Starting phenix.real_space_refine on Sun Mar 17 00:55:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uiy_26557/03_2024/7uiy_26557_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uiy_26557/03_2024/7uiy_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_26557/03_2024/7uiy_26557.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uiy_26557/03_2024/7uiy_26557.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uiy_26557/03_2024/7uiy_26557_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uiy_26557/03_2024/7uiy_26557_trim_updated.pdb" } resolution = 3.22 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 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. 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: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 24.37, per 1000 atoms: 0.32 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: 50.81 Conformation dependent library (CDL) restraints added in 5.8 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: 8.59 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: 25.64 Time building geometry restraints manager: 53.39 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: 34130 28.99 - 57.98: 1325 57.98 - 86.97: 100 86.97 - 115.96: 15 115.96 - 144.95: 18 Dihedral angle restraints: 35588 sinusoidal: 20083 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 35585 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 Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.850 Extract box with map and model: 4.800 Check model and map are aligned: 0.820 Set scattering table: 0.530 Process input model: 184.370 Find NCS groups from input model: 3.260 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 197.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 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 : 14.468 144.954 14693 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Rotamer: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 229 HIS 0.010 0.001 HIS D 393 PHE 0.038 0.002 PHE M 82 TYR 0.014 0.001 TYR F 540 ARG 0.006 0.000 ARG K 15 *********************** 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 : 4.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 GLN cc_start: 0.8008 (mt0) cc_final: 0.7795 (mt0) REVERT: A 286 GLU cc_start: 0.7142 (mm-30) cc_final: 0.6672 (mm-30) REVERT: A 432 ARG cc_start: 0.6907 (mtm-85) cc_final: 0.6691 (mtm180) REVERT: A 507 GLN cc_start: 0.7865 (mm110) cc_final: 0.7614 (mp10) REVERT: A 565 GLU cc_start: 0.7092 (mt-10) cc_final: 0.6873 (mt-10) REVERT: A 624 ASN cc_start: 0.6468 (p0) cc_final: 0.6248 (p0) REVERT: A 658 ILE cc_start: 0.7478 (mm) cc_final: 0.7230 (mm) REVERT: A 692 GLU cc_start: 0.6287 (tm-30) cc_final: 0.5988 (tp30) REVERT: B 370 ASP cc_start: 0.7244 (t0) cc_final: 0.6877 (t0) REVERT: B 425 ASP cc_start: 0.7208 (t70) cc_final: 0.6985 (t0) REVERT: C 207 LYS cc_start: 0.8767 (mtpt) cc_final: 0.8537 (mtpt) REVERT: C 229 TRP cc_start: 0.8196 (t60) cc_final: 0.7716 (t60) REVERT: C 674 ASP cc_start: 0.8034 (t70) cc_final: 0.7829 (t70) REVERT: D 178 GLN cc_start: 0.6844 (tp-100) cc_final: 0.6357 (tp40) REVERT: D 370 ASP cc_start: 0.7285 (t0) cc_final: 0.6944 (t0) REVERT: D 451 ASN cc_start: 0.8169 (m110) cc_final: 0.7886 (m110) REVERT: D 646 ASN cc_start: 0.9019 (t0) cc_final: 0.8811 (t0) REVERT: D 647 ILE cc_start: 0.8828 (mt) cc_final: 0.8625 (mp) REVERT: E 258 LYS cc_start: 0.8138 (pttp) cc_final: 0.7814 (ptmm) REVERT: E 383 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7727 (mt-10) REVERT: E 422 ASN cc_start: 0.7353 (t0) cc_final: 0.7041 (t0) REVERT: E 532 ARG cc_start: 0.7089 (mmm160) cc_final: 0.6835 (mmm160) REVERT: E 582 ASP cc_start: 0.7465 (t0) cc_final: 0.6920 (t70) REVERT: E 613 GLU cc_start: 0.8091 (pp20) cc_final: 0.7783 (pp20) REVERT: E 697 ARG cc_start: 0.7815 (tpt-90) cc_final: 0.7559 (ttm-80) REVERT: F 191 ARG cc_start: 0.7320 (mtt-85) cc_final: 0.6950 (mmt90) REVERT: F 197 ARG cc_start: 0.6975 (tpt-90) cc_final: 0.6765 (tpt90) REVERT: F 272 LYS cc_start: 0.8217 (mtmt) cc_final: 0.7763 (mmtm) REVERT: F 366 GLU cc_start: 0.7173 (mt-10) cc_final: 0.6961 (mt-10) REVERT: F 422 ASN cc_start: 0.6821 (m-40) cc_final: 0.6602 (m-40) REVERT: F 507 GLN cc_start: 0.8054 (mm-40) cc_final: 0.7818 (mm-40) REVERT: F 523 GLU cc_start: 0.9203 (tm-30) cc_final: 0.8601 (tm-30) REVERT: F 551 ASP cc_start: 0.6734 (m-30) cc_final: 0.6417 (m-30) REVERT: F 620 ILE cc_start: 0.5110 (tp) cc_final: 0.4867 (tp) REVERT: F 711 ASN cc_start: 0.7800 (t0) cc_final: 0.7489 (t0) REVERT: F 719 GLU cc_start: 0.7632 (tp30) cc_final: 0.6934 (tp30) REVERT: H 162 GLU cc_start: 0.6264 (tm-30) cc_final: 0.6044 (tm-30) REVERT: I 15 ARG cc_start: 0.6575 (ttm-80) cc_final: 0.6288 (mtp-110) REVERT: I 69 VAL cc_start: 0.8641 (t) cc_final: 0.8407 (p) REVERT: I 118 ARG cc_start: 0.7435 (mmt-90) cc_final: 0.7180 (ttm-80) REVERT: I 151 GLU cc_start: 0.7177 (tt0) cc_final: 0.6955 (tt0) REVERT: J 35 VAL cc_start: 0.8736 (t) cc_final: 0.8402 (t) REVERT: J 53 GLU cc_start: 0.7383 (mm-30) cc_final: 0.6862 (mm-30) REVERT: J 161 LEU cc_start: 0.7590 (pp) cc_final: 0.6872 (pp) REVERT: K 36 GLU cc_start: 0.7402 (tp30) cc_final: 0.7119 (tt0) REVERT: L 34 GLN cc_start: 0.7691 (tp-100) cc_final: 0.7467 (tp-100) REVERT: L 57 LYS cc_start: 0.7894 (mttm) cc_final: 0.7684 (mttm) REVERT: L 74 MET cc_start: 0.8084 (mmp) cc_final: 0.7769 (mmm) REVERT: L 78 ASP cc_start: 0.8052 (m-30) cc_final: 0.7793 (m-30) REVERT: L 149 MET cc_start: 0.7600 (mmt) cc_final: 0.7341 (mmt) REVERT: L 172 ARG cc_start: 0.7512 (ttt90) cc_final: 0.7290 (ttt180) REVERT: L 173 PHE cc_start: 0.8741 (m-80) cc_final: 0.8205 (m-80) REVERT: M 169 GLU cc_start: 0.7323 (tp30) cc_final: 0.7082 (tp30) REVERT: M 170 ARG cc_start: 0.7150 (mmt-90) cc_final: 0.5967 (mmt180) REVERT: N 42 LEU cc_start: 0.8869 (tp) cc_final: 0.8647 (tp) outliers start: 0 outliers final: 0 residues processed: 1263 average time/residue: 1.1383 time to fit residues: 2245.8828 Evaluate side-chains 1050 residues out of total 4057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1050 time to evaluate : 4.376 ------------------------------------------------------------------------------- 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: 9.9990 chunk 201 optimal weight: 5.9990 chunk 124 optimal weight: 8.9990 chunk 245 optimal weight: 5.9990 chunk 194 optimal weight: 0.9990 chunk 376 optimal weight: 7.9990 chunk 145 optimal weight: 5.9990 chunk 228 optimal weight: 7.9990 chunk 280 optimal weight: 9.9990 chunk 435 optimal weight: 3.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 483 HIS B 209 ASN B 528 HIS B 642 ASN C 325 GLN C 622 GLN C 642 ASN D 178 GLN 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 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 41 ASN K 41 ASN K 191 HIS L 116 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 38562 Z= 0.290 Angle : 0.587 8.847 52104 Z= 0.308 Chirality : 0.040 0.171 5979 Planarity : 0.004 0.049 6722 Dihedral : 9.779 152.867 5406 Min Nonbonded Distance : 1.762 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.26 % Allowed : 9.27 % Favored : 89.47 % 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: 0.39 (0.11), residues: 4789 helix: 1.02 (0.10), residues: 2378 sheet: -0.15 (0.19), residues: 689 loop : -0.51 (0.14), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 229 HIS 0.007 0.001 HIS M 138 PHE 0.018 0.001 PHE J 17 TYR 0.014 0.001 TYR E 540 ARG 0.007 0.000 ARG C 527 *********************** 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 1216 residues out of total 4057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 1165 time to evaluate : 4.403 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: A 215 GLU cc_start: 0.7312 (pt0) cc_final: 0.6906 (pt0) REVERT: A 279 ASN cc_start: 0.5730 (p0) cc_final: 0.5494 (p0) REVERT: A 362 LYS cc_start: 0.7033 (tttt) cc_final: 0.6792 (tttm) REVERT: A 503 GLU cc_start: 0.7018 (tp30) cc_final: 0.6012 (tp30) REVERT: A 507 GLN cc_start: 0.7905 (mm110) cc_final: 0.7666 (mp10) REVERT: A 528 HIS cc_start: 0.7854 (p90) cc_final: 0.7649 (p90) REVERT: A 624 ASN cc_start: 0.6513 (p0) cc_final: 0.6293 (p0) REVERT: A 692 GLU cc_start: 0.6500 (tm-30) cc_final: 0.6234 (tp30) REVERT: B 215 GLU cc_start: 0.7891 (mm-30) cc_final: 0.7600 (mm-30) REVERT: B 370 ASP cc_start: 0.7524 (t0) cc_final: 0.7106 (t0) REVERT: B 408 ARG cc_start: 0.8111 (ttt-90) cc_final: 0.7877 (ttt-90) REVERT: B 419 LYS cc_start: 0.8608 (ttpt) cc_final: 0.8165 (tttt) REVERT: B 425 ASP cc_start: 0.7494 (t70) cc_final: 0.7150 (t0) REVERT: B 613 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.8251 (pt0) REVERT: C 207 LYS cc_start: 0.8872 (mtpt) cc_final: 0.8629 (mtpt) REVERT: C 229 TRP cc_start: 0.8641 (t60) cc_final: 0.7457 (t60) REVERT: C 233 GLN cc_start: 0.8129 (mm-40) cc_final: 0.7908 (mm110) REVERT: C 280 SER cc_start: 0.7521 (m) cc_final: 0.7212 (m) REVERT: D 370 ASP cc_start: 0.7301 (t0) cc_final: 0.6973 (t0) REVERT: D 451 ASN cc_start: 0.8257 (m110) cc_final: 0.7979 (m110) REVERT: E 225 GLU cc_start: 0.8349 (mt-10) cc_final: 0.7724 (mt-10) REVERT: E 235 ASP cc_start: 0.6533 (t0) cc_final: 0.6105 (t0) REVERT: E 258 LYS cc_start: 0.8298 (pttp) cc_final: 0.7927 (ptmm) REVERT: E 348 GLU cc_start: 0.6874 (pt0) cc_final: 0.6353 (pt0) REVERT: E 387 LYS cc_start: 0.8741 (mtpt) cc_final: 0.8508 (mtpp) REVERT: E 422 ASN cc_start: 0.7320 (t0) cc_final: 0.6987 (t0) REVERT: E 520 ASP cc_start: 0.7285 (t0) cc_final: 0.6871 (t0) REVERT: E 532 ARG cc_start: 0.7068 (mmm160) cc_final: 0.6822 (mmm160) REVERT: E 582 ASP cc_start: 0.7636 (t0) cc_final: 0.7040 (t70) REVERT: E 611 GLU cc_start: 0.7876 (mp0) cc_final: 0.7537 (mp0) REVERT: E 704 MET cc_start: 0.6963 (ttt) cc_final: 0.6694 (ttt) REVERT: F 191 ARG cc_start: 0.7500 (mtt-85) cc_final: 0.6598 (mtt90) REVERT: F 268 LYS cc_start: 0.8061 (mtpp) cc_final: 0.7390 (ttmt) REVERT: F 272 LYS cc_start: 0.8366 (mtmt) cc_final: 0.7813 (mmmm) REVERT: F 366 GLU cc_start: 0.7286 (mt-10) cc_final: 0.7068 (mt-10) REVERT: F 523 GLU cc_start: 0.9187 (tm-30) cc_final: 0.8571 (tm-30) REVERT: F 551 ASP cc_start: 0.6942 (m-30) cc_final: 0.6594 (m-30) REVERT: F 719 GLU cc_start: 0.7767 (tp30) cc_final: 0.7031 (tp30) REVERT: H 141 GLU cc_start: 0.8213 (tp30) cc_final: 0.7892 (tp30) REVERT: I 25 LYS cc_start: 0.8879 (mtpt) cc_final: 0.8510 (mtpp) REVERT: I 56 GLU cc_start: 0.7859 (mp0) cc_final: 0.7517 (mm-30) REVERT: I 69 VAL cc_start: 0.8606 (t) cc_final: 0.8294 (p) REVERT: I 118 ARG cc_start: 0.7420 (mmt-90) cc_final: 0.7093 (mpt180) REVERT: J 146 LYS cc_start: 0.8692 (ttpt) cc_final: 0.8415 (ttpp) REVERT: K 18 ASP cc_start: 0.7992 (p0) cc_final: 0.7756 (p0) REVERT: K 178 GLU cc_start: 0.8076 (mp0) cc_final: 0.7867 (mt-10) REVERT: L 34 GLN cc_start: 0.7823 (tp-100) cc_final: 0.7566 (mm-40) REVERT: L 140 ARG cc_start: 0.7759 (mtp85) cc_final: 0.7390 (ttm110) REVERT: L 149 MET cc_start: 0.7930 (mmt) cc_final: 0.7703 (mmt) REVERT: L 172 ARG cc_start: 0.7442 (ttt90) cc_final: 0.7128 (ttt180) REVERT: L 173 PHE cc_start: 0.8696 (m-80) cc_final: 0.8201 (m-80) REVERT: N 41 ASN cc_start: 0.8249 (m110) cc_final: 0.7771 (m110) REVERT: N 140 ARG cc_start: 0.8174 (mmm-85) cc_final: 0.7843 (mmm-85) REVERT: N 144 LYS cc_start: 0.8375 (mtpt) cc_final: 0.8026 (mptt) outliers start: 51 outliers final: 40 residues processed: 1184 average time/residue: 1.1369 time to fit residues: 2104.1562 Evaluate side-chains 1155 residues out of total 4057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 1114 time to evaluate : 4.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 659 HIS Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain B residue 613 GLU Chi-restraints excluded: chain B residue 642 ASN Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 642 ASN Chi-restraints excluded: chain C residue 651 ASP Chi-restraints excluded: chain C residue 657 VAL Chi-restraints excluded: chain C residue 697 ARG Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 196 GLU Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain D residue 599 VAL Chi-restraints excluded: chain D residue 654 SER Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 384 LEU Chi-restraints excluded: chain E residue 612 THR Chi-restraints excluded: chain F residue 177 ASN Chi-restraints excluded: chain F residue 310 LEU Chi-restraints excluded: chain F residue 353 GLU Chi-restraints excluded: chain F residue 622 GLN Chi-restraints excluded: chain F residue 746 PHE Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain I residue 134 ASP Chi-restraints excluded: chain J residue 18 ASP Chi-restraints excluded: chain J residue 37 ASP Chi-restraints excluded: chain M residue 37 ASP Chi-restraints excluded: chain M residue 79 THR Chi-restraints excluded: chain M residue 142 ILE Chi-restraints excluded: chain M residue 184 LEU Chi-restraints excluded: chain M residue 186 ASP Chi-restraints excluded: chain N residue 75 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 242 optimal weight: 4.9990 chunk 135 optimal weight: 9.9990 chunk 362 optimal weight: 10.0000 chunk 296 optimal weight: 10.0000 chunk 120 optimal weight: 3.9990 chunk 436 optimal weight: 9.9990 chunk 471 optimal weight: 10.0000 chunk 388 optimal weight: 4.9990 chunk 433 optimal weight: 10.0000 chunk 148 optimal weight: 6.9990 chunk 350 optimal weight: 9.9990 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 359 ASN A 483 HIS A 507 GLN C 342 GLN C 422 ASN C 528 HIS D 606 ASN D 659 HIS E 273 GLN F 659 HIS I 41 ASN J 150 ASN K 191 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 38562 Z= 0.349 Angle : 0.569 9.746 52104 Z= 0.295 Chirality : 0.041 0.160 5979 Planarity : 0.004 0.057 6722 Dihedral : 9.896 162.740 5406 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.38 % Allowed : 11.95 % Favored : 86.67 % 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 (0.12), residues: 4789 helix: 0.94 (0.10), residues: 2385 sheet: -0.18 (0.18), residues: 736 loop : -0.59 (0.14), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 229 HIS 0.008 0.001 HIS A 288 PHE 0.017 0.001 PHE M 82 TYR 0.013 0.001 TYR C 365 ARG 0.011 0.000 ARG A 706 *********************** 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 1218 residues out of total 4057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 1162 time to evaluate : 4.371 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: A 307 ILE cc_start: 0.8607 (pt) cc_final: 0.8192 (mt) REVERT: A 359 ASN cc_start: 0.7901 (m-40) cc_final: 0.7666 (m-40) REVERT: A 387 LYS cc_start: 0.8924 (ttmt) cc_final: 0.8644 (ttmm) REVERT: A 503 GLU cc_start: 0.7252 (tp30) cc_final: 0.6377 (tp30) REVERT: A 507 GLN cc_start: 0.7876 (mm-40) cc_final: 0.7657 (mp10) REVERT: A 528 HIS cc_start: 0.7830 (p90) cc_final: 0.7620 (p90) REVERT: A 624 ASN cc_start: 0.6540 (p0) cc_final: 0.6297 (p0) REVERT: A 699 MET cc_start: 0.5255 (mmp) cc_final: 0.4686 (mmt) REVERT: A 730 GLN cc_start: 0.5857 (mp10) cc_final: 0.5531 (mp10) REVERT: B 247 SER cc_start: 0.8573 (t) cc_final: 0.8283 (p) REVERT: B 275 GLU cc_start: 0.7623 (pp20) cc_final: 0.7388 (pp20) REVERT: B 342 GLN cc_start: 0.8461 (tp40) cc_final: 0.8183 (tp40) REVERT: B 370 ASP cc_start: 0.7587 (t0) cc_final: 0.7182 (t0) REVERT: B 408 ARG cc_start: 0.8180 (ttt-90) cc_final: 0.7837 (ttt-90) REVERT: B 419 LYS cc_start: 0.8610 (ttpt) cc_final: 0.8131 (tttt) REVERT: C 207 LYS cc_start: 0.8878 (mtpt) cc_final: 0.8631 (mtpt) REVERT: C 622 GLN cc_start: 0.8180 (mt0) cc_final: 0.7975 (mt0) REVERT: C 718 ASN cc_start: 0.7902 (m-40) cc_final: 0.7691 (m-40) REVERT: D 370 ASP cc_start: 0.7343 (t0) cc_final: 0.7023 (t0) REVERT: D 451 ASN cc_start: 0.8319 (m110) cc_final: 0.8066 (m110) REVERT: E 225 GLU cc_start: 0.8526 (mt-10) cc_final: 0.8104 (mt-10) REVERT: E 230 ARG cc_start: 0.7327 (mtp180) cc_final: 0.7104 (mtm180) REVERT: E 348 GLU cc_start: 0.7480 (pt0) cc_final: 0.6762 (pt0) REVERT: E 387 LYS cc_start: 0.8820 (mtpt) cc_final: 0.8617 (mtpp) REVERT: E 422 ASN cc_start: 0.7417 (t0) cc_final: 0.7134 (t0) REVERT: E 520 ASP cc_start: 0.7415 (t0) cc_final: 0.7027 (t0) REVERT: E 532 ARG cc_start: 0.7112 (mmm160) cc_final: 0.6848 (mmm160) REVERT: E 582 ASP cc_start: 0.7863 (t0) cc_final: 0.7547 (t0) REVERT: E 613 GLU cc_start: 0.8170 (pp20) cc_final: 0.7875 (pp20) REVERT: E 704 MET cc_start: 0.7079 (ttt) cc_final: 0.6824 (ttt) REVERT: F 268 LYS cc_start: 0.8093 (mtpp) cc_final: 0.7415 (ttmt) REVERT: F 272 LYS cc_start: 0.8393 (mtmt) cc_final: 0.7844 (mmmm) REVERT: F 523 GLU cc_start: 0.9218 (tm-30) cc_final: 0.8592 (tm-30) REVERT: F 551 ASP cc_start: 0.6953 (m-30) cc_final: 0.6620 (m-30) REVERT: F 719 GLU cc_start: 0.7761 (tp30) cc_final: 0.7036 (tp30) REVERT: S 17 LYS cc_start: 0.7500 (mtmt) cc_final: 0.7240 (mtmt) REVERT: H 22 ARG cc_start: 0.9057 (tpt90) cc_final: 0.8648 (tpt90) REVERT: H 162 GLU cc_start: 0.5629 (tm-30) cc_final: 0.4777 (tm-30) REVERT: H 178 GLU cc_start: 0.7755 (mp0) cc_final: 0.7471 (mp0) REVERT: I 19 ILE cc_start: 0.9246 (tp) cc_final: 0.9045 (tp) REVERT: I 25 LYS cc_start: 0.8943 (mtpt) cc_final: 0.8594 (mtpp) REVERT: I 56 GLU cc_start: 0.7947 (mp0) cc_final: 0.7672 (mm-30) REVERT: I 118 ARG cc_start: 0.7443 (mmt-90) cc_final: 0.7195 (mpt180) REVERT: I 136 GLU cc_start: 0.6926 (tm-30) cc_final: 0.6480 (tm-30) REVERT: I 172 ARG cc_start: 0.7326 (ttt180) cc_final: 0.6891 (ttm-80) REVERT: J 123 GLN cc_start: 0.8311 (pt0) cc_final: 0.7941 (pt0) REVERT: J 146 LYS cc_start: 0.8568 (ttpt) cc_final: 0.8352 (ttpp) REVERT: J 149 MET cc_start: 0.8118 (mmp) cc_final: 0.7694 (mmp) REVERT: K 18 ASP cc_start: 0.8130 (p0) cc_final: 0.7917 (p0) REVERT: K 26 GLU cc_start: 0.8413 (mm-30) cc_final: 0.8209 (mm-30) REVERT: K 172 ARG cc_start: 0.8120 (ttt90) cc_final: 0.7827 (ttt90) REVERT: L 34 GLN cc_start: 0.7950 (tp-100) cc_final: 0.7696 (mm-40) REVERT: L 144 LYS cc_start: 0.8138 (mttm) cc_final: 0.7806 (mtpp) REVERT: L 149 MET cc_start: 0.8134 (mmt) cc_final: 0.7848 (mmt) REVERT: L 172 ARG cc_start: 0.7580 (ttt90) cc_final: 0.7198 (ttt180) REVERT: M 101 PHE cc_start: 0.8424 (t80) cc_final: 0.8007 (t80) REVERT: M 169 GLU cc_start: 0.7231 (tp30) cc_final: 0.6811 (tp30) REVERT: M 170 ARG cc_start: 0.7335 (mmt-90) cc_final: 0.7127 (mmt180) REVERT: N 41 ASN cc_start: 0.8233 (m110) cc_final: 0.7985 (m110) REVERT: N 140 ARG cc_start: 0.8179 (mmm-85) cc_final: 0.7977 (mmm-85) REVERT: N 144 LYS cc_start: 0.8460 (mtpt) cc_final: 0.8081 (mptt) outliers start: 56 outliers final: 44 residues processed: 1182 average time/residue: 1.1265 time to fit residues: 2083.8373 Evaluate side-chains 1165 residues out of total 4057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 1121 time to evaluate : 4.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 TYR Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 659 HIS Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain B residue 525 MET Chi-restraints excluded: chain B residue 679 SER Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 454 ASP Chi-restraints excluded: chain C residue 497 THR Chi-restraints excluded: chain C residue 651 ASP Chi-restraints excluded: chain C residue 657 VAL Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain D residue 599 VAL Chi-restraints excluded: chain D residue 632 ILE Chi-restraints excluded: chain D residue 654 SER Chi-restraints excluded: chain D residue 708 ILE Chi-restraints excluded: chain E residue 186 ASP Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 474 ILE Chi-restraints excluded: chain E residue 612 THR Chi-restraints excluded: chain F residue 177 ASN Chi-restraints excluded: chain F residue 216 SER Chi-restraints excluded: chain F residue 285 ASP Chi-restraints excluded: chain F residue 310 LEU Chi-restraints excluded: chain F residue 322 THR Chi-restraints excluded: chain F residue 564 ASP Chi-restraints excluded: chain F residue 606 ASN Chi-restraints excluded: chain F residue 622 GLN Chi-restraints excluded: chain F residue 746 PHE Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain I residue 134 ASP Chi-restraints excluded: chain J residue 18 ASP Chi-restraints excluded: chain J residue 37 ASP Chi-restraints excluded: chain J residue 157 THR Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain M residue 37 ASP Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain M residue 184 LEU Chi-restraints excluded: chain M residue 186 ASP Chi-restraints excluded: chain N residue 75 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 431 optimal weight: 10.0000 chunk 328 optimal weight: 50.0000 chunk 226 optimal weight: 10.0000 chunk 48 optimal weight: 20.0000 chunk 208 optimal weight: 6.9990 chunk 293 optimal weight: 7.9990 chunk 438 optimal weight: 9.9990 chunk 463 optimal weight: 7.9990 chunk 228 optimal weight: 8.9990 chunk 415 optimal weight: 8.9990 chunk 125 optimal weight: 8.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 483 HIS A 747 GLN B 642 ASN C 422 ASN C 483 HIS C 575 ASN ** D 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 356 GLN D 485 HIS D 606 ASN D 659 HIS ** F 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 659 HIS H 41 ASN I 41 ASN K 191 HIS M 41 ASN N 129 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 38562 Z= 0.445 Angle : 0.617 8.366 52104 Z= 0.320 Chirality : 0.042 0.156 5979 Planarity : 0.004 0.049 6722 Dihedral : 10.132 179.405 5406 Min Nonbonded Distance : 1.745 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.19 % Allowed : 13.24 % Favored : 84.57 % 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: -0.12 (0.12), residues: 4789 helix: 0.58 (0.10), residues: 2436 sheet: -0.45 (0.18), residues: 686 loop : -0.74 (0.14), residues: 1667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 229 HIS 0.008 0.001 HIS A 288 PHE 0.022 0.002 PHE I 101 TYR 0.016 0.002 TYR C 695 ARG 0.017 0.001 ARG M 22 *********************** 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 1261 residues out of total 4057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 1172 time to evaluate : 4.527 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: A 307 ILE cc_start: 0.8636 (pt) cc_final: 0.8212 (mt) REVERT: A 359 ASN cc_start: 0.7918 (m-40) cc_final: 0.7622 (m-40) REVERT: A 387 LYS cc_start: 0.8960 (ttmt) cc_final: 0.8670 (ttmm) REVERT: A 408 ARG cc_start: 0.8024 (ttm-80) cc_final: 0.7771 (ttm-80) REVERT: A 427 GLU cc_start: 0.7314 (pt0) cc_final: 0.6787 (pt0) REVERT: A 439 LYS cc_start: 0.7810 (mptt) cc_final: 0.7558 (ttpp) REVERT: A 478 ARG cc_start: 0.7215 (mmt-90) cc_final: 0.6890 (mmp-170) REVERT: A 483 HIS cc_start: 0.6685 (OUTLIER) cc_final: 0.6020 (m-70) REVERT: A 503 GLU cc_start: 0.7410 (tp30) cc_final: 0.6575 (tp30) REVERT: A 507 GLN cc_start: 0.7791 (mm-40) cc_final: 0.7584 (mp10) REVERT: A 624 ASN cc_start: 0.6642 (p0) cc_final: 0.6385 (p0) REVERT: B 206 ARG cc_start: 0.7224 (tpt170) cc_final: 0.6932 (mmt180) REVERT: B 230 ARG cc_start: 0.7902 (mtp85) cc_final: 0.7643 (mtp85) REVERT: B 247 SER cc_start: 0.8584 (t) cc_final: 0.8290 (p) REVERT: B 275 GLU cc_start: 0.7835 (pp20) cc_final: 0.7610 (pp20) REVERT: B 342 GLN cc_start: 0.8472 (tp40) cc_final: 0.8223 (tp40) REVERT: B 370 ASP cc_start: 0.7647 (t0) cc_final: 0.7241 (t0) REVERT: B 408 ARG cc_start: 0.8340 (ttt-90) cc_final: 0.8067 (ttt-90) REVERT: B 425 ASP cc_start: 0.7965 (t70) cc_final: 0.7473 (t0) REVERT: B 544 ASP cc_start: 0.7385 (t70) cc_final: 0.6314 (t0) REVERT: B 674 ASP cc_start: 0.7469 (m-30) cc_final: 0.7180 (m-30) REVERT: C 207 LYS cc_start: 0.8983 (mtpt) cc_final: 0.8726 (mtpt) REVERT: C 259 TYR cc_start: 0.8697 (m-80) cc_final: 0.7840 (m-80) REVERT: C 565 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7532 (mt-10) REVERT: C 697 ARG cc_start: 0.8462 (OUTLIER) cc_final: 0.7765 (ttp-110) REVERT: C 718 ASN cc_start: 0.8034 (m-40) cc_final: 0.7759 (m-40) REVERT: D 370 ASP cc_start: 0.7360 (t0) cc_final: 0.7009 (t0) REVERT: D 396 ASP cc_start: 0.8216 (t70) cc_final: 0.7799 (t0) REVERT: D 420 THR cc_start: 0.8705 (OUTLIER) cc_final: 0.8428 (m) REVERT: E 225 GLU cc_start: 0.8621 (mt-10) cc_final: 0.8229 (mt-10) REVERT: E 235 ASP cc_start: 0.7428 (t0) cc_final: 0.7025 (t70) REVERT: E 387 LYS cc_start: 0.8865 (mtpt) cc_final: 0.8661 (mttp) REVERT: E 422 ASN cc_start: 0.7492 (t0) cc_final: 0.7213 (t0) REVERT: E 532 ARG cc_start: 0.7136 (mmm160) cc_final: 0.6913 (mmm160) REVERT: E 617 ILE cc_start: 0.9028 (OUTLIER) cc_final: 0.8801 (mt) REVERT: E 697 ARG cc_start: 0.7881 (tpp80) cc_final: 0.7623 (ttm-80) REVERT: E 704 MET cc_start: 0.7141 (ttt) cc_final: 0.6769 (ttt) REVERT: F 177 ASN cc_start: 0.8505 (OUTLIER) cc_final: 0.8299 (t0) REVERT: F 268 LYS cc_start: 0.8157 (mtpp) cc_final: 0.7507 (ttmt) REVERT: F 272 LYS cc_start: 0.8421 (mtmt) cc_final: 0.7915 (mmtm) REVERT: F 353 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7542 (mt-10) REVERT: F 523 GLU cc_start: 0.9254 (tm-30) cc_final: 0.8647 (tm-30) REVERT: F 551 ASP cc_start: 0.6898 (m-30) cc_final: 0.6559 (m-30) REVERT: S 17 LYS cc_start: 0.7642 (mtmt) cc_final: 0.7374 (mtmt) REVERT: H 22 ARG cc_start: 0.9050 (tpt90) cc_final: 0.8680 (tpt90) REVERT: H 141 GLU cc_start: 0.8359 (tp30) cc_final: 0.8005 (tp30) REVERT: H 162 GLU cc_start: 0.5879 (tm-30) cc_final: 0.5242 (tm-30) REVERT: H 172 ARG cc_start: 0.7364 (ttm170) cc_final: 0.6874 (tpp80) REVERT: H 192 ARG cc_start: 0.4522 (mmt-90) cc_final: 0.4319 (mpt180) REVERT: I 25 LYS cc_start: 0.8971 (mtpt) cc_final: 0.8741 (mtpp) REVERT: I 118 ARG cc_start: 0.7448 (mmt-90) cc_final: 0.7071 (mpt180) REVERT: I 136 GLU cc_start: 0.6946 (tm-30) cc_final: 0.6544 (tm-30) REVERT: J 140 ARG cc_start: 0.6966 (mtt-85) cc_final: 0.6368 (mtt-85) REVERT: L 140 ARG cc_start: 0.7854 (mtp-110) cc_final: 0.7621 (ttm-80) REVERT: L 144 LYS cc_start: 0.8225 (mttm) cc_final: 0.7765 (mtpp) REVERT: L 149 MET cc_start: 0.8162 (mmt) cc_final: 0.7872 (mmt) REVERT: L 172 ARG cc_start: 0.7613 (ttt90) cc_final: 0.7162 (ttt180) REVERT: M 101 PHE cc_start: 0.8548 (t80) cc_final: 0.8022 (t80) REVERT: M 169 GLU cc_start: 0.7285 (tp30) cc_final: 0.6633 (tp30) REVERT: M 170 ARG cc_start: 0.7324 (mmt-90) cc_final: 0.6816 (mmt180) REVERT: N 140 ARG cc_start: 0.8256 (mmm-85) cc_final: 0.8032 (mmm-85) REVERT: N 144 LYS cc_start: 0.8511 (mtpt) cc_final: 0.8148 (mptt) REVERT: N 151 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7307 (mt-10) outliers start: 89 outliers final: 62 residues processed: 1210 average time/residue: 1.1261 time to fit residues: 2114.7239 Evaluate side-chains 1192 residues out of total 4057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 1123 time to evaluate : 4.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 ASP Chi-restraints excluded: chain A residue 483 HIS Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 583 ASN Chi-restraints excluded: chain A residue 659 HIS Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 525 MET Chi-restraints excluded: chain B residue 531 SER Chi-restraints excluded: chain B residue 613 GLU Chi-restraints excluded: chain B residue 642 ASN Chi-restraints excluded: chain B residue 679 SER Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 497 THR Chi-restraints excluded: chain C residue 565 GLU Chi-restraints excluded: chain C residue 651 ASP Chi-restraints excluded: chain C residue 657 VAL Chi-restraints excluded: chain C residue 697 ARG Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 272 LYS Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain D residue 599 VAL Chi-restraints excluded: chain D residue 632 ILE Chi-restraints excluded: chain D residue 654 SER Chi-restraints excluded: chain D residue 663 ASP Chi-restraints excluded: chain D residue 708 ILE Chi-restraints excluded: chain D residue 710 ASP Chi-restraints excluded: chain D residue 727 ASP Chi-restraints excluded: chain E residue 186 ASP Chi-restraints excluded: chain E residue 242 ASP Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 440 SER Chi-restraints excluded: chain E residue 474 ILE Chi-restraints excluded: chain E residue 612 THR Chi-restraints excluded: chain E residue 617 ILE Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 177 ASN Chi-restraints excluded: chain F residue 216 SER Chi-restraints excluded: chain F residue 285 ASP Chi-restraints excluded: chain F residue 310 LEU Chi-restraints excluded: chain F residue 322 THR Chi-restraints excluded: chain F residue 564 ASP Chi-restraints excluded: chain F residue 606 ASN Chi-restraints excluded: chain F residue 622 GLN Chi-restraints excluded: chain F residue 746 PHE Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain I residue 134 ASP Chi-restraints excluded: chain J residue 18 ASP Chi-restraints excluded: chain J residue 37 ASP Chi-restraints excluded: chain J residue 157 THR Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain L residue 188 ILE Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain M residue 37 ASP Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain M residue 82 PHE Chi-restraints excluded: chain M residue 116 ASN Chi-restraints excluded: chain M residue 186 ASP Chi-restraints excluded: chain N residue 75 SER Chi-restraints excluded: chain N residue 151 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 386 optimal weight: 10.0000 chunk 263 optimal weight: 7.9990 chunk 6 optimal weight: 30.0000 chunk 345 optimal weight: 5.9990 chunk 191 optimal weight: 2.9990 chunk 395 optimal weight: 7.9990 chunk 320 optimal weight: 50.0000 chunk 0 optimal weight: 20.0000 chunk 236 optimal weight: 4.9990 chunk 416 optimal weight: 5.9990 chunk 117 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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 356 GLN C 606 ASN C 622 GLN ** D 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 329 ASN D 451 ASN D 606 ASN D 659 HIS D 688 ASN D 718 ASN F 369 HIS F 393 HIS F 422 ASN I 9 GLN K 191 HIS L 159 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.3360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 38562 Z= 0.300 Angle : 0.551 7.139 52104 Z= 0.283 Chirality : 0.040 0.157 5979 Planarity : 0.004 0.052 6722 Dihedral : 10.055 176.679 5406 Min Nonbonded Distance : 1.764 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.05 % Allowed : 14.37 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.12), residues: 4789 helix: 0.77 (0.10), residues: 2425 sheet: -0.46 (0.18), residues: 741 loop : -0.67 (0.15), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 649 HIS 0.020 0.001 HIS A 483 PHE 0.016 0.001 PHE I 101 TYR 0.014 0.001 TYR D 324 ARG 0.006 0.000 ARG D 706 *********************** 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 1235 residues out of total 4057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 1152 time to evaluate : 4.413 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: A 279 ASN cc_start: 0.5934 (p0) cc_final: 0.5590 (p0) REVERT: A 307 ILE cc_start: 0.8617 (pt) cc_final: 0.8194 (mt) REVERT: A 362 LYS cc_start: 0.7728 (mttp) cc_final: 0.7485 (mttp) REVERT: A 387 LYS cc_start: 0.8962 (ttmt) cc_final: 0.8667 (ttmm) REVERT: A 400 ASP cc_start: 0.7671 (m-30) cc_final: 0.7359 (m-30) REVERT: A 427 GLU cc_start: 0.7337 (pt0) cc_final: 0.6800 (pt0) REVERT: A 478 ARG cc_start: 0.7169 (mmt-90) cc_final: 0.6786 (mmp-170) REVERT: A 503 GLU cc_start: 0.7431 (tp30) cc_final: 0.6615 (tp30) REVERT: A 507 GLN cc_start: 0.7824 (mm-40) cc_final: 0.7514 (mp10) REVERT: A 624 ASN cc_start: 0.6651 (p0) cc_final: 0.6435 (p0) REVERT: B 206 ARG cc_start: 0.7208 (tpt170) cc_final: 0.6899 (mmt180) REVERT: B 247 SER cc_start: 0.8547 (t) cc_final: 0.8275 (p) REVERT: B 370 ASP cc_start: 0.7643 (t0) cc_final: 0.7219 (t0) REVERT: B 408 ARG cc_start: 0.8348 (ttt-90) cc_final: 0.8118 (ttt-90) REVERT: B 425 ASP cc_start: 0.7940 (t70) cc_final: 0.7435 (t0) REVERT: B 674 ASP cc_start: 0.7434 (m-30) cc_final: 0.7152 (m-30) REVERT: C 193 LYS cc_start: 0.8556 (mtpp) cc_final: 0.8231 (mtpp) REVERT: C 207 LYS cc_start: 0.8973 (mtpt) cc_final: 0.8705 (mtpt) REVERT: C 259 TYR cc_start: 0.8677 (m-80) cc_final: 0.7830 (m-80) REVERT: C 718 ASN cc_start: 0.7999 (m-40) cc_final: 0.7747 (m-40) REVERT: D 370 ASP cc_start: 0.7337 (t0) cc_final: 0.7004 (t0) REVERT: D 396 ASP cc_start: 0.8181 (t70) cc_final: 0.7818 (t0) REVERT: D 420 THR cc_start: 0.8730 (OUTLIER) cc_final: 0.8451 (m) REVERT: E 225 GLU cc_start: 0.8525 (mt-10) cc_final: 0.8079 (mt-10) REVERT: E 235 ASP cc_start: 0.7397 (t0) cc_final: 0.6966 (t70) REVERT: E 348 GLU cc_start: 0.8098 (pt0) cc_final: 0.7216 (pt0) REVERT: E 387 LYS cc_start: 0.8873 (mtpt) cc_final: 0.8604 (mttm) REVERT: E 422 ASN cc_start: 0.7497 (t0) cc_final: 0.7207 (t0) REVERT: E 532 ARG cc_start: 0.7147 (mmm160) cc_final: 0.6919 (mmm160) REVERT: E 617 ILE cc_start: 0.8954 (OUTLIER) cc_final: 0.8734 (mt) REVERT: E 704 MET cc_start: 0.7150 (ttt) cc_final: 0.6812 (ttt) REVERT: F 177 ASN cc_start: 0.8534 (OUTLIER) cc_final: 0.7980 (t0) REVERT: F 268 LYS cc_start: 0.8154 (mtpp) cc_final: 0.7811 (tttm) REVERT: F 272 LYS cc_start: 0.8412 (mtmt) cc_final: 0.7936 (mmtm) REVERT: F 348 GLU cc_start: 0.7059 (pp20) cc_final: 0.6794 (pp20) REVERT: F 523 GLU cc_start: 0.9276 (tm-30) cc_final: 0.8648 (tm-30) REVERT: F 551 ASP cc_start: 0.6861 (m-30) cc_final: 0.6529 (m-30) REVERT: S 17 LYS cc_start: 0.7641 (mtmt) cc_final: 0.7367 (mtmt) REVERT: H 22 ARG cc_start: 0.9037 (tpt90) cc_final: 0.8678 (tpt90) REVERT: H 141 GLU cc_start: 0.8307 (tp30) cc_final: 0.7979 (tp30) REVERT: H 162 GLU cc_start: 0.5870 (tm-30) cc_final: 0.5355 (tm-30) REVERT: H 172 ARG cc_start: 0.7374 (ttm170) cc_final: 0.7169 (tpp80) REVERT: H 190 THR cc_start: 0.7888 (m) cc_final: 0.7623 (p) REVERT: H 192 ARG cc_start: 0.4576 (mmt-90) cc_final: 0.4367 (mpt180) REVERT: I 118 ARG cc_start: 0.7458 (mmt-90) cc_final: 0.7078 (mpt180) REVERT: I 141 GLU cc_start: 0.7952 (tm-30) cc_final: 0.7466 (tm-30) REVERT: J 149 MET cc_start: 0.8203 (mmt) cc_final: 0.7660 (mmp) REVERT: L 140 ARG cc_start: 0.7859 (mtp-110) cc_final: 0.7341 (mtp85) REVERT: L 149 MET cc_start: 0.8192 (mmt) cc_final: 0.7923 (mmt) REVERT: L 172 ARG cc_start: 0.7590 (ttt90) cc_final: 0.7134 (ttt180) REVERT: M 101 PHE cc_start: 0.8628 (t80) cc_final: 0.8060 (t80) REVERT: M 169 GLU cc_start: 0.7300 (tp30) cc_final: 0.6707 (tp30) REVERT: M 170 ARG cc_start: 0.7335 (mmt-90) cc_final: 0.6852 (mmt180) REVERT: N 140 ARG cc_start: 0.8234 (mmm-85) cc_final: 0.8015 (mmm-85) REVERT: N 144 LYS cc_start: 0.8525 (mtpt) cc_final: 0.8154 (mptt) outliers start: 83 outliers final: 62 residues processed: 1188 average time/residue: 1.1198 time to fit residues: 2056.4789 Evaluate side-chains 1183 residues out of total 4057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 1118 time to evaluate : 4.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 483 HIS Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 583 ASN Chi-restraints excluded: chain A residue 659 HIS Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 679 SER Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 345 ASP Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 454 ASP Chi-restraints excluded: chain C residue 497 THR Chi-restraints excluded: chain C residue 651 ASP Chi-restraints excluded: chain C residue 657 VAL Chi-restraints excluded: chain C residue 678 VAL Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 178 GLN Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 265 LYS Chi-restraints excluded: chain D residue 272 LYS Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain D residue 599 VAL Chi-restraints excluded: chain D residue 708 ILE Chi-restraints excluded: chain D residue 710 ASP Chi-restraints excluded: chain D residue 722 PHE Chi-restraints excluded: chain E residue 186 ASP Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 347 THR Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 438 GLU Chi-restraints excluded: chain E residue 600 VAL Chi-restraints excluded: chain E residue 612 THR Chi-restraints excluded: chain E residue 617 ILE Chi-restraints excluded: chain F residue 177 ASN Chi-restraints excluded: chain F residue 225 GLU Chi-restraints excluded: chain F residue 285 ASP Chi-restraints excluded: chain F residue 310 LEU Chi-restraints excluded: chain F residue 316 ILE Chi-restraints excluded: chain F residue 322 THR Chi-restraints excluded: chain F residue 369 HIS Chi-restraints excluded: chain F residue 564 ASP Chi-restraints excluded: chain F residue 606 ASN Chi-restraints excluded: chain F residue 622 GLN Chi-restraints excluded: chain F residue 746 PHE Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain J residue 37 ASP Chi-restraints excluded: chain J residue 58 ASP Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 157 THR Chi-restraints excluded: chain J residue 159 GLN Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain L residue 188 ILE Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain M residue 37 ASP Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain M residue 82 PHE Chi-restraints excluded: chain M residue 171 ASP Chi-restraints excluded: chain M residue 184 LEU Chi-restraints excluded: chain M residue 186 ASP Chi-restraints excluded: chain N residue 75 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 156 optimal weight: 6.9990 chunk 417 optimal weight: 9.9990 chunk 91 optimal weight: 5.9990 chunk 272 optimal weight: 9.9990 chunk 114 optimal weight: 4.9990 chunk 464 optimal weight: 10.0000 chunk 385 optimal weight: 5.9990 chunk 215 optimal weight: 10.0000 chunk 38 optimal weight: 40.0000 chunk 153 optimal weight: 0.7980 chunk 243 optimal weight: 7.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 483 HIS B 642 ASN C 622 GLN C 684 GLN ** D 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 606 ASN D 659 HIS F 393 HIS I 156 HIS 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: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 38562 Z= 0.291 Angle : 0.541 7.314 52104 Z= 0.277 Chirality : 0.040 0.157 5979 Planarity : 0.004 0.055 6722 Dihedral : 9.971 179.718 5406 Min Nonbonded Distance : 1.748 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.14 % Allowed : 14.52 % Favored : 83.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.12), residues: 4789 helix: 0.80 (0.10), residues: 2439 sheet: -0.38 (0.18), residues: 737 loop : -0.64 (0.15), residues: 1613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 649 HIS 0.014 0.001 HIS F 369 PHE 0.010 0.001 PHE E 596 TYR 0.015 0.001 TYR K 60 ARG 0.008 0.000 ARG F 372 *********************** 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 1229 residues out of total 4057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 1142 time to evaluate : 4.443 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: A 279 ASN cc_start: 0.5961 (p0) cc_final: 0.5629 (p0) REVERT: A 307 ILE cc_start: 0.8605 (pt) cc_final: 0.8180 (mt) REVERT: A 362 LYS cc_start: 0.7729 (mttp) cc_final: 0.7515 (mttp) REVERT: A 387 LYS cc_start: 0.8960 (ttmt) cc_final: 0.8657 (ttmm) REVERT: A 393 HIS cc_start: 0.6452 (m-70) cc_final: 0.6193 (m-70) REVERT: A 427 GLU cc_start: 0.7350 (pt0) cc_final: 0.6818 (pt0) REVERT: A 478 ARG cc_start: 0.7092 (mmt-90) cc_final: 0.6692 (mmp-170) REVERT: A 503 GLU cc_start: 0.7512 (tp30) cc_final: 0.6743 (tp30) REVERT: A 507 GLN cc_start: 0.7800 (mm-40) cc_final: 0.7475 (mp10) REVERT: B 206 ARG cc_start: 0.7140 (tpt170) cc_final: 0.6813 (mmt180) REVERT: B 215 GLU cc_start: 0.8074 (mm-30) cc_final: 0.7834 (mm-30) REVERT: B 230 ARG cc_start: 0.7854 (mtp85) cc_final: 0.7638 (mtp85) REVERT: B 247 SER cc_start: 0.8539 (t) cc_final: 0.8283 (p) REVERT: B 370 ASP cc_start: 0.7663 (t0) cc_final: 0.7231 (t0) REVERT: B 408 ARG cc_start: 0.8368 (ttt-90) cc_final: 0.8141 (ttt-90) REVERT: B 425 ASP cc_start: 0.7975 (t70) cc_final: 0.7479 (t0) REVERT: B 674 ASP cc_start: 0.7438 (m-30) cc_final: 0.7162 (m-30) REVERT: C 207 LYS cc_start: 0.8968 (mtpt) cc_final: 0.8706 (mtpt) REVERT: C 259 TYR cc_start: 0.8684 (m-80) cc_final: 0.7821 (m-80) REVERT: C 394 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8152 (tp) REVERT: C 451 ASN cc_start: 0.8808 (m-40) cc_final: 0.8543 (m110) REVERT: D 370 ASP cc_start: 0.7343 (t0) cc_final: 0.7016 (t0) REVERT: D 396 ASP cc_start: 0.8183 (t70) cc_final: 0.7816 (t0) REVERT: D 420 THR cc_start: 0.8719 (OUTLIER) cc_final: 0.8446 (m) REVERT: D 706 ARG cc_start: 0.8493 (mtm-85) cc_final: 0.8283 (mtm-85) REVERT: E 225 GLU cc_start: 0.8526 (mt-10) cc_final: 0.8075 (mt-10) REVERT: E 235 ASP cc_start: 0.7457 (t0) cc_final: 0.6981 (t70) REVERT: E 348 GLU cc_start: 0.8168 (pt0) cc_final: 0.7364 (pt0) REVERT: E 387 LYS cc_start: 0.8894 (mtpt) cc_final: 0.8628 (mttm) REVERT: E 422 ASN cc_start: 0.7519 (t0) cc_final: 0.7218 (t0) REVERT: E 532 ARG cc_start: 0.7164 (mmm160) cc_final: 0.6909 (mmm160) REVERT: E 611 GLU cc_start: 0.7979 (mp0) cc_final: 0.7689 (mp0) REVERT: E 704 MET cc_start: 0.7179 (ttt) cc_final: 0.6841 (ttt) REVERT: F 177 ASN cc_start: 0.8545 (OUTLIER) cc_final: 0.7976 (t0) REVERT: F 268 LYS cc_start: 0.8207 (mtpp) cc_final: 0.7878 (tttm) REVERT: F 272 LYS cc_start: 0.8405 (mtmt) cc_final: 0.7936 (mmtm) REVERT: F 348 GLU cc_start: 0.7095 (pp20) cc_final: 0.6876 (pp20) REVERT: F 523 GLU cc_start: 0.9277 (tm-30) cc_final: 0.8651 (tm-30) REVERT: F 551 ASP cc_start: 0.6871 (m-30) cc_final: 0.6538 (m-30) REVERT: H 22 ARG cc_start: 0.9054 (tpt90) cc_final: 0.8690 (tpt90) REVERT: H 141 GLU cc_start: 0.8325 (tp30) cc_final: 0.8011 (tp30) REVERT: H 162 GLU cc_start: 0.6058 (tm-30) cc_final: 0.5584 (tm-30) REVERT: H 190 THR cc_start: 0.7887 (m) cc_final: 0.7630 (p) REVERT: H 192 ARG cc_start: 0.4647 (mmt-90) cc_final: 0.4414 (mpt180) REVERT: I 118 ARG cc_start: 0.7470 (mmt-90) cc_final: 0.7095 (mpt180) REVERT: L 140 ARG cc_start: 0.7869 (mtp-110) cc_final: 0.7326 (mtp85) REVERT: L 149 MET cc_start: 0.8193 (mmt) cc_final: 0.7829 (mmt) REVERT: L 172 ARG cc_start: 0.7584 (ttt90) cc_final: 0.7120 (ttt180) REVERT: M 169 GLU cc_start: 0.7304 (tp30) cc_final: 0.6716 (tp30) REVERT: M 170 ARG cc_start: 0.7355 (mmt-90) cc_final: 0.6835 (mmt180) REVERT: N 102 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8826 (mm) REVERT: N 140 ARG cc_start: 0.8258 (mmm-85) cc_final: 0.8030 (mmm-85) REVERT: N 144 LYS cc_start: 0.8538 (mtpt) cc_final: 0.8169 (mptt) REVERT: N 151 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7247 (mt-10) outliers start: 87 outliers final: 71 residues processed: 1181 average time/residue: 1.0987 time to fit residues: 2010.9695 Evaluate side-chains 1190 residues out of total 4057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 1114 time to evaluate : 4.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 583 ASN Chi-restraints excluded: chain A residue 659 HIS Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 613 GLU Chi-restraints excluded: chain B residue 642 ASN Chi-restraints excluded: chain B residue 679 SER Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 345 ASP Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 454 ASP Chi-restraints excluded: chain C residue 497 THR Chi-restraints excluded: chain C residue 588 ASP Chi-restraints excluded: chain C residue 590 ASN Chi-restraints excluded: chain C residue 651 ASP Chi-restraints excluded: chain C residue 657 VAL Chi-restraints excluded: chain C residue 678 VAL Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 178 GLN Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 265 LYS Chi-restraints excluded: chain D residue 272 LYS Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain D residue 599 VAL Chi-restraints excluded: chain D residue 609 VAL Chi-restraints excluded: chain D residue 654 SER Chi-restraints excluded: chain D residue 708 ILE Chi-restraints excluded: chain D residue 722 PHE Chi-restraints excluded: chain E residue 186 ASP Chi-restraints excluded: chain E residue 313 SER Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 347 THR Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 438 GLU Chi-restraints excluded: chain E residue 440 SER Chi-restraints excluded: chain E residue 600 VAL Chi-restraints excluded: chain E residue 612 THR Chi-restraints excluded: chain F residue 177 ASN Chi-restraints excluded: chain F residue 225 GLU Chi-restraints excluded: chain F residue 285 ASP Chi-restraints excluded: chain F residue 310 LEU Chi-restraints excluded: chain F residue 316 ILE Chi-restraints excluded: chain F residue 322 THR Chi-restraints excluded: chain F residue 564 ASP Chi-restraints excluded: chain F residue 606 ASN Chi-restraints excluded: chain F residue 622 GLN Chi-restraints excluded: chain F residue 746 PHE Chi-restraints excluded: chain S residue 23 LYS Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain H residue 168 THR Chi-restraints excluded: chain J residue 37 ASP Chi-restraints excluded: chain J residue 58 ASP Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 157 THR Chi-restraints excluded: chain J residue 159 GLN Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain L residue 188 ILE Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain M residue 36 GLU Chi-restraints excluded: chain M residue 37 ASP Chi-restraints excluded: chain M residue 41 ASN Chi-restraints excluded: chain M residue 82 PHE Chi-restraints excluded: chain M residue 171 ASP Chi-restraints excluded: chain M residue 184 LEU Chi-restraints excluded: chain M residue 186 ASP Chi-restraints excluded: chain N residue 75 SER Chi-restraints excluded: chain N residue 102 LEU Chi-restraints excluded: chain N residue 151 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 447 optimal weight: 10.0000 chunk 52 optimal weight: 20.0000 chunk 264 optimal weight: 4.9990 chunk 339 optimal weight: 30.0000 chunk 262 optimal weight: 9.9990 chunk 390 optimal weight: 3.9990 chunk 259 optimal weight: 9.9990 chunk 462 optimal weight: 9.9990 chunk 289 optimal weight: 9.9990 chunk 282 optimal weight: 0.9980 chunk 213 optimal weight: 0.8980 overall best weight: 4.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 356 GLN ** D 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 606 ASN D 659 HIS ** F 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 393 HIS F 422 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: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 38562 Z= 0.253 Angle : 0.526 7.677 52104 Z= 0.267 Chirality : 0.039 0.157 5979 Planarity : 0.004 0.057 6722 Dihedral : 9.874 178.960 5406 Min Nonbonded Distance : 1.756 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.00 % Allowed : 15.11 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.12), residues: 4789 helix: 0.91 (0.11), residues: 2430 sheet: -0.36 (0.18), residues: 724 loop : -0.62 (0.15), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 649 HIS 0.006 0.001 HIS A 288 PHE 0.012 0.001 PHE I 101 TYR 0.015 0.001 TYR K 60 ARG 0.007 0.000 ARG A 706 *********************** 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 1216 residues out of total 4057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 1135 time to evaluate : 4.452 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: A 279 ASN cc_start: 0.5974 (p0) cc_final: 0.5646 (p0) REVERT: A 307 ILE cc_start: 0.8591 (pt) cc_final: 0.8170 (mt) REVERT: A 362 LYS cc_start: 0.7731 (mttp) cc_final: 0.7525 (mttp) REVERT: A 387 LYS cc_start: 0.8960 (ttmt) cc_final: 0.8659 (ttmm) REVERT: A 393 HIS cc_start: 0.6401 (m-70) cc_final: 0.6119 (m-70) REVERT: A 427 GLU cc_start: 0.7349 (pt0) cc_final: 0.6830 (pt0) REVERT: A 475 LYS cc_start: 0.8430 (mttt) cc_final: 0.7964 (mtpt) REVERT: A 503 GLU cc_start: 0.7470 (tp30) cc_final: 0.6742 (tp30) REVERT: A 507 GLN cc_start: 0.7800 (mm-40) cc_final: 0.7568 (mp10) REVERT: B 206 ARG cc_start: 0.7131 (tpt170) cc_final: 0.6809 (mmt180) REVERT: B 230 ARG cc_start: 0.7844 (mtp85) cc_final: 0.7634 (mtp85) REVERT: B 247 SER cc_start: 0.8517 (t) cc_final: 0.8270 (p) REVERT: B 370 ASP cc_start: 0.7642 (t0) cc_final: 0.7210 (t0) REVERT: B 408 ARG cc_start: 0.8370 (ttt-90) cc_final: 0.8065 (ttt-90) REVERT: B 425 ASP cc_start: 0.7968 (t70) cc_final: 0.7608 (t70) REVERT: B 674 ASP cc_start: 0.7440 (m-30) cc_final: 0.7197 (m-30) REVERT: C 207 LYS cc_start: 0.8957 (mtpt) cc_final: 0.8680 (mtpt) REVERT: C 259 TYR cc_start: 0.8681 (m-80) cc_final: 0.7822 (m-80) REVERT: C 451 ASN cc_start: 0.8796 (m-40) cc_final: 0.8535 (m110) REVERT: D 370 ASP cc_start: 0.7345 (t0) cc_final: 0.7019 (t0) REVERT: D 396 ASP cc_start: 0.8171 (t70) cc_final: 0.7825 (t0) REVERT: D 674 ASP cc_start: 0.7269 (m-30) cc_final: 0.6853 (m-30) REVERT: D 706 ARG cc_start: 0.8490 (mtm-85) cc_final: 0.8235 (mtm-85) REVERT: E 225 GLU cc_start: 0.8524 (mt-10) cc_final: 0.8068 (mt-10) REVERT: E 235 ASP cc_start: 0.7478 (t0) cc_final: 0.7007 (t70) REVERT: E 348 GLU cc_start: 0.8170 (pt0) cc_final: 0.7379 (pt0) REVERT: E 387 LYS cc_start: 0.8871 (mtpt) cc_final: 0.8636 (mttm) REVERT: E 408 ARG cc_start: 0.8165 (ttp80) cc_final: 0.7935 (ttt-90) REVERT: E 422 ASN cc_start: 0.7499 (t0) cc_final: 0.7204 (t0) REVERT: E 532 ARG cc_start: 0.7182 (mmm160) cc_final: 0.6928 (mmm160) REVERT: E 611 GLU cc_start: 0.7967 (mp0) cc_final: 0.7661 (mp0) REVERT: E 704 MET cc_start: 0.7189 (ttt) cc_final: 0.6869 (ttt) REVERT: F 177 ASN cc_start: 0.8529 (OUTLIER) cc_final: 0.7968 (t0) REVERT: F 268 LYS cc_start: 0.8222 (mtpp) cc_final: 0.7887 (tttm) REVERT: F 272 LYS cc_start: 0.8408 (mtmt) cc_final: 0.7941 (mmtm) REVERT: F 348 GLU cc_start: 0.7078 (pp20) cc_final: 0.6840 (pp20) REVERT: F 523 GLU cc_start: 0.9268 (tm-30) cc_final: 0.8649 (tm-30) REVERT: F 551 ASP cc_start: 0.6923 (m-30) cc_final: 0.6593 (m-30) REVERT: H 22 ARG cc_start: 0.9040 (tpt90) cc_final: 0.8689 (tpt90) REVERT: H 141 GLU cc_start: 0.8336 (tp30) cc_final: 0.8123 (tp30) REVERT: H 162 GLU cc_start: 0.5966 (tm-30) cc_final: 0.5592 (tm-30) REVERT: H 190 THR cc_start: 0.7880 (m) cc_final: 0.7644 (p) REVERT: H 192 ARG cc_start: 0.4634 (mmt-90) cc_final: 0.4399 (mpt180) REVERT: I 118 ARG cc_start: 0.7486 (mmt-90) cc_final: 0.7091 (mpt180) REVERT: L 144 LYS cc_start: 0.8196 (mttm) cc_final: 0.7893 (mtpp) REVERT: L 172 ARG cc_start: 0.7596 (ttt90) cc_final: 0.7103 (ttt180) REVERT: M 26 GLU cc_start: 0.8490 (mm-30) cc_final: 0.8270 (mm-30) REVERT: M 169 GLU cc_start: 0.7320 (tp30) cc_final: 0.6757 (tp30) REVERT: M 170 ARG cc_start: 0.7354 (mmt-90) cc_final: 0.6835 (mmt180) REVERT: N 102 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8804 (mm) REVERT: N 140 ARG cc_start: 0.8247 (mmm-85) cc_final: 0.8017 (mmm-85) REVERT: N 144 LYS cc_start: 0.8549 (mtpt) cc_final: 0.8189 (mptt) outliers start: 81 outliers final: 67 residues processed: 1166 average time/residue: 1.1425 time to fit residues: 2069.2600 Evaluate side-chains 1186 residues out of total 4057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 1117 time to evaluate : 4.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 531 SER Chi-restraints excluded: chain B residue 613 GLU Chi-restraints excluded: chain B residue 679 SER Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 345 ASP Chi-restraints excluded: chain C residue 651 ASP Chi-restraints excluded: chain C residue 657 VAL Chi-restraints excluded: chain C residue 678 VAL Chi-restraints excluded: chain C residue 692 GLU Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain C residue 708 ILE Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 178 GLN Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 265 LYS Chi-restraints excluded: chain D residue 599 VAL Chi-restraints excluded: chain D residue 609 VAL Chi-restraints excluded: chain D residue 708 ILE Chi-restraints excluded: chain D residue 710 ASP Chi-restraints excluded: chain D residue 722 PHE Chi-restraints excluded: chain E residue 186 ASP Chi-restraints excluded: chain E residue 313 SER Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 347 THR Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 438 GLU Chi-restraints excluded: chain E residue 440 SER Chi-restraints excluded: chain E residue 600 VAL Chi-restraints excluded: chain E residue 612 THR Chi-restraints excluded: chain F residue 177 ASN Chi-restraints excluded: chain F residue 285 ASP Chi-restraints excluded: chain F residue 310 LEU Chi-restraints excluded: chain F residue 316 ILE Chi-restraints excluded: chain F residue 322 THR Chi-restraints excluded: chain F residue 393 HIS Chi-restraints excluded: chain F residue 564 ASP Chi-restraints excluded: chain F residue 606 ASN Chi-restraints excluded: chain F residue 622 GLN Chi-restraints excluded: chain F residue 746 PHE Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain H residue 168 THR Chi-restraints excluded: chain J residue 37 ASP Chi-restraints excluded: chain J residue 58 ASP Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 157 THR Chi-restraints excluded: chain J residue 159 GLN Chi-restraints excluded: chain J residue 184 LEU Chi-restraints excluded: chain K residue 70 ILE Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain L residue 188 ILE Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain M residue 36 GLU Chi-restraints excluded: chain M residue 41 ASN Chi-restraints excluded: chain M residue 82 PHE Chi-restraints excluded: chain M residue 171 ASP Chi-restraints excluded: chain M residue 184 LEU Chi-restraints excluded: chain M residue 186 ASP Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 75 SER Chi-restraints excluded: chain N residue 102 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 286 optimal weight: 5.9990 chunk 184 optimal weight: 2.9990 chunk 276 optimal weight: 9.9990 chunk 139 optimal weight: 3.9990 chunk 90 optimal weight: 6.9990 chunk 89 optimal weight: 0.9990 chunk 294 optimal weight: 10.0000 chunk 315 optimal weight: 0.9990 chunk 228 optimal weight: 7.9990 chunk 43 optimal weight: 20.0000 chunk 363 optimal weight: 10.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 642 ASN ** D 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 606 ASN D 659 HIS F 393 HIS H 41 ASN I 131 GLN K 191 HIS L 159 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 38562 Z= 0.206 Angle : 0.513 7.461 52104 Z= 0.258 Chirality : 0.039 0.158 5979 Planarity : 0.004 0.079 6722 Dihedral : 9.752 177.547 5406 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.77 % Allowed : 15.68 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.12), residues: 4789 helix: 1.02 (0.11), residues: 2439 sheet: -0.32 (0.18), residues: 725 loop : -0.60 (0.15), residues: 1625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 649 HIS 0.005 0.001 HIS A 288 PHE 0.012 0.001 PHE I 101 TYR 0.014 0.001 TYR K 60 ARG 0.014 0.000 ARG C 410 *********************** 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 1197 residues out of total 4057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 1125 time to evaluate : 4.473 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: A 279 ASN cc_start: 0.5951 (p0) cc_final: 0.5739 (p0) REVERT: A 307 ILE cc_start: 0.8599 (pt) cc_final: 0.8180 (mt) REVERT: A 387 LYS cc_start: 0.8955 (ttmt) cc_final: 0.8652 (ttmm) REVERT: A 393 HIS cc_start: 0.6336 (m-70) cc_final: 0.6040 (m-70) REVERT: A 427 GLU cc_start: 0.7384 (pt0) cc_final: 0.6848 (pt0) REVERT: A 432 ARG cc_start: 0.7301 (mtt90) cc_final: 0.7055 (mtm180) REVERT: A 439 LYS cc_start: 0.7758 (mptt) cc_final: 0.7528 (ttpp) REVERT: A 475 LYS cc_start: 0.8394 (mttt) cc_final: 0.7972 (mtpt) REVERT: A 503 GLU cc_start: 0.7456 (tp30) cc_final: 0.6761 (tp30) REVERT: B 206 ARG cc_start: 0.7094 (tpt170) cc_final: 0.6744 (mmt180) REVERT: B 230 ARG cc_start: 0.7785 (mtp85) cc_final: 0.7584 (mtp85) REVERT: B 247 SER cc_start: 0.8493 (t) cc_final: 0.8265 (p) REVERT: B 370 ASP cc_start: 0.7633 (t0) cc_final: 0.7198 (t0) REVERT: B 425 ASP cc_start: 0.7949 (t70) cc_final: 0.7609 (t70) REVERT: B 674 ASP cc_start: 0.7438 (m-30) cc_final: 0.7204 (m-30) REVERT: C 207 LYS cc_start: 0.8940 (mtpt) cc_final: 0.8662 (mtpt) REVERT: C 451 ASN cc_start: 0.8786 (m-40) cc_final: 0.8527 (m110) REVERT: D 370 ASP cc_start: 0.7326 (t0) cc_final: 0.7006 (t0) REVERT: D 396 ASP cc_start: 0.8099 (t70) cc_final: 0.7746 (t0) REVERT: D 674 ASP cc_start: 0.7291 (m-30) cc_final: 0.6860 (m-30) REVERT: D 706 ARG cc_start: 0.8483 (mtm-85) cc_final: 0.8269 (mtm-85) REVERT: E 225 GLU cc_start: 0.8490 (mt-10) cc_final: 0.8028 (mt-10) REVERT: E 235 ASP cc_start: 0.7454 (t0) cc_final: 0.6993 (t70) REVERT: E 348 GLU cc_start: 0.8161 (pt0) cc_final: 0.7416 (pt0) REVERT: E 387 LYS cc_start: 0.8881 (mtpt) cc_final: 0.8639 (mttm) REVERT: E 422 ASN cc_start: 0.7487 (t0) cc_final: 0.7195 (t0) REVERT: E 532 ARG cc_start: 0.7135 (mmm160) cc_final: 0.6882 (mmm160) REVERT: E 611 GLU cc_start: 0.7951 (mp0) cc_final: 0.7652 (mp0) REVERT: E 704 MET cc_start: 0.7197 (ttt) cc_final: 0.6894 (ttt) REVERT: F 268 LYS cc_start: 0.8215 (mtpp) cc_final: 0.7892 (tttm) REVERT: F 272 LYS cc_start: 0.8410 (mtmt) cc_final: 0.7941 (mmtm) REVERT: F 353 GLU cc_start: 0.7726 (mt-10) cc_final: 0.7521 (mt-10) REVERT: F 523 GLU cc_start: 0.9260 (tm-30) cc_final: 0.8646 (tm-30) REVERT: F 551 ASP cc_start: 0.6917 (m-30) cc_final: 0.6581 (m-30) REVERT: H 22 ARG cc_start: 0.9013 (tpt90) cc_final: 0.8654 (tpt90) REVERT: H 141 GLU cc_start: 0.8344 (tp30) cc_final: 0.8104 (tp30) REVERT: H 162 GLU cc_start: 0.5969 (tm-30) cc_final: 0.5642 (tm-30) REVERT: H 190 THR cc_start: 0.7868 (m) cc_final: 0.7640 (p) REVERT: I 118 ARG cc_start: 0.7440 (mmt-90) cc_final: 0.7060 (mpt180) REVERT: L 140 ARG cc_start: 0.7725 (mtp85) cc_final: 0.7275 (ttm110) REVERT: L 172 ARG cc_start: 0.7591 (ttt90) cc_final: 0.7168 (ttt180) REVERT: M 169 GLU cc_start: 0.7314 (tp30) cc_final: 0.6752 (tp30) REVERT: M 170 ARG cc_start: 0.7349 (mmt-90) cc_final: 0.6808 (mmt180) REVERT: N 102 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8798 (mm) REVERT: N 140 ARG cc_start: 0.8247 (mmm-85) cc_final: 0.8004 (mmm-85) REVERT: N 144 LYS cc_start: 0.8561 (mtpt) cc_final: 0.8151 (mptt) REVERT: N 148 ARG cc_start: 0.7180 (tpt170) cc_final: 0.6707 (mmm160) outliers start: 72 outliers final: 65 residues processed: 1155 average time/residue: 1.1153 time to fit residues: 2006.5585 Evaluate side-chains 1175 residues out of total 4057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 1109 time to evaluate : 4.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 583 ASN Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 659 HIS Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 531 SER Chi-restraints excluded: chain B residue 613 GLU Chi-restraints excluded: chain B residue 679 SER Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 345 ASP Chi-restraints excluded: chain C residue 651 ASP Chi-restraints excluded: chain C residue 657 VAL Chi-restraints excluded: chain C residue 692 GLU Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain C residue 708 ILE Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 178 GLN Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 265 LYS Chi-restraints excluded: chain D residue 609 VAL Chi-restraints excluded: chain D residue 708 ILE Chi-restraints excluded: chain D residue 722 PHE Chi-restraints excluded: chain E residue 186 ASP Chi-restraints excluded: chain E residue 313 SER Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 347 THR Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 438 GLU Chi-restraints excluded: chain E residue 440 SER Chi-restraints excluded: chain E residue 600 VAL Chi-restraints excluded: chain E residue 612 THR Chi-restraints excluded: chain F residue 177 ASN Chi-restraints excluded: chain F residue 285 ASP Chi-restraints excluded: chain F residue 310 LEU Chi-restraints excluded: chain F residue 322 THR Chi-restraints excluded: chain F residue 393 HIS Chi-restraints excluded: chain F residue 564 ASP Chi-restraints excluded: chain F residue 606 ASN Chi-restraints excluded: chain F residue 622 GLN Chi-restraints excluded: chain F residue 746 PHE Chi-restraints excluded: chain S residue 23 LYS Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain H residue 168 THR Chi-restraints excluded: chain J residue 58 ASP Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 157 THR Chi-restraints excluded: chain J residue 159 GLN Chi-restraints excluded: chain J residue 184 LEU Chi-restraints excluded: chain K residue 70 ILE Chi-restraints excluded: chain L residue 151 GLU Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain L residue 188 ILE Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain M residue 36 GLU Chi-restraints excluded: chain M residue 41 ASN Chi-restraints excluded: chain M residue 82 PHE Chi-restraints excluded: chain M residue 171 ASP Chi-restraints excluded: chain M residue 184 LEU Chi-restraints excluded: chain M residue 186 ASP Chi-restraints excluded: chain N residue 74 MET Chi-restraints excluded: chain N residue 75 SER Chi-restraints excluded: chain N residue 102 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 420 optimal weight: 1.9990 chunk 443 optimal weight: 6.9990 chunk 404 optimal weight: 0.9980 chunk 431 optimal weight: 0.9990 chunk 259 optimal weight: 9.9990 chunk 187 optimal weight: 6.9990 chunk 338 optimal weight: 7.9990 chunk 132 optimal weight: 0.7980 chunk 389 optimal weight: 3.9990 chunk 407 optimal weight: 6.9990 chunk 429 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 507 GLN C 356 GLN ** D 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 606 ASN D 659 HIS F 393 HIS F 422 ASN K 191 HIS L 159 GLN ** M 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.3715 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= 0.154 Angle : 0.500 7.305 52104 Z= 0.250 Chirality : 0.039 0.159 5979 Planarity : 0.003 0.060 6722 Dihedral : 9.565 176.275 5406 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.45 % Allowed : 15.95 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.12), residues: 4789 helix: 1.15 (0.11), residues: 2443 sheet: -0.23 (0.18), residues: 725 loop : -0.50 (0.15), residues: 1621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 229 HIS 0.017 0.001 HIS F 393 PHE 0.014 0.001 PHE I 101 TYR 0.017 0.001 TYR M 77 ARG 0.008 0.000 ARG C 527 *********************** 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 1195 residues out of total 4057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 1136 time to evaluate : 4.532 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: A 279 ASN cc_start: 0.5889 (p0) cc_final: 0.5663 (p0) REVERT: A 307 ILE cc_start: 0.8591 (pt) cc_final: 0.8165 (mt) REVERT: A 376 LYS cc_start: 0.7816 (mtpt) cc_final: 0.7551 (mtpp) REVERT: A 387 LYS cc_start: 0.8947 (ttmt) cc_final: 0.8642 (ttmm) REVERT: A 393 HIS cc_start: 0.6131 (m-70) cc_final: 0.5917 (m-70) REVERT: A 427 GLU cc_start: 0.7382 (pt0) cc_final: 0.6849 (pt0) REVERT: A 432 ARG cc_start: 0.7284 (mtt90) cc_final: 0.7012 (mtm180) REVERT: A 439 LYS cc_start: 0.7693 (mptt) cc_final: 0.7488 (ttpp) REVERT: A 475 LYS cc_start: 0.8414 (mttt) cc_final: 0.7986 (mtpt) REVERT: A 503 GLU cc_start: 0.7218 (tp30) cc_final: 0.6761 (tp30) REVERT: B 206 ARG cc_start: 0.7054 (tpt170) cc_final: 0.6726 (mmt180) REVERT: B 247 SER cc_start: 0.8389 (t) cc_final: 0.8189 (p) REVERT: B 370 ASP cc_start: 0.7597 (t0) cc_final: 0.7165 (t0) REVERT: B 425 ASP cc_start: 0.7913 (t70) cc_final: 0.7623 (t70) REVERT: B 674 ASP cc_start: 0.7434 (m-30) cc_final: 0.7200 (m-30) REVERT: C 207 LYS cc_start: 0.8921 (mtpt) cc_final: 0.8642 (mtpt) REVERT: C 451 ASN cc_start: 0.8760 (m-40) cc_final: 0.8499 (m110) REVERT: C 719 GLU cc_start: 0.7675 (mm-30) cc_final: 0.7460 (mm-30) REVERT: D 370 ASP cc_start: 0.7302 (t0) cc_final: 0.7024 (t0) REVERT: D 396 ASP cc_start: 0.8040 (t70) cc_final: 0.7678 (t0) REVERT: D 674 ASP cc_start: 0.7329 (m-30) cc_final: 0.6893 (m-30) REVERT: E 225 GLU cc_start: 0.8429 (mt-10) cc_final: 0.7932 (mt-10) REVERT: E 235 ASP cc_start: 0.7413 (t0) cc_final: 0.6966 (t70) REVERT: E 422 ASN cc_start: 0.7473 (t0) cc_final: 0.7177 (t0) REVERT: E 532 ARG cc_start: 0.7143 (mmm160) cc_final: 0.6881 (mmm160) REVERT: E 611 GLU cc_start: 0.7895 (mp0) cc_final: 0.7593 (mp0) REVERT: E 704 MET cc_start: 0.7261 (ttt) cc_final: 0.6943 (ttt) REVERT: F 268 LYS cc_start: 0.8205 (mtpp) cc_final: 0.7878 (tttm) REVERT: F 272 LYS cc_start: 0.8405 (mtmt) cc_final: 0.7932 (mmtm) REVERT: F 340 ARG cc_start: 0.7532 (mmt-90) cc_final: 0.7005 (mmt90) REVERT: F 353 GLU cc_start: 0.7729 (mt-10) cc_final: 0.7492 (mt-10) REVERT: F 523 GLU cc_start: 0.9262 (tm-30) cc_final: 0.8627 (tm-30) REVERT: F 551 ASP cc_start: 0.6944 (m-30) cc_final: 0.6596 (m-30) REVERT: H 22 ARG cc_start: 0.8998 (tpt90) cc_final: 0.8641 (tpt90) REVERT: H 141 GLU cc_start: 0.8283 (tp30) cc_final: 0.8058 (tp30) REVERT: H 172 ARG cc_start: 0.7519 (tpp80) cc_final: 0.7307 (tpp80) REVERT: H 190 THR cc_start: 0.7869 (m) cc_final: 0.7646 (p) REVERT: I 118 ARG cc_start: 0.7456 (mmt-90) cc_final: 0.7096 (mpt180) REVERT: K 149 MET cc_start: 0.8993 (mmp) cc_final: 0.8451 (mmp) REVERT: L 140 ARG cc_start: 0.7709 (mtp85) cc_final: 0.7335 (ttm110) REVERT: L 172 ARG cc_start: 0.7565 (ttt90) cc_final: 0.7147 (ttt180) REVERT: M 169 GLU cc_start: 0.7334 (tp30) cc_final: 0.6731 (tp30) REVERT: M 170 ARG cc_start: 0.7349 (mmt-90) cc_final: 0.6820 (mmt180) REVERT: N 102 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8779 (mm) REVERT: N 140 ARG cc_start: 0.8239 (mmm-85) cc_final: 0.7989 (mmm-85) REVERT: N 144 LYS cc_start: 0.8564 (mtpt) cc_final: 0.8154 (mptt) REVERT: N 148 ARG cc_start: 0.7169 (tpt170) cc_final: 0.6703 (mmm160) outliers start: 59 outliers final: 56 residues processed: 1161 average time/residue: 1.1255 time to fit residues: 2040.8245 Evaluate side-chains 1176 residues out of total 4057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 1119 time to evaluate : 4.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 507 GLN Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 659 HIS Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 613 GLU Chi-restraints excluded: chain B residue 679 SER Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 345 ASP Chi-restraints excluded: chain C residue 651 ASP Chi-restraints excluded: chain C residue 657 VAL Chi-restraints excluded: chain C residue 692 GLU Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain C residue 708 ILE Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 178 GLN Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 265 LYS Chi-restraints excluded: chain D residue 708 ILE Chi-restraints excluded: chain D residue 722 PHE Chi-restraints excluded: chain E residue 313 SER Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 438 GLU Chi-restraints excluded: chain E residue 600 VAL Chi-restraints excluded: chain E residue 612 THR Chi-restraints excluded: chain F residue 177 ASN Chi-restraints excluded: chain F residue 225 GLU Chi-restraints excluded: chain F residue 310 LEU Chi-restraints excluded: chain F residue 322 THR Chi-restraints excluded: chain F residue 564 ASP Chi-restraints excluded: chain F residue 606 ASN Chi-restraints excluded: chain F residue 622 GLN Chi-restraints excluded: chain F residue 746 PHE Chi-restraints excluded: chain S residue 23 LYS Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain H residue 168 THR Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain J residue 58 ASP Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 157 THR Chi-restraints excluded: chain J residue 159 GLN Chi-restraints excluded: chain J residue 184 LEU Chi-restraints excluded: chain K residue 70 ILE Chi-restraints excluded: chain L residue 151 GLU Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain M residue 36 GLU Chi-restraints excluded: chain M residue 41 ASN Chi-restraints excluded: chain M residue 82 PHE Chi-restraints excluded: chain M residue 171 ASP Chi-restraints excluded: chain M residue 184 LEU Chi-restraints excluded: chain M residue 186 ASP Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 74 MET Chi-restraints excluded: chain N residue 102 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 283 optimal weight: 20.0000 chunk 455 optimal weight: 0.8980 chunk 278 optimal weight: 9.9990 chunk 216 optimal weight: 5.9990 chunk 316 optimal weight: 20.0000 chunk 478 optimal weight: 7.9990 chunk 440 optimal weight: 6.9990 chunk 380 optimal weight: 9.9990 chunk 39 optimal weight: 20.0000 chunk 294 optimal weight: 10.0000 chunk 233 optimal weight: 7.9990 overall best weight: 5.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 709 GLN D 606 ASN D 659 HIS ** F 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 393 HIS ** J 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 150 ASN K 191 HIS L 159 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.3810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 38562 Z= 0.338 Angle : 0.551 9.442 52104 Z= 0.280 Chirality : 0.040 0.161 5979 Planarity : 0.004 0.064 6722 Dihedral : 9.720 173.348 5406 Min Nonbonded Distance : 1.729 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.58 % Allowed : 16.00 % Favored : 82.43 % 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: 0.38 (0.12), residues: 4789 helix: 1.01 (0.11), residues: 2448 sheet: -0.25 (0.18), residues: 725 loop : -0.54 (0.15), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 229 HIS 0.006 0.001 HIS A 288 PHE 0.016 0.001 PHE C 172 TYR 0.021 0.001 TYR K 60 ARG 0.009 0.000 ARG I 140 ********************** 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 1181 residues out of total 4057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 1117 time to evaluate : 4.375 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: A 215 GLU cc_start: 0.7101 (pt0) cc_final: 0.6802 (pt0) REVERT: A 279 ASN cc_start: 0.5971 (p0) cc_final: 0.5733 (p0) REVERT: A 307 ILE cc_start: 0.8611 (pt) cc_final: 0.8188 (mt) REVERT: A 376 LYS cc_start: 0.7824 (mtpt) cc_final: 0.7556 (mtpp) REVERT: A 387 LYS cc_start: 0.8972 (ttmt) cc_final: 0.8657 (ttmm) REVERT: A 427 GLU cc_start: 0.7427 (pt0) cc_final: 0.6879 (pt0) REVERT: A 432 ARG cc_start: 0.7288 (mtt90) cc_final: 0.7014 (mtm180) REVERT: A 439 LYS cc_start: 0.7775 (mptt) cc_final: 0.7555 (ttpp) REVERT: A 472 GLU cc_start: 0.7859 (mm-30) cc_final: 0.7458 (mm-30) REVERT: A 475 LYS cc_start: 0.8405 (mttt) cc_final: 0.8145 (mtpt) REVERT: A 503 GLU cc_start: 0.7371 (tp30) cc_final: 0.6811 (tp30) REVERT: B 206 ARG cc_start: 0.7111 (tpt170) cc_final: 0.6756 (mmt180) REVERT: B 247 SER cc_start: 0.8497 (t) cc_final: 0.8255 (p) REVERT: B 273 GLN cc_start: 0.7663 (tt0) cc_final: 0.7353 (tp-100) REVERT: B 370 ASP cc_start: 0.7666 (t0) cc_final: 0.7230 (t0) REVERT: B 404 GLU cc_start: 0.8617 (tp30) cc_final: 0.7299 (tp30) REVERT: B 425 ASP cc_start: 0.8016 (t70) cc_final: 0.7680 (t70) REVERT: B 674 ASP cc_start: 0.7447 (m-30) cc_final: 0.7213 (m-30) REVERT: C 207 LYS cc_start: 0.8967 (mtpt) cc_final: 0.8701 (mtpt) REVERT: C 259 TYR cc_start: 0.8705 (m-80) cc_final: 0.7855 (m-80) REVERT: C 394 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8180 (tp) REVERT: C 451 ASN cc_start: 0.8803 (m-40) cc_final: 0.8521 (m110) REVERT: C 544 ASP cc_start: 0.7366 (t0) cc_final: 0.6933 (t0) REVERT: D 370 ASP cc_start: 0.7356 (t0) cc_final: 0.7050 (t0) REVERT: D 396 ASP cc_start: 0.8202 (t70) cc_final: 0.7859 (t0) REVERT: D 412 MET cc_start: 0.5402 (ttp) cc_final: 0.5116 (ttp) REVERT: D 565 GLU cc_start: 0.8772 (mm-30) cc_final: 0.8555 (mm-30) REVERT: D 674 ASP cc_start: 0.7312 (m-30) cc_final: 0.6871 (m-30) REVERT: E 225 GLU cc_start: 0.8512 (mt-10) cc_final: 0.8074 (mt-10) REVERT: E 235 ASP cc_start: 0.7513 (t0) cc_final: 0.7052 (t0) REVERT: E 348 GLU cc_start: 0.8237 (pt0) cc_final: 0.7540 (pt0) REVERT: E 422 ASN cc_start: 0.7525 (t0) cc_final: 0.7260 (t0) REVERT: E 532 ARG cc_start: 0.7160 (mmm160) cc_final: 0.6897 (mmm160) REVERT: E 611 GLU cc_start: 0.7940 (mp0) cc_final: 0.7654 (mp0) REVERT: E 633 LYS cc_start: 0.7992 (mttt) cc_final: 0.7669 (mttp) REVERT: E 704 MET cc_start: 0.7232 (ttt) cc_final: 0.6945 (ttt) REVERT: F 177 ASN cc_start: 0.8522 (OUTLIER) cc_final: 0.7973 (t0) REVERT: F 268 LYS cc_start: 0.8244 (mtpp) cc_final: 0.7920 (tttm) REVERT: F 272 LYS cc_start: 0.8416 (mtmt) cc_final: 0.7950 (mmtm) REVERT: F 340 ARG cc_start: 0.7601 (mmt-90) cc_final: 0.7056 (mmt90) REVERT: F 353 GLU cc_start: 0.7758 (mt-10) cc_final: 0.7531 (mt-10) REVERT: F 523 GLU cc_start: 0.9276 (tm-30) cc_final: 0.8662 (tm-30) REVERT: F 551 ASP cc_start: 0.6956 (m-30) cc_final: 0.6613 (m-30) REVERT: H 22 ARG cc_start: 0.9022 (tpt90) cc_final: 0.8649 (tpt90) REVERT: H 172 ARG cc_start: 0.7546 (tpp80) cc_final: 0.7333 (tpp80) REVERT: H 190 THR cc_start: 0.7902 (m) cc_final: 0.7674 (p) REVERT: I 118 ARG cc_start: 0.7476 (mmt-90) cc_final: 0.7128 (mpt180) REVERT: K 149 MET cc_start: 0.8999 (mmp) cc_final: 0.8470 (mmp) REVERT: L 172 ARG cc_start: 0.7610 (ttt90) cc_final: 0.7194 (ttt180) REVERT: M 169 GLU cc_start: 0.7318 (tp30) cc_final: 0.6770 (tp30) REVERT: M 170 ARG cc_start: 0.7351 (mmt-90) cc_final: 0.6807 (mmt180) REVERT: N 102 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8801 (mm) REVERT: N 140 ARG cc_start: 0.8279 (mmm-85) cc_final: 0.8023 (mmm-85) REVERT: N 144 LYS cc_start: 0.8594 (mtpt) cc_final: 0.8198 (mptt) REVERT: N 148 ARG cc_start: 0.7286 (tpt170) cc_final: 0.6795 (mmm160) REVERT: N 151 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7422 (tt0) outliers start: 64 outliers final: 56 residues processed: 1144 average time/residue: 1.0930 time to fit residues: 1933.8359 Evaluate side-chains 1171 residues out of total 4057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 1111 time to evaluate : 4.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 659 HIS Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 531 SER Chi-restraints excluded: chain B residue 613 GLU Chi-restraints excluded: chain B residue 679 SER Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 345 ASP Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 590 ASN Chi-restraints excluded: chain C residue 651 ASP Chi-restraints excluded: chain C residue 657 VAL Chi-restraints excluded: chain C residue 681 GLU Chi-restraints excluded: chain C residue 692 GLU Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain C residue 708 ILE Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 178 GLN Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 265 LYS Chi-restraints excluded: chain D residue 609 VAL Chi-restraints excluded: chain D residue 708 ILE Chi-restraints excluded: chain D residue 722 PHE Chi-restraints excluded: chain E residue 313 SER Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 438 GLU Chi-restraints excluded: chain E residue 600 VAL Chi-restraints excluded: chain E residue 612 THR Chi-restraints excluded: chain F residue 177 ASN Chi-restraints excluded: chain F residue 225 GLU Chi-restraints excluded: chain F residue 285 ASP Chi-restraints excluded: chain F residue 310 LEU Chi-restraints excluded: chain F residue 322 THR Chi-restraints excluded: chain F residue 564 ASP Chi-restraints excluded: chain F residue 606 ASN Chi-restraints excluded: chain F residue 622 GLN Chi-restraints excluded: chain F residue 746 PHE Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 168 THR Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain I residue 134 ASP Chi-restraints excluded: chain J residue 58 ASP Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 157 THR Chi-restraints excluded: chain J residue 159 GLN Chi-restraints excluded: chain K residue 70 ILE Chi-restraints excluded: chain L residue 151 GLU Chi-restraints excluded: chain M residue 3 VAL Chi-restraints excluded: chain M residue 36 GLU Chi-restraints excluded: chain M residue 41 ASN Chi-restraints excluded: chain M residue 82 PHE Chi-restraints excluded: chain M residue 171 ASP Chi-restraints excluded: chain M residue 184 LEU Chi-restraints excluded: chain M residue 186 ASP Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 74 MET Chi-restraints excluded: chain N residue 102 LEU Chi-restraints excluded: chain N residue 151 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 302 optimal weight: 10.0000 chunk 405 optimal weight: 0.6980 chunk 116 optimal weight: 2.9990 chunk 351 optimal weight: 4.9990 chunk 56 optimal weight: 7.9990 chunk 105 optimal weight: 3.9990 chunk 381 optimal weight: 10.0000 chunk 159 optimal weight: 10.0000 chunk 391 optimal weight: 4.9990 chunk 48 optimal weight: 10.0000 chunk 70 optimal weight: 8.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 709 GLN ** D 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 606 ASN D 659 HIS F 422 ASN ** J 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 191 HIS L 159 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.156444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.112193 restraints weight = 142734.043| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 2.50 r_work: 0.2948 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.3867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 38562 Z= 0.223 Angle : 0.520 8.956 52104 Z= 0.262 Chirality : 0.039 0.159 5979 Planarity : 0.004 0.063 6722 Dihedral : 9.680 176.269 5406 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.50 % Allowed : 16.42 % Favored : 82.08 % 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: 1.08 (0.11), residues: 2452 sheet: -0.21 (0.18), residues: 711 loop : -0.51 (0.15), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 229 HIS 0.007 0.001 HIS A 570 PHE 0.012 0.001 PHE I 101 TYR 0.017 0.001 TYR M 77 ARG 0.010 0.000 ARG C 527 =============================================================================== Job complete usr+sys time: 28140.88 seconds wall clock time: 484 minutes 8.06 seconds (29048.06 seconds total)