.9990 chunk 105 optimal weight: 0.8980 chunk 381 optimal weight: 10.0000 chunk 159 optimal weight: 7.9990 chunk 391 optimal weight: 0.9980 chunk 48 optimal weight: 10.0000 chunk 70 optimal weight: 8.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 483 HIS ** A 570 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 485 HIS C 606 ASN D 606 ASN K 191 HIS L 122 HIS L 159 GLN ** M 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.158953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.114736 restraints weight = 141666.619| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 2.46 r_work: 0.2954 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.3984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 38562 Z= 0.180 Angle : 0.522 7.606 52104 Z= 0.264 Chirality : 0.039 0.157 5979 Planarity : 0.003 0.071 6722 Dihedral : 8.971 179.097 5329 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer Outliers : 0.10 % 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: 0.46 (0.12), residues: 4789 helix: 1.14 (0.11), residues: 2431 sheet: -0.31 (0.18), residues: 739 loop : -0.54 (0.16), residues: 1619 =============================================================================== Job complete usr+sys time: 26090.76 seconds wall clock time: 447 minutes 50.71 seconds (26870.71 seconds total)