Starting phenix.real_space_refine on Sun Mar 17 01:33:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uj0_26559/03_2024/7uj0_26559_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uj0_26559/03_2024/7uj0_26559.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uj0_26559/03_2024/7uj0_26559.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uj0_26559/03_2024/7uj0_26559.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uj0_26559/03_2024/7uj0_26559_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uj0_26559/03_2024/7uj0_26559_trim_updated.pdb" } resolution = 3.26 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 9 5.21 5 S 169 5.16 5 C 23836 2.51 5 N 6725 2.21 5 O 7236 1.98 5 H 38308 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 186": "OD1" <-> "OD2" Residue "A GLU 196": "OE1" <-> "OE2" Residue "A GLU 215": "OE1" <-> "OE2" Residue "A GLU 225": "OE1" <-> "OE2" Residue "A GLU 238": "OE1" <-> "OE2" Residue "A ASP 242": "OD1" <-> "OD2" 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 GLU 264": "OE1" <-> "OE2" Residue "A GLU 286": "OE1" <-> "OE2" Residue "A PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 334": "OD1" <-> "OD2" Residue "A GLU 348": "OE1" <-> "OE2" Residue "A GLU 353": "OE1" <-> "OE2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 370": "OD1" <-> "OD2" Residue "A ASP 396": "OD1" <-> "OD2" Residue "A ASP 400": "OD1" <-> "OD2" Residue "A GLU 404": "OE1" <-> "OE2" Residue "A ASP 425": "OD1" <-> "OD2" Residue "A GLU 438": "OE1" <-> "OE2" Residue "A PHE 461": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 468": "OE1" <-> "OE2" Residue "A GLU 484": "OE1" <-> "OE2" Residue "A PHE 493": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 ASP 544": "OD1" <-> "OD2" Residue "A ASP 551": "OD1" <-> "OD2" Residue "A GLU 565": "OE1" <-> "OE2" Residue "A PHE 596": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 630": "OE1" <-> "OE2" Residue "A GLU 639": "OE1" <-> "OE2" Residue "A ASP 645": "OD1" <-> "OD2" Residue "A PHE 650": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 674": "OD1" <-> "OD2" Residue "A GLU 738": "OE1" <-> "OE2" Residue "A GLU 741": "OE1" <-> "OE2" Residue "A PHE 746": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 186": "OD1" <-> "OD2" Residue "B GLU 194": "OE1" <-> "OE2" Residue "B TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 334": "OD1" <-> "OD2" Residue "B TYR 373": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 388": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 461": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 484": "OE1" <-> "OE2" Residue "B PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 540": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 565": "OE1" <-> "OE2" Residue "B PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 582": "OD1" <-> "OD2" Residue "B ASP 627": "OD1" <-> "OD2" 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 GLU 685": "OE1" <-> "OE2" Residue "C ASP 186": "OD1" <-> "OD2" Residue "C TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 326": "OE1" <-> "OE2" Residue "C PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 373": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 388": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 400": "OD1" <-> "OD2" Residue "C GLU 472": "OE1" <-> "OE2" Residue "C PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 540": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 567": "OE1" <-> "OE2" Residue "C PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 613": "OE1" <-> "OE2" Residue "C PHE 636": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 640": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 674": "OD1" <-> "OD2" Residue "C TYR 744": "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 ASP 262": "OD1" <-> "OD2" Residue "D PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 373": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 400": "OD1" <-> "OD2" Residue "D ASP 403": "OD1" <-> "OD2" Residue "D PHE 461": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 565": "OE1" <-> "OE2" Residue "D GLU 611": "OE1" <-> "OE2" Residue "D ASP 623": "OD1" <-> "OD2" Residue "D PHE 636": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 665": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 736": "OD1" <-> "OD2" Residue "E GLU 192": "OE1" <-> "OE2" Residue "E TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 249": "OD1" <-> "OD2" Residue "E TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 260": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ASP 285": "OD1" <-> "OD2" Residue "E PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E 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 391": "OD1" <-> "OD2" Residue "E GLU 404": "OE1" <-> "OE2" Residue "E ASP 445": "OD1" <-> "OD2" Residue "E ASP 447": "OD1" <-> "OD2" Residue "E PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 520": "OD1" <-> "OD2" Residue "E TYR 524": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 540": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 544": "OD1" <-> "OD2" Residue "E PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 582": "OD1" <-> "OD2" Residue "E ASP 627": "OD1" <-> "OD2" Residue "E GLU 630": "OE1" <-> "OE2" Residue "E PHE 636": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 656": "OD1" <-> "OD2" Residue "E PHE 665": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 668": "OE1" <-> "OE2" Residue "E ASP 674": "OD1" <-> "OD2" Residue "E ASP 710": "OD1" <-> "OD2" Residue "E PHE 722": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 727": "OD1" <-> "OD2" Residue "F TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 249": "OD1" <-> "OD2" Residue "F ARG 260": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F GLU 286": "OE1" <-> "OE2" Residue "F PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 332": "OE1" <-> "OE2" Residue "F ASP 334": "OD1" <-> "OD2" Residue "F GLU 352": "OE1" <-> "OE2" Residue "F TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 373": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 388": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 403": "OD1" <-> "OD2" Residue "F ASP 445": "OD1" <-> "OD2" Residue "F ASP 447": "OD1" <-> "OD2" Residue "F GLU 503": "OE1" <-> "OE2" Residue "F PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 520": "OD1" <-> "OD2" Residue "F ASP 544": "OD1" <-> "OD2" Residue "F GLU 565": "OE1" <-> "OE2" Residue "F PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 582": "OD1" <-> "OD2" Residue "F ASP 595": "OD1" <-> "OD2" Residue "F GLU 611": "OE1" <-> "OE2" Residue "F ASP 627": "OD1" <-> "OD2" Residue "F GLU 631": "OE1" <-> "OE2" Residue "F PHE 636": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 650": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 663": "OD1" <-> "OD2" Residue "F PHE 665": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 681": "OE1" <-> "OE2" Residue "F GLU 685": "OE1" <-> "OE2" Residue "F ASP 710": "OD1" <-> "OD2" Residue "S ASP 20": "OD1" <-> "OD2" Residue "H ARG 12": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 51": "OE1" <-> "OE2" Residue "H ASP 78": "OD1" <-> "OD2" Residue "H PHE 82": "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 ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ASP 167": "OD1" <-> "OD2" Residue "H ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I GLU 8": "OE1" <-> "OE2" Residue "I ARG 12": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I GLU 165": "OE1" <-> "OE2" Residue "I ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I GLU 169": "OE1" <-> "OE2" Residue "I ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I PHE 173": "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 ASP 37": "OD1" <-> "OD2" Residue "J ASP 134": "OD1" <-> "OD2" Residue "J GLU 136": "OE1" <-> "OE2" Residue "J ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J GLU 165": "OE1" <-> "OE2" Residue "J ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" 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 ASP 78": "OD1" <-> "OD2" Residue "K GLU 136": "OE1" <-> "OE2" Residue "K ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 37": "OD1" <-> "OD2" Residue "L TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ASP 78": "OD1" <-> "OD2" Residue "L ARG 118": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ASP 134": "OD1" <-> "OD2" Residue "L GLU 141": "OE1" <-> "OE2" Residue "L ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M ARG 12": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M GLU 14": "OE1" <-> "OE2" Residue "M ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M GLU 51": "OE1" <-> "OE2" Residue "M TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N ARG 12": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" 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 101": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N GLU 151": "OE1" <-> "OE2" Residue "N GLU 165": "OE1" <-> "OE2" Residue "N ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 76314 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: 9140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 580, 9140 Classifications: {'peptide': 580} Link IDs: {'PTRANS': 18, 'TRANS': 561} Chain: "C" Number of atoms: 9152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 581, 9152 Classifications: {'peptide': 581} Link IDs: {'PTRANS': 18, 'TRANS': 562} Chain: "D" Number of atoms: 9142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 580, 9142 Classifications: {'peptide': 580} Link IDs: {'PTRANS': 18, 'TRANS': 561} Chain: "E" Number of atoms: 9143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 580, 9143 Classifications: {'peptide': 580} Link IDs: {'PTRANS': 18, 'TRANS': 561} Chain: "F" Number of atoms: 9130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 9130 Classifications: {'peptide': 579} Link IDs: {'PTRANS': 18, 'TRANS': 560} Chain: "S" Number of atoms: 179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 179 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: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 2, 'ADP': 1, 'AGS': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 55 Unusual residues: {' MG': 1, 'ADP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" 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} Time building chain proxies: 28.91, per 1000 atoms: 0.38 Number of scatterers: 76314 At special positions: 0 Unit cell: (151.38, 151.38, 164.43, 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 9 11.99 O 7236 8.00 N 6725 7.00 C 23836 6.00 H 38308 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: 48.40 Conformation dependent library (CDL) restraints added in 5.7 seconds 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8908 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 216 helices and 43 sheets defined 48.0% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.64 Creating SS restraints... Processing helix chain 'A' and resid 177 through 182 Processing helix chain 'A' and resid 192 through 202 removed outlier: 3.844A pdb=" N VAL A 201 " --> pdb=" O ARG A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 233 removed outlier: 3.763A pdb=" N ALA A 224 " --> pdb=" O LYS A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 241 No H-bonds generated for 'chain 'A' and resid 238 through 241' Processing helix chain 'A' and resid 250 through 255 Processing helix chain 'A' and resid 262 through 274 Processing helix chain 'A' and resid 303 through 313 removed outlier: 3.568A pdb=" N ILE A 307 " --> pdb=" O ALA A 303 " (cutoff:3.500A) Proline residue: A 309 - end of helix removed outlier: 3.932A pdb=" N SER A 313 " --> pdb=" O PRO A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 329 removed outlier: 3.689A pdb=" N SER A 328 " --> pdb=" O TYR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 340 Processing helix chain 'A' and resid 351 through 369 removed outlier: 3.867A pdb=" N GLN A 356 " --> pdb=" O GLU A 352 " (cutoff:3.500A) Proline residue: A 363 - end of helix removed outlier: 4.119A pdb=" N HIS A 368 " --> pdb=" O LYS A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 388 removed outlier: 4.095A pdb=" N VAL A 382 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU A 383 " --> pdb=" O ARG A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 411 Processing helix chain 'A' and resid 423 through 434 removed outlier: 3.934A pdb=" N ALA A 431 " --> pdb=" O GLU A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 459 removed outlier: 3.734A pdb=" N LYS A 450 " --> pdb=" O ARG A 446 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY A 453 " --> pdb=" O LEU A 449 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ASP A 454 " --> pdb=" O LYS A 450 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG A 455 " --> pdb=" O ASN A 451 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS A 457 " --> pdb=" O GLY A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 479 removed outlier: 3.517A pdb=" N GLU A 468 " --> pdb=" O ASP A 464 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA A 469 " --> pdb=" O LYS A 465 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 512 removed outlier: 3.878A pdb=" N THR A 505 " --> pdb=" O LYS A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 534 removed outlier: 3.918A pdb=" N ILE A 534 " --> pdb=" O VAL A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 555 removed outlier: 3.540A pdb=" N VAL A 553 " --> pdb=" O LEU A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 583 removed outlier: 3.775A pdb=" N ILE A 576 " --> pdb=" O ASP A 572 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN A 579 " --> pdb=" O ASN A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 635 removed outlier: 3.683A pdb=" N LYS A 634 " --> pdb=" O GLU A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 643 Processing helix chain 'A' and resid 655 through 675 removed outlier: 4.024A pdb=" N ASP A 663 " --> pdb=" O HIS A 659 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS A 664 " --> pdb=" O GLN A 660 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU A 669 " --> pdb=" O PHE A 665 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLN A 675 " --> pdb=" O VAL A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 684 through 694 removed outlier: 3.519A pdb=" N TRP A 689 " --> pdb=" O GLU A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 711 Processing helix chain 'A' and resid 713 through 721 removed outlier: 3.824A pdb=" N ASN A 718 " --> pdb=" O LYS A 714 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLU A 719 " --> pdb=" O PRO A 715 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 182 removed outlier: 3.726A 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: 3.555A pdb=" N ALA B 224 " --> pdb=" O LYS B 220 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA B 228 " --> pdb=" O ALA B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 241 No H-bonds generated for 'chain 'B' and resid 238 through 241' Processing helix chain 'B' and resid 250 through 253 No H-bonds generated for 'chain 'B' and resid 250 through 253' Processing helix chain 'B' and resid 262 through 277 Processing helix chain 'B' and resid 287 through 291 Processing helix chain 'B' and resid 303 through 313 Proline residue: B 309 - end of helix removed outlier: 3.632A pdb=" N SER B 313 " --> pdb=" O PRO B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 329 Processing helix chain 'B' and resid 335 through 340 Processing helix chain 'B' and resid 351 through 369 removed outlier: 3.662A 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: 3.529A 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 451 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: 3.903A pdb=" N ARG B 532 " --> pdb=" O HIS B 528 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU B 533 " --> pdb=" O THR B 529 " (cutoff:3.500A) removed outlier: 3.839A 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 566 through 568 No H-bonds generated for 'chain 'B' and resid 566 through 568' Processing helix chain 'B' and resid 571 through 583 removed outlier: 3.847A pdb=" N LEU B 578 " --> pdb=" O ASN B 575 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N MET B 581 " --> pdb=" O LEU B 578 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASP B 582 " --> pdb=" O GLN B 579 " (cutoff:3.500A) removed outlier: 3.606A 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 removed outlier: 3.524A pdb=" N GLU B 631 " --> pdb=" O ASP B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 643 Processing helix chain 'B' and resid 655 through 676 removed outlier: 3.693A pdb=" N GLN B 660 " --> pdb=" O ASP B 656 " (cutoff:3.500A) removed outlier: 3.965A 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: 3.506A pdb=" N ARG B 706 " --> pdb=" O ARG B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 721 removed outlier: 3.502A pdb=" N ASN B 718 " --> pdb=" O LYS B 714 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU B 719 " --> pdb=" O PRO B 715 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 182 Processing helix chain 'C' and resid 192 through 202 Processing helix chain 'C' and resid 220 through 233 removed outlier: 3.512A pdb=" N ALA C 224 " --> pdb=" O LYS C 220 " (cutoff:3.500A) removed outlier: 3.738A 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 335 through 340 removed outlier: 3.591A pdb=" N ARG C 340 " --> pdb=" O ALA C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 369 removed outlier: 3.594A 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 Processing helix chain 'C' and resid 394 through 410 removed outlier: 3.697A pdb=" N VAL C 401 " --> pdb=" O LYS C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 423 through 433 Processing helix chain 'C' and resid 443 through 450 Processing helix chain 'C' and resid 452 through 457 Processing helix chain 'C' and resid 464 through 479 Processing helix chain 'C' and resid 503 through 512 removed outlier: 3.566A pdb=" N SER C 509 " --> pdb=" O THR C 505 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS C 510 " --> pdb=" O VAL C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 527 through 534 removed outlier: 3.606A pdb=" N SER C 531 " --> pdb=" O ARG C 527 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ARG C 532 " --> pdb=" O HIS C 528 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU C 533 " --> pdb=" O THR C 529 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ILE C 534 " --> pdb=" O VAL C 530 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 527 through 534' Processing helix chain 'C' and resid 550 through 555 Processing helix chain 'C' and resid 566 through 568 No H-bonds generated for 'chain 'C' and resid 566 through 568' Processing helix chain 'C' and resid 571 through 576 Processing helix chain 'C' and resid 578 through 582 Processing helix chain 'C' and resid 609 through 613 Processing helix chain 'C' and resid 625 through 635 removed outlier: 3.613A pdb=" N MET C 629 " --> pdb=" O SER C 625 " (cutoff:3.500A) Processing helix chain 'C' and resid 638 through 643 Processing helix chain 'C' and resid 655 through 676 removed outlier: 3.713A pdb=" N HIS C 659 " --> pdb=" O THR C 655 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLN C 660 " --> pdb=" O ASP C 656 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN C 675 " --> pdb=" O VAL C 671 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS C 676 " --> pdb=" O GLN C 672 " (cutoff:3.500A) Processing helix chain 'C' and resid 684 through 694 Processing helix chain 'C' and resid 702 through 711 removed outlier: 3.508A pdb=" N ARG C 706 " --> pdb=" O ARG C 702 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 721 Processing helix chain 'D' and resid 176 through 182 removed outlier: 3.522A pdb=" N ARG D 181 " --> pdb=" O ASN D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 203 Processing helix chain 'D' and resid 220 through 233 removed outlier: 3.889A pdb=" N ALA D 224 " --> pdb=" O LYS D 220 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA D 228 " --> pdb=" O ALA D 224 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN D 233 " --> pdb=" O TRP D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 253 No H-bonds generated for 'chain 'D' and resid 250 through 253' Processing helix chain 'D' and resid 262 through 277 removed outlier: 3.505A pdb=" N GLN D 273 " --> pdb=" O ALA D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 290 Processing helix chain 'D' and resid 303 through 313 Proline residue: D 309 - end of helix Processing helix chain 'D' and resid 324 through 329 Processing helix chain 'D' and resid 331 through 333 No H-bonds generated for 'chain 'D' and resid 331 through 333' Processing helix chain 'D' and resid 335 through 340 removed outlier: 3.593A pdb=" N ARG D 339 " --> pdb=" O ARG D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 369 removed outlier: 3.708A pdb=" N GLN D 356 " --> pdb=" O GLU D 352 " (cutoff:3.500A) Proline residue: D 363 - end of helix Processing helix chain 'D' and resid 375 through 388 Processing helix chain 'D' and resid 394 through 411 Processing helix chain 'D' and resid 423 through 434 Processing helix chain 'D' and resid 443 through 450 removed outlier: 3.597A pdb=" N THR D 448 " --> pdb=" O SER D 444 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 459 removed outlier: 3.560A pdb=" N MET D 458 " --> pdb=" O ASP D 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 464 through 478 Processing helix chain 'D' and resid 503 through 512 removed outlier: 3.640A pdb=" N LYS D 510 " --> pdb=" O VAL D 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 527 through 532 removed outlier: 3.618A pdb=" N SER D 531 " --> pdb=" O ARG D 527 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N ARG D 532 " --> pdb=" O HIS D 528 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 527 through 532' Processing helix chain 'D' and resid 548 through 555 Processing helix chain 'D' and resid 571 through 582 removed outlier: 3.580A pdb=" N LEU D 578 " --> pdb=" O ASN D 575 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLN D 579 " --> pdb=" O ILE D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 609 through 613 Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 643 Processing helix chain 'D' and resid 655 through 676 removed outlier: 3.550A pdb=" N GLN D 660 " --> pdb=" O ASP D 656 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS D 676 " --> pdb=" O GLN D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 684 through 694 Processing helix chain 'D' and resid 702 through 711 removed outlier: 3.527A pdb=" N ARG D 706 " --> pdb=" O ARG D 702 " (cutoff:3.500A) Processing helix chain 'D' and resid 713 through 721 removed outlier: 3.975A pdb=" N ASN D 718 " --> pdb=" O LYS D 714 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU D 719 " --> pdb=" O PRO D 715 " (cutoff:3.500A) Processing helix chain 'D' and resid 724 through 726 No H-bonds generated for 'chain 'D' and resid 724 through 726' Processing helix chain 'E' and resid 177 through 182 removed outlier: 3.555A 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 233 removed outlier: 3.678A pdb=" N ALA E 224 " --> pdb=" O LYS E 220 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA E 228 " --> pdb=" O ALA E 224 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 254 Processing helix chain 'E' and resid 262 through 276 Processing helix chain 'E' and resid 287 through 291 Processing helix chain 'E' and resid 303 through 313 Proline residue: E 309 - end of helix Processing helix chain 'E' and resid 324 through 329 Processing helix chain 'E' and resid 335 through 340 removed outlier: 3.598A pdb=" N ARG E 340 " --> pdb=" O ALA E 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 369 removed outlier: 3.693A pdb=" N GLN E 356 " --> pdb=" O GLU E 352 " (cutoff:3.500A) Proline residue: E 363 - end of helix Processing helix chain 'E' and resid 375 through 388 removed outlier: 3.778A pdb=" N ARG E 379 " --> pdb=" O ALA E 375 " (cutoff:3.500A) Processing helix chain 'E' and resid 394 through 412 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 478 removed outlier: 3.841A pdb=" N ALA E 469 " --> pdb=" O LYS E 465 " (cutoff:3.500A) Processing helix chain 'E' and resid 501 through 512 removed outlier: 3.528A pdb=" N THR E 505 " --> pdb=" O LYS E 501 " (cutoff:3.500A) Processing helix chain 'E' and resid 527 through 532 removed outlier: 3.844A pdb=" N SER E 531 " --> pdb=" O ARG E 527 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ARG E 532 " --> pdb=" O HIS E 528 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 527 through 532' Processing helix chain 'E' and resid 550 through 555 removed outlier: 3.739A pdb=" N ILE E 554 " --> pdb=" O THR E 550 " (cutoff:3.500A) Processing helix chain 'E' and resid 571 through 583 removed outlier: 4.149A pdb=" N GLN E 579 " --> pdb=" O ASN E 575 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL E 580 " --> pdb=" O ILE E 576 " (cutoff:3.500A) Processing helix chain 'E' and resid 608 through 613 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: 3.677A pdb=" N GLN E 660 " --> pdb=" O ASP E 656 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL E 662 " --> pdb=" O ILE E 658 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN E 672 " --> pdb=" O GLU E 668 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLN E 675 " --> pdb=" O VAL E 671 " (cutoff:3.500A) Processing helix chain 'E' and resid 684 through 694 Processing helix chain 'E' and resid 702 through 721 removed outlier: 4.188A pdb=" N ARG E 706 " --> pdb=" O ARG E 702 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLN E 709 " --> pdb=" O ALA E 705 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LYS E 714 " --> pdb=" O ASP E 710 " (cutoff:3.500A) Proline residue: E 715 - end of helix removed outlier: 4.009A pdb=" N ASN E 718 " --> pdb=" O LYS E 714 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLU E 719 " --> pdb=" O PRO E 715 " (cutoff:3.500A) Processing helix chain 'E' and resid 724 through 726 No H-bonds generated for 'chain 'E' and resid 724 through 726' Processing helix chain 'F' and resid 176 through 182 removed outlier: 3.744A pdb=" N ARG F 181 " --> pdb=" O ASN F 177 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL F 182 " --> pdb=" O GLN F 178 " (cutoff:3.500A) Processing helix chain 'F' and resid 192 through 202 Processing helix chain 'F' and resid 220 through 233 removed outlier: 3.758A pdb=" N ALA F 224 " --> pdb=" O LYS F 220 " (cutoff:3.500A) removed outlier: 3.529A 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 256 Processing helix chain 'F' and resid 262 through 276 Processing helix chain 'F' and resid 288 through 291 No H-bonds generated for 'chain 'F' and resid 288 through 291' Processing helix chain 'F' and resid 301 through 313 removed outlier: 3.916A pdb=" N LYS F 308 " --> pdb=" O ASN F 305 " (cutoff:3.500A) Proline residue: F 309 - end of helix removed outlier: 3.577A pdb=" N SER F 313 " --> pdb=" O LEU F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 324 through 330 Processing helix chain 'F' and resid 335 through 338 No H-bonds generated for 'chain 'F' and resid 335 through 338' Processing helix chain 'F' and resid 351 through 369 removed outlier: 3.618A pdb=" N GLN F 356 " --> pdb=" O GLU F 352 " (cutoff:3.500A) Proline residue: F 363 - end of helix removed outlier: 3.591A pdb=" N HIS F 369 " --> pdb=" O TYR F 365 " (cutoff:3.500A) Processing helix chain 'F' and resid 375 through 388 Processing helix chain 'F' and resid 394 through 412 removed outlier: 3.652A pdb=" N ILE F 399 " --> pdb=" O PRO F 395 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASP F 400 " --> pdb=" O ASP F 396 " (cutoff:3.500A) Processing helix chain 'F' and resid 423 through 434 removed outlier: 3.694A pdb=" N SER F 428 " --> pdb=" O ALA F 424 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL F 429 " --> pdb=" O ASP F 425 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG F 432 " --> pdb=" O SER F 428 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ILE F 433 " --> pdb=" O VAL F 429 " (cutoff:3.500A) Processing helix chain 'F' and resid 438 through 441 No H-bonds generated for 'chain 'F' and resid 438 through 441' Processing helix chain 'F' and resid 445 through 459 removed outlier: 4.104A pdb=" N GLY F 453 " --> pdb=" O LEU F 449 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ASP F 454 " --> pdb=" O LYS F 450 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS F 457 " --> pdb=" O GLY F 453 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N MET F 458 " --> pdb=" O ASP F 454 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU F 459 " --> pdb=" O ARG F 455 " (cutoff:3.500A) Processing helix chain 'F' and resid 464 through 478 removed outlier: 3.508A pdb=" N ALA F 477 " --> pdb=" O ALA F 473 " (cutoff:3.500A) Processing helix chain 'F' and resid 500 through 512 removed outlier: 3.591A pdb=" N THR F 505 " --> pdb=" O LYS F 501 " (cutoff:3.500A) Processing helix chain 'F' and resid 528 through 532 Processing helix chain 'F' and resid 548 through 555 Processing helix chain 'F' and resid 571 through 582 removed outlier: 3.545A pdb=" N GLN F 579 " --> pdb=" O ASN F 575 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL F 580 " --> pdb=" O ILE F 576 " (cutoff:3.500A) Processing helix chain 'F' and resid 607 through 613 removed outlier: 3.566A pdb=" N GLU F 613 " --> pdb=" O VAL F 609 " (cutoff:3.500A) Processing helix chain 'F' and resid 628 through 635 removed outlier: 3.963A pdb=" N ILE F 632 " --> pdb=" O ALA F 628 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LYS F 634 " --> pdb=" O GLU F 630 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 643 Processing helix chain 'F' and resid 655 through 676 Processing helix chain 'F' and resid 684 through 694 Processing helix chain 'F' and resid 704 through 720 removed outlier: 3.731A pdb=" N GLN F 709 " --> pdb=" O ALA F 705 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LEU F 712 " --> pdb=" O ILE F 708 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LYS F 714 " --> pdb=" O ASP F 710 " (cutoff:3.500A) Proline residue: F 715 - end of helix removed outlier: 3.974A pdb=" N ASN F 718 " --> pdb=" O LYS F 714 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLU F 719 " --> pdb=" O PRO F 715 " (cutoff:3.500A) Processing helix chain 'F' and resid 724 through 726 No H-bonds generated for 'chain 'F' and resid 724 through 726' Processing helix chain 'H' and resid 19 through 26 removed outlier: 3.875A pdb=" N GLU H 26 " --> pdb=" O ARG H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 53 removed outlier: 3.581A pdb=" N ALA H 52 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU H 53 " --> pdb=" O PHE H 49 " (cutoff:3.500A) Processing helix chain 'H' and resid 70 through 82 removed outlier: 3.714A pdb=" N SER H 75 " --> pdb=" O THR H 71 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE H 76 " --> pdb=" O ALA H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 104 Processing helix chain 'H' and resid 132 through 157 removed outlier: 3.610A pdb=" N ILE H 137 " --> pdb=" O THR H 133 " (cutoff:3.500A) Processing helix chain 'H' and resid 161 through 168 Processing helix chain 'H' and resid 176 through 182 removed outlier: 3.706A pdb=" N VAL H 180 " --> pdb=" O ALA H 176 " (cutoff:3.500A) Processing helix chain 'I' and resid 19 through 26 removed outlier: 3.568A pdb=" N GLU I 26 " --> pdb=" O ARG I 22 " (cutoff:3.500A) Processing helix chain 'I' and resid 37 through 53 Processing helix chain 'I' and resid 70 through 82 Processing helix chain 'I' and resid 97 through 104 Processing helix chain 'I' and resid 132 through 157 Processing helix chain 'I' and resid 161 through 169 Processing helix chain 'I' and resid 176 through 182 removed outlier: 3.555A pdb=" N VAL I 180 " --> pdb=" O ALA I 176 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU I 181 " --> pdb=" O PRO I 177 " (cutoff:3.500A) Processing helix chain 'J' and resid 19 through 26 removed outlier: 3.698A 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: 3.600A pdb=" N SER J 75 " --> pdb=" O THR J 71 " (cutoff:3.500A) removed outlier: 3.797A 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 Processing helix chain 'K' and resid 19 through 26 Processing helix chain 'K' and resid 37 through 53 Processing helix chain 'K' and resid 70 through 82 removed outlier: 3.626A pdb=" N SER K 75 " --> pdb=" O THR K 71 " (cutoff:3.500A) removed outlier: 3.740A 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: 3.610A pdb=" N VAL K 180 " --> pdb=" O ALA K 176 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU K 181 " --> pdb=" O PRO K 177 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 26 removed outlier: 3.691A 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: 3.798A pdb=" N SER L 75 " --> pdb=" O THR L 71 " (cutoff:3.500A) removed outlier: 3.758A 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 removed outlier: 3.510A pdb=" N VAL L 180 " --> pdb=" O ALA L 176 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU L 181 " --> pdb=" O PRO L 177 " (cutoff:3.500A) Processing helix chain 'M' and resid 19 through 25 Processing helix chain 'M' and resid 37 through 53 removed outlier: 3.748A pdb=" N ASN M 41 " --> pdb=" O ASP M 37 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU M 42 " --> pdb=" O HIS M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 70 through 81 removed outlier: 3.856A pdb=" N ILE M 76 " --> pdb=" O ALA M 72 " (cutoff:3.500A) Processing helix chain 'M' and resid 97 through 103 Processing helix chain 'M' and resid 132 through 157 Processing helix chain 'M' and resid 161 through 168 Processing helix chain 'M' and resid 176 through 182 Processing helix chain 'N' and resid 19 through 26 removed outlier: 3.668A 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: 3.699A pdb=" N SER N 75 " --> pdb=" O THR N 71 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE N 76 " --> pdb=" O ALA N 72 " (cutoff:3.500A) Processing helix chain 'N' and resid 97 through 105 removed outlier: 3.615A pdb=" N LEU N 103 " --> pdb=" O GLY N 99 " (cutoff:3.500A) Processing helix chain 'N' and resid 132 through 157 removed outlier: 3.517A pdb=" N ILE N 137 " --> pdb=" O THR N 133 " (cutoff:3.500A) Processing helix chain 'N' and resid 161 through 168 Processing helix chain 'N' and resid 176 through 182 removed outlier: 3.758A pdb=" N VAL N 180 " --> pdb=" O ALA N 176 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU N 181 " --> pdb=" O PRO N 177 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 341 through 345 removed outlier: 6.620A pdb=" N ASN A 209 " --> pdb=" O GLN A 342 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N ILE A 344 " --> pdb=" O ASN A 209 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N LEU A 211 " --> pdb=" O ILE A 344 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL A 318 " --> pdb=" O PRO A 210 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N LEU A 212 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N GLY A 320 " --> pdb=" O LEU A 212 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N LEU A 282 " --> pdb=" O ILE A 319 " (cutoff:3.500A) removed outlier: 8.882A pdb=" N SER A 321 " --> pdb=" O LEU A 282 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N ILE A 284 " --> pdb=" O SER A 321 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 648 through 650 removed outlier: 6.417A pdb=" N LEU A 601 " --> pdb=" O PHE A 491 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N PHE A 493 " --> pdb=" O LEU A 601 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N MET A 603 " --> pdb=" O PHE A 493 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N GLY A 495 " --> pdb=" O MET A 603 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N THR A 605 " --> pdb=" O GLY A 495 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASP A 564 " --> pdb=" O PHE A 519 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 679 through 681 removed outlier: 3.506A pdb=" N VAL A 733 " --> pdb=" O GLU A 681 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 173 through 175 removed outlier: 6.120A pdb=" N ILE B 281 " --> pdb=" O TYR B 246 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N LEU B 248 " --> pdb=" O ILE B 281 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N PHE B 283 " --> pdb=" O LEU B 248 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N ARG B 317 " --> pdb=" O LEU B 282 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N ILE B 284 " --> pdb=" O ARG B 317 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N ILE B 319 " --> pdb=" O ILE B 284 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR B 322 " --> pdb=" O LEU B 212 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N GLN B 342 " --> pdb=" O LEU B 211 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL B 213 " --> pdb=" O GLN B 342 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N ILE B 344 " --> pdb=" O VAL B 213 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 646 through 650 removed outlier: 6.776A pdb=" N LEU B 601 " --> pdb=" O PHE B 491 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N PHE B 493 " --> pdb=" O LEU B 601 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N MET B 603 " --> pdb=" O PHE B 493 " (cutoff:3.500A) removed outlier: 8.547A pdb=" N GLY B 495 " --> pdb=" O MET B 603 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 680 through 682 removed outlier: 6.431A pdb=" N VAL B 731 " --> pdb=" O GLU B 681 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 173 through 175 removed outlier: 5.086A pdb=" N ASP C 285 " --> pdb=" O LEU C 248 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ARG C 317 " --> pdb=" O LEU C 282 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N ILE C 284 " --> pdb=" O ARG C 317 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ILE C 319 " --> pdb=" O ILE C 284 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N GLN C 342 " --> pdb=" O LEU C 211 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL C 213 " --> pdb=" O GLN C 342 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N ILE C 344 " --> pdb=" O VAL C 213 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 490 through 494 removed outlier: 6.864A pdb=" N LEU C 601 " --> pdb=" O PHE C 491 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N PHE C 493 " --> pdb=" O LEU C 601 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N MET C 603 " --> pdb=" O PHE C 493 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 680 through 682 removed outlier: 6.175A pdb=" N VAL C 731 " --> pdb=" O GLU C 681 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASP C 736 " --> pdb=" O GLU C 741 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLU C 741 " --> pdb=" O ASP C 736 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 173 through 175 removed outlier: 6.559A pdb=" N ILE D 281 " --> pdb=" O TYR D 246 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N LEU D 248 " --> pdb=" O ILE D 281 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N PHE D 283 " --> pdb=" O LEU D 248 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ARG D 317 " --> pdb=" O LEU D 282 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N ILE D 284 " --> pdb=" O ARG D 317 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE D 319 " --> pdb=" O ILE D 284 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N GLN D 342 " --> pdb=" O LEU D 211 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL D 213 " --> pdb=" O GLN D 342 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N ILE D 344 " --> pdb=" O VAL D 213 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 489 through 494 removed outlier: 4.129A pdb=" N GLY D 489 " --> pdb=" O VAL D 599 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N ALA D 559 " --> pdb=" O VAL D 600 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N VAL D 602 " --> pdb=" O ALA D 559 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LEU D 561 " --> pdb=" O VAL D 602 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N THR D 604 " --> pdb=" O LEU D 561 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N LEU D 563 " --> pdb=" O THR D 604 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 585 through 587 Processing sheet with id= M, first strand: chain 'D' and resid 732 through 736 removed outlier: 3.561A pdb=" N GLU D 741 " --> pdb=" O ASP D 736 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 211 through 214 removed outlier: 7.257A pdb=" N GLY E 320 " --> pdb=" O LEU E 212 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N GLY E 214 " --> pdb=" O GLY E 320 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N THR E 322 " --> pdb=" O GLY E 214 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'E' and resid 245 through 247 removed outlier: 6.494A pdb=" N ILE E 281 " --> pdb=" O TYR E 246 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'E' and resid 646 through 650 removed outlier: 6.090A pdb=" N LEU E 601 " --> pdb=" O PHE E 491 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N PHE E 493 " --> pdb=" O LEU E 601 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N MET E 603 " --> pdb=" O PHE E 493 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N GLY E 495 " --> pdb=" O MET E 603 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N THR E 605 " --> pdb=" O GLY E 495 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N VAL E 602 " --> pdb=" O ALA E 559 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N LEU E 561 " --> pdb=" O VAL E 602 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N THR E 604 " --> pdb=" O LEU E 561 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N LEU E 563 " --> pdb=" O THR E 604 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N GLU E 515 " --> pdb=" O VAL E 560 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N LEU E 562 " --> pdb=" O GLU E 515 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LEU E 517 " --> pdb=" O LEU E 562 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N ASP E 564 " --> pdb=" O LEU E 517 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N PHE E 519 " --> pdb=" O ASP E 564 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 585 through 587 Processing sheet with id= R, first strand: chain 'E' and resid 733 through 735 Processing sheet with id= S, first strand: chain 'F' and resid 211 through 213 removed outlier: 7.979A pdb=" N LEU F 212 " --> pdb=" O VAL F 318 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N GLY F 320 " --> pdb=" O LEU F 212 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ARG F 317 " --> pdb=" O SER F 280 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER F 321 " --> pdb=" O ILE F 284 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N THR F 244 " --> pdb=" O ILE F 281 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N PHE F 283 " --> pdb=" O THR F 244 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N TYR F 246 " --> pdb=" O PHE F 283 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'F' and resid 490 through 492 removed outlier: 6.663A pdb=" N LEU F 601 " --> pdb=" O PHE F 491 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'F' and resid 517 through 520 Processing sheet with id= V, first strand: chain 'F' and resid 680 through 682 removed outlier: 6.869A pdb=" N VAL F 731 " --> pdb=" O GLU F 681 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA F 734 " --> pdb=" O THR F 743 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'H' and resid 5 through 8 Processing sheet with id= X, first strand: chain 'H' and resid 28 through 32 removed outlier: 6.384A pdb=" N TYR H 60 " --> pdb=" O ILE H 29 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N LEU H 31 " --> pdb=" O TYR H 60 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N TYR H 62 " --> pdb=" O LEU H 31 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'H' and resid 118 through 121 Processing sheet with id= Z, first strand: chain 'I' and resid 5 through 7 Processing sheet with id= AA, first strand: chain 'I' and resid 28 through 32 removed outlier: 6.534A pdb=" N TYR I 60 " --> pdb=" O ILE I 29 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N LEU I 31 " --> pdb=" O TYR I 60 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N TYR I 62 " --> pdb=" O LEU I 31 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'I' and resid 118 through 121 Processing sheet with id= AC, first strand: chain 'J' and resid 5 through 9 Processing sheet with id= AD, first strand: chain 'J' and resid 28 through 32 removed outlier: 6.566A pdb=" N TYR J 60 " --> pdb=" O ILE J 29 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N LEU J 31 " --> pdb=" O TYR J 60 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N TYR J 62 " --> pdb=" O LEU J 31 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'J' and resid 119 through 121 Processing sheet with id= AF, first strand: chain 'K' and resid 5 through 9 Processing sheet with id= AG, first strand: chain 'K' and resid 28 through 32 removed outlier: 6.613A pdb=" N TYR K 60 " --> pdb=" O ILE K 29 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N LEU K 31 " --> pdb=" O TYR K 60 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N TYR K 62 " --> pdb=" O LEU K 31 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'K' and resid 118 through 121 Processing sheet with id= AI, first strand: chain 'L' and resid 5 through 9 removed outlier: 3.570A pdb=" N ARG L 15 " --> pdb=" O GLU L 8 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'L' and resid 28 through 32 removed outlier: 6.691A pdb=" N TYR L 60 " --> pdb=" O ILE L 29 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N LEU L 31 " --> pdb=" O TYR L 60 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N TYR L 62 " --> pdb=" O LEU L 31 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'L' and resid 118 through 121 Processing sheet with id= AL, first strand: chain 'M' and resid 5 through 9 Processing sheet with id= AM, first strand: chain 'M' and resid 28 through 32 removed outlier: 6.464A pdb=" N TYR M 60 " --> pdb=" O ILE M 29 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N LEU M 31 " --> pdb=" O TYR M 60 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N TYR M 62 " --> pdb=" O LEU M 31 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'M' and resid 119 through 121 Processing sheet with id= AO, first strand: chain 'N' and resid 5 through 8 Processing sheet with id= AP, first strand: chain 'N' and resid 59 through 63 Processing sheet with id= AQ, first strand: chain 'N' and resid 119 through 121 1443 hydrogen bonds defined for protein. 4188 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 26.07 Time building geometry restraints manager: 50.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.06: 38282 1.06 - 1.28: 6539 1.28 - 1.50: 15836 1.50 - 1.73: 15932 1.73 - 1.95: 305 Bond restraints: 76894 Sorted by residual: bond pdb=" C4 ADP E 801 " pdb=" C5 ADP E 801 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.99e+01 bond pdb=" C4 ADP E 802 " pdb=" C5 ADP E 802 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.97e+01 bond pdb=" C4 ADP A 802 " pdb=" C5 ADP A 802 " ideal model delta sigma weight residual 1.490 1.382 0.108 2.00e-02 2.50e+03 2.94e+01 bond pdb=" C4 ADP F 801 " pdb=" C5 ADP F 801 " ideal model delta sigma weight residual 1.490 1.382 0.108 2.00e-02 2.50e+03 2.92e+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 2.92e+01 ... (remaining 76889 not shown) Histogram of bond angle deviations from ideal: 98.31 - 105.44: 756 105.44 - 112.57: 90917 112.57 - 119.70: 19981 119.70 - 126.84: 27305 126.84 - 133.97: 411 Bond angle restraints: 139370 Sorted by residual: angle pdb=" PA ADP E 801 " pdb=" O3A ADP E 801 " pdb=" PB ADP E 801 " ideal model delta sigma weight residual 120.50 132.89 -12.39 3.00e+00 1.11e-01 1.71e+01 angle pdb=" PA ADP A 802 " pdb=" O3A ADP A 802 " pdb=" PB ADP A 802 " ideal model delta sigma weight residual 120.50 132.72 -12.22 3.00e+00 1.11e-01 1.66e+01 angle pdb=" PA ADP F 802 " pdb=" O3A ADP F 802 " pdb=" PB ADP F 802 " ideal model delta sigma weight residual 120.50 132.44 -11.94 3.00e+00 1.11e-01 1.58e+01 angle pdb=" PB AGS A 801 " pdb=" O3B AGS A 801 " pdb=" PG AGS A 801 " ideal model delta sigma weight residual 120.12 132.02 -11.90 3.00e+00 1.11e-01 1.57e+01 angle pdb=" PB AGS C 802 " pdb=" O3B AGS C 802 " pdb=" PG AGS C 802 " ideal model delta sigma weight residual 120.12 132.00 -11.88 3.00e+00 1.11e-01 1.57e+01 ... (remaining 139365 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.42: 34113 28.42 - 56.85: 1342 56.85 - 85.27: 132 85.27 - 113.69: 12 113.69 - 142.12: 14 Dihedral angle restraints: 35613 sinusoidal: 20094 harmonic: 15519 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 74.16 -134.15 1 2.00e+01 2.50e-03 4.07e+01 dihedral pdb=" C5' ADP A 802 " pdb=" O5' ADP A 802 " pdb=" PA ADP A 802 " pdb=" O2A ADP A 802 " ideal model delta sinusoidal sigma weight residual 300.00 166.98 133.02 1 2.00e+01 2.50e-03 4.04e+01 dihedral pdb=" O1B ADP F 801 " pdb=" O3A ADP F 801 " pdb=" PB ADP F 801 " pdb=" PA ADP F 801 " ideal model delta sinusoidal sigma weight residual -60.00 62.98 -122.98 1 2.00e+01 2.50e-03 3.71e+01 ... (remaining 35610 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 4451 0.045 - 0.091: 1210 0.091 - 0.136: 288 0.136 - 0.182: 27 0.182 - 0.227: 5 Chirality restraints: 5981 Sorted by residual: 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 -2.74 0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" C3' ADP F 802 " pdb=" C2' ADP F 802 " pdb=" C4' ADP F 802 " pdb=" O3' ADP F 802 " 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=" C3' ADP A 802 " pdb=" C2' ADP A 802 " pdb=" C4' ADP A 802 " pdb=" O3' ADP A 802 " both_signs ideal model delta sigma weight residual False -2.51 -2.72 0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 5978 not shown) Planarity restraints: 11378 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE F 436 " -0.048 5.00e-02 4.00e+02 7.32e-02 8.56e+00 pdb=" N PRO F 437 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO F 437 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO F 437 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS E 465 " 0.012 2.00e-02 2.50e+03 2.42e-02 5.83e+00 pdb=" C LYS E 465 " -0.042 2.00e-02 2.50e+03 pdb=" O LYS E 465 " 0.016 2.00e-02 2.50e+03 pdb=" N ALA E 466 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS A 570 " -0.039 5.00e-02 4.00e+02 5.85e-02 5.48e+00 pdb=" N PRO A 571 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 571 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 571 " -0.033 5.00e-02 4.00e+02 ... (remaining 11375 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.22: 6288 2.22 - 2.82: 171600 2.82 - 3.41: 203067 3.41 - 4.01: 277133 4.01 - 4.60: 431040 Nonbonded interactions: 1089128 Sorted by model distance: nonbonded pdb=" O ALA L 96 " pdb=" H ALA L 100 " model vdw 1.630 1.850 nonbonded pdb=" HG1 THR B 221 " pdb="MG MG B 803 " model vdw 1.659 1.700 nonbonded pdb=" O ALA I 96 " pdb=" H ALA I 100 " model vdw 1.661 1.850 nonbonded pdb=" H PHE E 493 " pdb=" O MET E 603 " model vdw 1.674 1.850 nonbonded pdb=" O VAL A 580 " pdb=" H GLY A 584 " model vdw 1.676 1.850 ... (remaining 1089123 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 501 or (resid 50 \ 2 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 resi \ d 503 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 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 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 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 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 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 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 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: 0.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.830 Extract box with map and model: 4.640 Check model and map are aligned: 0.820 Set scattering table: 0.520 Process input model: 186.920 Find NCS groups from input model: 3.330 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:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 200.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 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 : 0.005 0.109 38586 Z= 0.366 Angle : 0.830 12.394 52137 Z= 0.423 Chirality : 0.044 0.227 5981 Planarity : 0.004 0.073 6728 Dihedral : 14.411 142.116 14702 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Rotamer: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % 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: -1.04 (0.11), residues: 4795 helix: -0.13 (0.09), residues: 2317 sheet: -1.25 (0.19), residues: 638 loop : -1.02 (0.13), residues: 1840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 649 HIS 0.017 0.001 HIS D 528 PHE 0.021 0.002 PHE E 331 TYR 0.013 0.001 TYR F 540 ARG 0.010 0.001 ARG E 340 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Evaluate side-chains 1515 residues out of total 4059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1515 time to evaluate : 4.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 MET cc_start: 0.8139 (mmp) cc_final: 0.7926 (mmp) REVERT: A 284 ILE cc_start: 0.7686 (mp) cc_final: 0.7142 (mt) REVERT: A 327 PHE cc_start: 0.7796 (t80) cc_final: 0.7526 (t80) REVERT: A 335 ARG cc_start: 0.6071 (ttt-90) cc_final: 0.5581 (ttt-90) REVERT: A 348 GLU cc_start: 0.8631 (pt0) cc_final: 0.8317 (tt0) REVERT: A 352 GLU cc_start: 0.8374 (tp30) cc_final: 0.8172 (tp30) REVERT: A 379 ARG cc_start: 0.8609 (ptm160) cc_final: 0.7925 (ptm-80) REVERT: A 404 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7514 (mm-30) REVERT: A 501 LYS cc_start: 0.8011 (mtmt) cc_final: 0.7808 (mtmt) REVERT: A 503 GLU cc_start: 0.8366 (mp0) cc_final: 0.7835 (tt0) REVERT: A 520 ASP cc_start: 0.7588 (t0) cc_final: 0.7256 (t70) REVERT: A 525 MET cc_start: 0.8427 (tmm) cc_final: 0.8000 (tmm) REVERT: A 744 TYR cc_start: 0.8627 (m-80) cc_final: 0.8345 (m-80) REVERT: B 286 GLU cc_start: 0.7797 (mt-10) cc_final: 0.7585 (mt-10) REVERT: C 196 GLU cc_start: 0.7572 (tt0) cc_final: 0.7236 (tt0) REVERT: C 697 ARG cc_start: 0.8037 (mtp180) cc_final: 0.7788 (mtm180) REVERT: C 699 MET cc_start: 0.7276 (mmm) cc_final: 0.6980 (mmp) REVERT: D 265 LYS cc_start: 0.8620 (tttm) cc_final: 0.8407 (ttpp) REVERT: D 332 GLU cc_start: 0.8203 (tt0) cc_final: 0.7951 (tt0) REVERT: D 503 GLU cc_start: 0.7158 (tp30) cc_final: 0.6764 (tp30) REVERT: E 194 GLU cc_start: 0.8638 (mp0) cc_final: 0.8237 (mp0) REVERT: E 258 LYS cc_start: 0.8762 (tmtt) cc_final: 0.8373 (tptt) REVERT: E 432 ARG cc_start: 0.7969 (ptm-80) cc_final: 0.7754 (ptm-80) REVERT: E 527 ARG cc_start: 0.7712 (mtp-110) cc_final: 0.7408 (ttm-80) REVERT: E 551 ASP cc_start: 0.6186 (m-30) cc_final: 0.5955 (m-30) REVERT: F 233 GLN cc_start: 0.7351 (mm110) cc_final: 0.6821 (tp40) REVERT: F 271 LEU cc_start: 0.8779 (mt) cc_final: 0.8578 (mt) REVERT: F 343 LYS cc_start: 0.7943 (tttt) cc_final: 0.7644 (ttmm) REVERT: F 390 ASN cc_start: 0.7225 (p0) cc_final: 0.6700 (t0) REVERT: F 503 GLU cc_start: 0.8910 (tp30) cc_final: 0.8523 (tp30) REVERT: F 564 ASP cc_start: 0.8532 (t0) cc_final: 0.8124 (t0) REVERT: F 668 GLU cc_start: 0.8610 (mp0) cc_final: 0.8240 (mp0) REVERT: F 706 ARG cc_start: 0.9047 (ttp80) cc_final: 0.8842 (ttp80) REVERT: H 9 GLN cc_start: 0.8592 (mm110) cc_final: 0.8351 (mm110) REVERT: H 110 LYS cc_start: 0.8634 (mmmt) cc_final: 0.8413 (mmmm) REVERT: H 140 ARG cc_start: 0.8005 (mtp85) cc_final: 0.7785 (mtp85) REVERT: H 149 MET cc_start: 0.8385 (mmp) cc_final: 0.8013 (mmp) REVERT: I 108 LYS cc_start: 0.7593 (ptmm) cc_final: 0.7390 (ptmm) REVERT: I 144 LYS cc_start: 0.8493 (mttp) cc_final: 0.8243 (mttp) REVERT: I 167 ASP cc_start: 0.8037 (m-30) cc_final: 0.7799 (m-30) REVERT: J 15 ARG cc_start: 0.7136 (mmm160) cc_final: 0.6810 (mmm160) REVERT: J 150 ASN cc_start: 0.9041 (m110) cc_final: 0.8654 (m-40) REVERT: K 26 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7769 (mm-30) REVERT: K 169 GLU cc_start: 0.7893 (tp30) cc_final: 0.7579 (tp30) REVERT: L 77 TYR cc_start: 0.8529 (t80) cc_final: 0.8217 (t80) REVERT: L 117 SER cc_start: 0.9177 (m) cc_final: 0.8920 (m) REVERT: L 166 ARG cc_start: 0.7689 (ptt-90) cc_final: 0.7103 (ptt-90) REVERT: L 169 GLU cc_start: 0.7681 (pt0) cc_final: 0.7309 (pt0) REVERT: M 123 GLN cc_start: 0.8397 (pt0) cc_final: 0.8065 (pt0) REVERT: M 138 HIS cc_start: 0.8423 (m90) cc_final: 0.8042 (m-70) REVERT: M 151 GLU cc_start: 0.7864 (tt0) cc_final: 0.7542 (tt0) REVERT: N 58 ASP cc_start: 0.7844 (p0) cc_final: 0.7421 (p0) REVERT: N 136 GLU cc_start: 0.8431 (tm-30) cc_final: 0.7796 (tm-30) outliers start: 0 outliers final: 0 residues processed: 1515 average time/residue: 1.1187 time to fit residues: 2649.3868 Evaluate side-chains 1288 residues out of total 4059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1288 time to evaluate : 4.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 405 optimal weight: 7.9990 chunk 363 optimal weight: 10.0000 chunk 201 optimal weight: 7.9990 chunk 124 optimal weight: 9.9990 chunk 245 optimal weight: 5.9990 chunk 194 optimal weight: 4.9990 chunk 376 optimal weight: 9.9990 chunk 145 optimal weight: 5.9990 chunk 228 optimal weight: 9.9990 chunk 280 optimal weight: 4.9990 chunk 435 optimal weight: 7.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 ASN A 606 ASN A 660 GLN A 711 ASN B 325 GLN B 642 ASN C 233 GLN C 356 GLN ** C 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 730 GLN ** E 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 684 GLN E 711 ASN E 740 ASN F 305 ASN ** F 659 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 672 GLN ** F 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 711 ASN H 41 ASN I 41 ASN I 116 ASN I 131 GLN K 122 HIS L 41 ASN ** N 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 38586 Z= 0.334 Angle : 0.611 8.129 52137 Z= 0.324 Chirality : 0.041 0.171 5981 Planarity : 0.004 0.053 6728 Dihedral : 9.237 158.525 5411 Min Nonbonded Distance : 1.704 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.50 % Allowed : 9.88 % Favored : 88.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.11), residues: 4795 helix: 0.63 (0.10), residues: 2413 sheet: -1.02 (0.20), residues: 589 loop : -0.80 (0.13), residues: 1793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 229 HIS 0.010 0.001 HIS A 556 PHE 0.029 0.001 PHE C 746 TYR 0.016 0.001 TYR C 259 ARG 0.007 0.001 ARG E 592 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Evaluate side-chains 1437 residues out of total 4059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 1376 time to evaluate : 4.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 ARG cc_start: 0.8373 (ttt90) cc_final: 0.8063 (ptm160) REVERT: A 240 MET cc_start: 0.8200 (mmp) cc_final: 0.7868 (mmp) REVERT: A 284 ILE cc_start: 0.7805 (mp) cc_final: 0.7185 (mt) REVERT: A 327 PHE cc_start: 0.7856 (t80) cc_final: 0.7541 (t80) REVERT: A 334 ASP cc_start: 0.7297 (t0) cc_final: 0.7083 (t0) REVERT: A 335 ARG cc_start: 0.6156 (ttt-90) cc_final: 0.5694 (ttt-90) REVERT: A 343 LYS cc_start: 0.8754 (tmmt) cc_final: 0.7998 (tmmt) REVERT: A 379 ARG cc_start: 0.8663 (ptm160) cc_final: 0.7909 (tpt90) REVERT: A 404 GLU cc_start: 0.7933 (mm-30) cc_final: 0.7502 (mm-30) REVERT: A 503 GLU cc_start: 0.8607 (mp0) cc_final: 0.7893 (tt0) REVERT: A 520 ASP cc_start: 0.7363 (t0) cc_final: 0.7150 (t70) REVERT: A 525 MET cc_start: 0.8466 (tmm) cc_final: 0.8072 (tmm) REVERT: A 744 TYR cc_start: 0.8709 (m-80) cc_final: 0.8134 (m-80) REVERT: B 370 ASP cc_start: 0.7934 (t0) cc_final: 0.7608 (t0) REVERT: B 593 LYS cc_start: 0.8690 (tppp) cc_final: 0.8353 (tptp) REVERT: B 727 ASP cc_start: 0.7069 (OUTLIER) cc_final: 0.6520 (m-30) REVERT: C 196 GLU cc_start: 0.7824 (tt0) cc_final: 0.7421 (tt0) REVERT: C 275 GLU cc_start: 0.7553 (tm-30) cc_final: 0.7353 (tm-30) REVERT: C 332 GLU cc_start: 0.7962 (tp30) cc_final: 0.7706 (tp30) REVERT: C 697 ARG cc_start: 0.8274 (mtp180) cc_final: 0.8048 (mtm180) REVERT: C 699 MET cc_start: 0.7603 (mmm) cc_final: 0.7402 (mmm) REVERT: C 704 MET cc_start: 0.8067 (tpp) cc_final: 0.7833 (mmm) REVERT: D 503 GLU cc_start: 0.7373 (tp30) cc_final: 0.6921 (tp30) REVERT: D 675 GLN cc_start: 0.8183 (mm-40) cc_final: 0.7947 (tp40) REVERT: D 727 ASP cc_start: 0.6742 (OUTLIER) cc_final: 0.6509 (m-30) REVERT: E 258 LYS cc_start: 0.8799 (tmtt) cc_final: 0.8442 (tptt) REVERT: E 432 ARG cc_start: 0.8372 (ptm-80) cc_final: 0.7856 (tmm160) REVERT: E 527 ARG cc_start: 0.7743 (mtp-110) cc_final: 0.7477 (ttm-80) REVERT: E 551 ASP cc_start: 0.6520 (m-30) cc_final: 0.6287 (m-30) REVERT: E 699 MET cc_start: 0.7976 (mmp) cc_final: 0.7756 (mmp) REVERT: F 195 LEU cc_start: 0.9015 (tp) cc_final: 0.8782 (mp) REVERT: F 215 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7457 (mm-30) REVERT: F 352 GLU cc_start: 0.7637 (mp0) cc_final: 0.7323 (mp0) REVERT: F 390 ASN cc_start: 0.7157 (p0) cc_final: 0.6607 (t0) REVERT: F 503 GLU cc_start: 0.8861 (tp30) cc_final: 0.8545 (tp30) REVERT: F 631 GLU cc_start: 0.8486 (mp0) cc_final: 0.8230 (mp0) REVERT: F 706 ARG cc_start: 0.9089 (ttp80) cc_final: 0.8799 (tpt-90) REVERT: H 101 PHE cc_start: 0.8714 (t80) cc_final: 0.8264 (t80) REVERT: H 140 ARG cc_start: 0.8136 (mtp85) cc_final: 0.7897 (mmm-85) REVERT: H 149 MET cc_start: 0.8582 (mmp) cc_final: 0.8106 (mmp) REVERT: I 136 GLU cc_start: 0.8419 (tm-30) cc_final: 0.7986 (tm-30) REVERT: J 60 TYR cc_start: 0.8584 (m-80) cc_final: 0.8350 (m-10) REVERT: J 74 MET cc_start: 0.8372 (mmm) cc_final: 0.8056 (mmt) REVERT: J 123 GLN cc_start: 0.8409 (pt0) cc_final: 0.7945 (pt0) REVERT: J 172 ARG cc_start: 0.8122 (tpp80) cc_final: 0.7910 (tpt90) REVERT: K 144 LYS cc_start: 0.8623 (mmmt) cc_final: 0.8336 (mttp) REVERT: K 151 GLU cc_start: 0.7437 (mt-10) cc_final: 0.7196 (mt-10) REVERT: K 169 GLU cc_start: 0.8106 (tp30) cc_final: 0.7757 (tp30) REVERT: L 17 PHE cc_start: 0.8127 (m-80) cc_final: 0.7763 (m-80) REVERT: L 34 GLN cc_start: 0.8491 (tp40) cc_final: 0.8252 (tp40) REVERT: L 117 SER cc_start: 0.9053 (m) cc_final: 0.8835 (m) REVERT: L 141 GLU cc_start: 0.7591 (tm-30) cc_final: 0.7233 (tm-30) REVERT: M 8 GLU cc_start: 0.7317 (tt0) cc_final: 0.7091 (tt0) REVERT: M 87 VAL cc_start: 0.9338 (t) cc_final: 0.9085 (p) REVERT: M 151 GLU cc_start: 0.7958 (tt0) cc_final: 0.7610 (tt0) REVERT: N 58 ASP cc_start: 0.7944 (p0) cc_final: 0.7554 (p0) REVERT: N 136 GLU cc_start: 0.8606 (tm-30) cc_final: 0.8351 (tm-30) outliers start: 61 outliers final: 44 residues processed: 1391 average time/residue: 1.1650 time to fit residues: 2534.8791 Evaluate side-chains 1350 residues out of total 4059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 1304 time to evaluate : 4.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 ASN Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain B residue 523 GLU Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 727 ASP Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 383 GLU Chi-restraints excluded: chain C residue 391 ASP Chi-restraints excluded: chain C residue 585 THR Chi-restraints excluded: chain C residue 637 THR Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain D residue 720 LEU Chi-restraints excluded: chain D residue 722 PHE Chi-restraints excluded: chain D residue 727 ASP Chi-restraints excluded: chain D residue 735 LEU Chi-restraints excluded: chain E residue 215 GLU Chi-restraints excluded: chain E residue 459 LEU Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain E residue 606 ASN Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 280 SER Chi-restraints excluded: chain F residue 310 LEU Chi-restraints excluded: chain F residue 598 ASN Chi-restraints excluded: chain F residue 676 LYS Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain I residue 116 ASN Chi-restraints excluded: chain I residue 171 ASP Chi-restraints excluded: chain J residue 160 SER Chi-restraints excluded: chain J residue 191 HIS Chi-restraints excluded: chain K residue 16 SER Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain L residue 137 ILE Chi-restraints excluded: chain L residue 155 LEU Chi-restraints excluded: chain L residue 160 SER Chi-restraints excluded: chain L residue 184 LEU Chi-restraints excluded: chain N residue 120 MET Chi-restraints excluded: chain N residue 160 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: 9.9990 chunk 120 optimal weight: 6.9990 chunk 436 optimal weight: 0.9990 chunk 471 optimal weight: 10.0000 chunk 388 optimal weight: 0.8980 chunk 433 optimal weight: 9.9990 chunk 148 optimal weight: 4.9990 chunk 350 optimal weight: 10.0000 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 652 HIS B 200 GLN C 177 ASN ** C 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 325 GLN E 288 HIS ** E 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 747 GLN F 178 GLN F 606 ASN ** F 659 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 747 GLN H 41 ASN H 150 ASN I 159 GLN I 163 GLN K 122 HIS L 41 ASN ** N 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 38586 Z= 0.225 Angle : 0.526 7.062 52137 Z= 0.271 Chirality : 0.039 0.145 5981 Planarity : 0.004 0.050 6728 Dihedral : 8.948 155.290 5411 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.50 % Allowed : 12.64 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.12), residues: 4795 helix: 0.84 (0.10), residues: 2438 sheet: -0.94 (0.20), residues: 588 loop : -0.61 (0.14), residues: 1769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 229 HIS 0.007 0.001 HIS F 652 PHE 0.015 0.001 PHE A 596 TYR 0.012 0.001 TYR C 259 ARG 0.006 0.000 ARG E 592 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Evaluate side-chains 1394 residues out of total 4059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 1333 time to evaluate : 4.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 MET cc_start: 0.8159 (mmp) cc_final: 0.7815 (mmp) REVERT: A 284 ILE cc_start: 0.7815 (mp) cc_final: 0.7192 (mt) REVERT: A 334 ASP cc_start: 0.7305 (t0) cc_final: 0.7102 (t0) REVERT: A 335 ARG cc_start: 0.6241 (ttt-90) cc_final: 0.5798 (ttt-90) REVERT: A 343 LYS cc_start: 0.8781 (tmmt) cc_final: 0.8077 (tmmt) REVERT: A 348 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8320 (tt0) REVERT: A 379 ARG cc_start: 0.8679 (ptm160) cc_final: 0.7873 (tpt90) REVERT: A 404 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7421 (mm-30) REVERT: A 410 ARG cc_start: 0.7373 (ptm160) cc_final: 0.7063 (ptm-80) REVERT: A 503 GLU cc_start: 0.8534 (mp0) cc_final: 0.7891 (tt0) REVERT: B 279 ASN cc_start: 0.7530 (t0) cc_final: 0.7015 (t0) REVERT: B 370 ASP cc_start: 0.7925 (t0) cc_final: 0.7599 (t0) REVERT: B 727 ASP cc_start: 0.7265 (m-30) cc_final: 0.6751 (m-30) REVERT: C 196 GLU cc_start: 0.7792 (tt0) cc_final: 0.7390 (tt0) REVERT: D 213 VAL cc_start: 0.9256 (t) cc_final: 0.9053 (p) REVERT: D 325 GLN cc_start: 0.7395 (OUTLIER) cc_final: 0.7051 (tp-100) REVERT: D 332 GLU cc_start: 0.8258 (tt0) cc_final: 0.8003 (tt0) REVERT: D 476 MET cc_start: 0.8643 (mtt) cc_final: 0.8434 (mtt) REVERT: D 727 ASP cc_start: 0.6784 (OUTLIER) cc_final: 0.6554 (m-30) REVERT: E 225 GLU cc_start: 0.8419 (mt-10) cc_final: 0.8041 (mt-10) REVERT: E 258 LYS cc_start: 0.8813 (tmtt) cc_final: 0.8434 (tptt) REVERT: E 352 GLU cc_start: 0.7438 (mm-30) cc_final: 0.7106 (mm-30) REVERT: E 366 GLU cc_start: 0.7419 (mt-10) cc_final: 0.6985 (mt-10) REVERT: E 432 ARG cc_start: 0.8378 (ptm-80) cc_final: 0.7886 (tmm160) REVERT: E 527 ARG cc_start: 0.7756 (mtp-110) cc_final: 0.7509 (ttm-80) REVERT: E 551 ASP cc_start: 0.6518 (m-30) cc_final: 0.6199 (m-30) REVERT: F 178 GLN cc_start: 0.8366 (OUTLIER) cc_final: 0.8094 (tm130) REVERT: F 215 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7422 (mm-30) REVERT: F 352 GLU cc_start: 0.7710 (mp0) cc_final: 0.7367 (mp0) REVERT: F 390 ASN cc_start: 0.7182 (p0) cc_final: 0.6612 (t0) REVERT: F 706 ARG cc_start: 0.9078 (ttp80) cc_final: 0.8785 (tpt-90) REVERT: H 78 ASP cc_start: 0.7844 (m-30) cc_final: 0.7500 (m-30) REVERT: H 86 ASP cc_start: 0.8203 (m-30) cc_final: 0.7914 (t0) REVERT: H 101 PHE cc_start: 0.8783 (t80) cc_final: 0.8246 (t80) REVERT: H 140 ARG cc_start: 0.8123 (mtp85) cc_final: 0.7837 (mtp85) REVERT: H 144 LYS cc_start: 0.8950 (OUTLIER) cc_final: 0.8715 (mtmm) REVERT: H 149 MET cc_start: 0.8618 (mmp) cc_final: 0.8097 (mmp) REVERT: I 136 GLU cc_start: 0.8331 (tm-30) cc_final: 0.7902 (tm-30) REVERT: I 144 LYS cc_start: 0.8602 (mttp) cc_final: 0.8304 (mttp) REVERT: I 165 GLU cc_start: 0.8224 (pt0) cc_final: 0.7728 (pm20) REVERT: I 169 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7686 (mm-30) REVERT: J 60 TYR cc_start: 0.8527 (m-80) cc_final: 0.8322 (m-10) REVERT: J 123 GLN cc_start: 0.8356 (pt0) cc_final: 0.7988 (pt0) REVERT: J 140 ARG cc_start: 0.8229 (ttm110) cc_final: 0.8002 (ttm-80) REVERT: J 162 GLU cc_start: 0.8144 (mp0) cc_final: 0.7897 (mp0) REVERT: J 172 ARG cc_start: 0.8104 (tpp80) cc_final: 0.7883 (tpt90) REVERT: K 144 LYS cc_start: 0.8643 (mmmt) cc_final: 0.8352 (mttp) REVERT: K 151 GLU cc_start: 0.7445 (mt-10) cc_final: 0.7141 (mt-10) REVERT: K 169 GLU cc_start: 0.8113 (tp30) cc_final: 0.7802 (tp30) REVERT: L 34 GLN cc_start: 0.8496 (tp40) cc_final: 0.8256 (tp40) REVERT: L 117 SER cc_start: 0.8988 (m) cc_final: 0.8784 (m) REVERT: L 141 GLU cc_start: 0.7481 (tm-30) cc_final: 0.7070 (tm-30) REVERT: M 151 GLU cc_start: 0.7990 (tt0) cc_final: 0.7606 (tt0) REVERT: N 34 GLN cc_start: 0.8060 (mm-40) cc_final: 0.7757 (mm-40) REVERT: N 58 ASP cc_start: 0.7951 (p0) cc_final: 0.7565 (p0) REVERT: N 136 GLU cc_start: 0.8567 (tm-30) cc_final: 0.8335 (tm-30) outliers start: 61 outliers final: 43 residues processed: 1350 average time/residue: 1.1749 time to fit residues: 2488.4019 Evaluate side-chains 1334 residues out of total 4059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 1286 time to evaluate : 4.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 362 LYS Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 710 ASP Chi-restraints excluded: chain B residue 564 ASP Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain C residue 233 GLN Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 637 THR Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 325 GLN Chi-restraints excluded: chain D residue 328 SER Chi-restraints excluded: chain D residue 722 PHE Chi-restraints excluded: chain D residue 727 ASP Chi-restraints excluded: chain D residue 735 LEU Chi-restraints excluded: chain D residue 742 LEU Chi-restraints excluded: chain E residue 209 ASN Chi-restraints excluded: chain E residue 459 LEU Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain F residue 178 GLN Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 280 SER Chi-restraints excluded: chain F residue 310 LEU Chi-restraints excluded: chain F residue 408 ARG Chi-restraints excluded: chain F residue 570 HIS Chi-restraints excluded: chain F residue 598 ASN Chi-restraints excluded: chain F residue 676 LYS Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 144 LYS Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 58 ASP Chi-restraints excluded: chain J residue 160 SER Chi-restraints excluded: chain J residue 191 HIS Chi-restraints excluded: chain K residue 16 SER Chi-restraints excluded: chain K residue 160 SER Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain L residue 184 LEU Chi-restraints excluded: chain N residue 63 ILE Chi-restraints excluded: chain N residue 117 SER Chi-restraints excluded: chain N residue 120 MET 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: 7.9990 chunk 226 optimal weight: 10.0000 chunk 48 optimal weight: 7.9990 chunk 208 optimal weight: 9.9990 chunk 293 optimal weight: 10.0000 chunk 438 optimal weight: 10.0000 chunk 463 optimal weight: 8.9990 chunk 228 optimal weight: 10.0000 chunk 415 optimal weight: 7.9990 chunk 125 optimal weight: 8.9990 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 606 ASN ** C 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 575 ASN D 325 GLN D 556 HIS ** E 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 747 GLN ** F 659 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 122 HIS M 41 ASN M 123 GLN ** N 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 81 GLN N 129 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 38586 Z= 0.416 Angle : 0.585 7.207 52137 Z= 0.307 Chirality : 0.042 0.158 5981 Planarity : 0.004 0.055 6728 Dihedral : 9.059 162.472 5411 Min Nonbonded Distance : 1.705 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.12 % Allowed : 13.70 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.12), residues: 4795 helix: 0.66 (0.10), residues: 2458 sheet: -0.83 (0.21), residues: 581 loop : -0.75 (0.14), residues: 1756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 229 HIS 0.007 0.001 HIS C 393 PHE 0.023 0.001 PHE M 17 TYR 0.017 0.001 TYR J 60 ARG 0.010 0.000 ARG B 643 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Evaluate side-chains 1409 residues out of total 4059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 1323 time to evaluate : 4.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 GLN cc_start: 0.8757 (mt0) cc_final: 0.8466 (tt0) REVERT: A 240 MET cc_start: 0.8263 (mmp) cc_final: 0.7929 (mmp) REVERT: A 335 ARG cc_start: 0.6472 (ttt-90) cc_final: 0.4777 (ttt90) REVERT: A 343 LYS cc_start: 0.8835 (tmmt) cc_final: 0.8254 (tmmt) REVERT: A 345 ASP cc_start: 0.7205 (p0) cc_final: 0.6970 (p0) REVERT: A 348 GLU cc_start: 0.8769 (pt0) cc_final: 0.8323 (tt0) REVERT: A 379 ARG cc_start: 0.8712 (ptm160) cc_final: 0.7900 (tpt90) REVERT: A 404 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7467 (mm-30) REVERT: A 410 ARG cc_start: 0.7421 (ptm160) cc_final: 0.7153 (ptm-80) REVERT: A 455 ARG cc_start: 0.8571 (tpp-160) cc_final: 0.8367 (tpp-160) REVERT: A 503 GLU cc_start: 0.8522 (mp0) cc_final: 0.7856 (tt0) REVERT: A 525 MET cc_start: 0.8541 (tmm) cc_final: 0.8082 (tmm) REVERT: B 247 SER cc_start: 0.8854 (t) cc_final: 0.8214 (p) REVERT: B 370 ASP cc_start: 0.8052 (t0) cc_final: 0.7732 (t0) REVERT: B 572 ASP cc_start: 0.8356 (m-30) cc_final: 0.8103 (m-30) REVERT: B 727 ASP cc_start: 0.7791 (OUTLIER) cc_final: 0.7289 (m-30) REVERT: C 410 ARG cc_start: 0.8626 (OUTLIER) cc_final: 0.8321 (ttm170) REVERT: D 476 MET cc_start: 0.8691 (mtt) cc_final: 0.8478 (mtt) REVERT: E 225 GLU cc_start: 0.8524 (mt-10) cc_final: 0.8200 (mt-10) REVERT: E 258 LYS cc_start: 0.8842 (tmtt) cc_final: 0.8403 (tptt) REVERT: E 352 GLU cc_start: 0.7592 (mm-30) cc_final: 0.7300 (mm-30) REVERT: E 366 GLU cc_start: 0.7509 (mt-10) cc_final: 0.7076 (mt-10) REVERT: E 633 LYS cc_start: 0.8638 (mttt) cc_final: 0.8221 (mttm) REVERT: F 215 GLU cc_start: 0.7912 (mm-30) cc_final: 0.7392 (mm-30) REVERT: F 220 LYS cc_start: 0.7981 (pttm) cc_final: 0.7757 (ptpp) REVERT: F 305 ASN cc_start: 0.7460 (m-40) cc_final: 0.7194 (m-40) REVERT: F 352 GLU cc_start: 0.7746 (mp0) cc_final: 0.7412 (mp0) REVERT: F 390 ASN cc_start: 0.7179 (p0) cc_final: 0.6546 (t0) REVERT: F 412 MET cc_start: 0.7013 (OUTLIER) cc_final: 0.6790 (ttp) REVERT: F 558 HIS cc_start: 0.6864 (OUTLIER) cc_final: 0.6459 (t-90) REVERT: F 706 ARG cc_start: 0.9085 (ttp80) cc_final: 0.8637 (tpt-90) REVERT: F 710 ASP cc_start: 0.8709 (t0) cc_final: 0.8250 (t0) REVERT: H 86 ASP cc_start: 0.8243 (m-30) cc_final: 0.7996 (t0) REVERT: H 149 MET cc_start: 0.8704 (mmp) cc_final: 0.8183 (mmp) REVERT: I 136 GLU cc_start: 0.8386 (tm-30) cc_final: 0.7974 (tm-30) REVERT: I 144 LYS cc_start: 0.8680 (mttp) cc_final: 0.8374 (mttp) REVERT: I 149 MET cc_start: 0.8526 (mmp) cc_final: 0.8153 (mmp) REVERT: I 169 GLU cc_start: 0.8016 (mm-30) cc_final: 0.7737 (mm-30) REVERT: J 123 GLN cc_start: 0.8444 (pt0) cc_final: 0.7944 (pt0) REVERT: J 150 ASN cc_start: 0.9093 (m110) cc_final: 0.8747 (m110) REVERT: J 172 ARG cc_start: 0.8129 (tpp80) cc_final: 0.7900 (tpt90) REVERT: K 140 ARG cc_start: 0.7832 (ttm-80) cc_final: 0.7478 (ttm-80) REVERT: K 144 LYS cc_start: 0.8675 (mmmt) cc_final: 0.8349 (mttp) REVERT: K 167 ASP cc_start: 0.7606 (m-30) cc_final: 0.7348 (m-30) REVERT: K 169 GLU cc_start: 0.8261 (tp30) cc_final: 0.7763 (tp30) REVERT: L 34 GLN cc_start: 0.8570 (tp40) cc_final: 0.8337 (tp40) REVERT: L 58 ASP cc_start: 0.7958 (p0) cc_final: 0.7643 (p0) REVERT: L 141 GLU cc_start: 0.7632 (tm-30) cc_final: 0.7265 (tm-30) REVERT: M 120 MET cc_start: 0.8465 (tmm) cc_final: 0.8161 (tmm) REVERT: M 146 LYS cc_start: 0.7287 (mttt) cc_final: 0.6899 (mttp) REVERT: M 151 GLU cc_start: 0.8039 (tt0) cc_final: 0.7642 (tt0) REVERT: M 171 ASP cc_start: 0.8646 (m-30) cc_final: 0.8416 (m-30) REVERT: N 58 ASP cc_start: 0.8157 (p0) cc_final: 0.7811 (p0) REVERT: N 136 GLU cc_start: 0.8585 (tm-30) cc_final: 0.8355 (tm-30) outliers start: 86 outliers final: 63 residues processed: 1359 average time/residue: 1.1242 time to fit residues: 2369.7579 Evaluate side-chains 1351 residues out of total 4059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 1284 time to evaluate : 4.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 491 PHE Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 710 ASP Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain B residue 523 GLU Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 642 ASN Chi-restraints excluded: chain B residue 727 ASP Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 391 ASP Chi-restraints excluded: chain C residue 410 ARG Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain C residue 585 THR Chi-restraints excluded: chain C residue 626 THR Chi-restraints excluded: chain C residue 637 THR Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain D residue 531 SER Chi-restraints excluded: chain D residue 727 ASP Chi-restraints excluded: chain D residue 742 LEU Chi-restraints excluded: chain D residue 746 PHE Chi-restraints excluded: chain E residue 209 ASN Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 345 ASP Chi-restraints excluded: chain E residue 459 LEU Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain E residue 606 ASN Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 243 CYS Chi-restraints excluded: chain F residue 280 SER Chi-restraints excluded: chain F residue 310 LEU Chi-restraints excluded: chain F residue 412 MET Chi-restraints excluded: chain F residue 558 HIS Chi-restraints excluded: chain F residue 570 HIS Chi-restraints excluded: chain F residue 623 ASP Chi-restraints excluded: chain F residue 676 LYS Chi-restraints excluded: chain F residue 696 ASP Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 58 ASP Chi-restraints excluded: chain I residue 116 ASN Chi-restraints excluded: chain I residue 117 SER Chi-restraints excluded: chain I residue 171 ASP Chi-restraints excluded: chain I residue 175 SER Chi-restraints excluded: chain J residue 81 GLN Chi-restraints excluded: chain J residue 160 SER Chi-restraints excluded: chain K residue 16 SER Chi-restraints excluded: chain K residue 160 SER Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain L residue 184 LEU Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain M residue 121 ILE Chi-restraints excluded: chain N residue 117 SER Chi-restraints excluded: chain N residue 120 MET Chi-restraints excluded: chain N residue 182 TYR 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: 0.9990 chunk 6 optimal weight: 6.9990 chunk 345 optimal weight: 9.9990 chunk 191 optimal weight: 5.9990 chunk 395 optimal weight: 8.9990 chunk 320 optimal weight: 50.0000 chunk 0 optimal weight: 40.0000 chunk 236 optimal weight: 7.9990 chunk 416 optimal weight: 9.9990 chunk 117 optimal weight: 4.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 575 ASN C 369 HIS ** C 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 558 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 747 GLN ** F 659 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 131 GLN I 159 GLN K 41 ASN K 122 HIS K 159 GLN M 123 GLN ** N 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.3397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 38586 Z= 0.277 Angle : 0.534 6.988 52137 Z= 0.276 Chirality : 0.040 0.147 5981 Planarity : 0.004 0.055 6728 Dihedral : 8.951 166.392 5411 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.02 % Allowed : 14.91 % Favored : 83.07 % 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: 0.02 (0.12), residues: 4795 helix: 0.79 (0.10), residues: 2452 sheet: -0.80 (0.21), residues: 578 loop : -0.67 (0.14), residues: 1765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 229 HIS 0.021 0.001 HIS E 558 PHE 0.028 0.001 PHE F 665 TYR 0.024 0.001 TYR C 259 ARG 0.007 0.000 ARG E 592 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Evaluate side-chains 1402 residues out of total 4059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 1320 time to evaluate : 4.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 MET cc_start: 0.8199 (mmp) cc_final: 0.7865 (mmp) REVERT: A 335 ARG cc_start: 0.6297 (ttt-90) cc_final: 0.4632 (ttt90) REVERT: A 343 LYS cc_start: 0.8851 (tmmt) cc_final: 0.8269 (tmmt) REVERT: A 345 ASP cc_start: 0.7218 (p0) cc_final: 0.6944 (p0) REVERT: A 348 GLU cc_start: 0.8811 (pt0) cc_final: 0.8219 (tt0) REVERT: A 379 ARG cc_start: 0.8761 (ptm160) cc_final: 0.7907 (tpt90) REVERT: A 404 GLU cc_start: 0.7915 (mm-30) cc_final: 0.7455 (mm-30) REVERT: A 503 GLU cc_start: 0.8580 (mp0) cc_final: 0.7903 (tt0) REVERT: B 247 SER cc_start: 0.8827 (t) cc_final: 0.8196 (p) REVERT: B 370 ASP cc_start: 0.8052 (t0) cc_final: 0.7743 (t0) REVERT: B 572 ASP cc_start: 0.8367 (m-30) cc_final: 0.8109 (m-30) REVERT: B 642 ASN cc_start: 0.8498 (OUTLIER) cc_final: 0.8113 (t0) REVERT: B 727 ASP cc_start: 0.7896 (OUTLIER) cc_final: 0.7661 (m-30) REVERT: D 329 ASN cc_start: 0.9047 (m110) cc_final: 0.8784 (m-40) REVERT: D 476 MET cc_start: 0.8655 (mtt) cc_final: 0.8454 (mtt) REVERT: D 503 GLU cc_start: 0.7310 (tp30) cc_final: 0.6915 (tp30) REVERT: E 258 LYS cc_start: 0.8774 (tmtt) cc_final: 0.8363 (tptt) REVERT: E 352 GLU cc_start: 0.7565 (mm-30) cc_final: 0.7260 (mm-30) REVERT: E 366 GLU cc_start: 0.7486 (mt-10) cc_final: 0.7039 (mt-10) REVERT: E 633 LYS cc_start: 0.8605 (mttt) cc_final: 0.8199 (mttp) REVERT: F 172 PHE cc_start: 0.7859 (m-80) cc_final: 0.7573 (m-80) REVERT: F 212 LEU cc_start: 0.8459 (mt) cc_final: 0.8112 (mp) REVERT: F 305 ASN cc_start: 0.7447 (m-40) cc_final: 0.7176 (m-40) REVERT: F 343 LYS cc_start: 0.8464 (ttpt) cc_final: 0.8153 (ttmm) REVERT: F 352 GLU cc_start: 0.7728 (mp0) cc_final: 0.7422 (mp0) REVERT: F 390 ASN cc_start: 0.7252 (p0) cc_final: 0.6595 (t0) REVERT: F 412 MET cc_start: 0.7024 (OUTLIER) cc_final: 0.6815 (ttp) REVERT: F 631 GLU cc_start: 0.8519 (mp0) cc_final: 0.7750 (pt0) REVERT: F 665 PHE cc_start: 0.8798 (m-80) cc_final: 0.8357 (m-80) REVERT: H 149 MET cc_start: 0.8703 (mmp) cc_final: 0.8263 (mmp) REVERT: I 136 GLU cc_start: 0.8385 (tm-30) cc_final: 0.7991 (tm-30) REVERT: I 144 LYS cc_start: 0.8666 (mttp) cc_final: 0.8355 (mttp) REVERT: I 149 MET cc_start: 0.8526 (mmp) cc_final: 0.8183 (mmp) REVERT: I 169 GLU cc_start: 0.8016 (mm-30) cc_final: 0.7720 (mm-30) REVERT: J 60 TYR cc_start: 0.8395 (m-10) cc_final: 0.8165 (m-10) REVERT: J 123 GLN cc_start: 0.8467 (pt0) cc_final: 0.7965 (pt0) REVERT: J 172 ARG cc_start: 0.8122 (tpp80) cc_final: 0.7884 (tpt90) REVERT: K 140 ARG cc_start: 0.7852 (ttm-80) cc_final: 0.7499 (ttm-80) REVERT: K 144 LYS cc_start: 0.8678 (mmmt) cc_final: 0.8367 (mttp) REVERT: K 151 GLU cc_start: 0.7484 (mt-10) cc_final: 0.7196 (mt-10) REVERT: K 169 GLU cc_start: 0.8310 (tp30) cc_final: 0.7867 (tp30) REVERT: L 34 GLN cc_start: 0.8535 (tp40) cc_final: 0.8297 (tp40) REVERT: L 69 VAL cc_start: 0.9095 (p) cc_final: 0.8885 (m) REVERT: L 86 ASP cc_start: 0.7787 (m-30) cc_final: 0.7465 (t0) REVERT: L 141 GLU cc_start: 0.7661 (tm-30) cc_final: 0.7214 (tm-30) REVERT: M 54 ASN cc_start: 0.8517 (t0) cc_final: 0.8133 (t0) REVERT: M 120 MET cc_start: 0.8400 (tmm) cc_final: 0.8102 (tmm) REVERT: M 151 GLU cc_start: 0.7990 (tt0) cc_final: 0.7616 (tt0) REVERT: M 171 ASP cc_start: 0.8672 (m-30) cc_final: 0.8423 (m-30) REVERT: N 58 ASP cc_start: 0.8157 (p0) cc_final: 0.7805 (p0) REVERT: N 136 GLU cc_start: 0.8578 (tm-30) cc_final: 0.8313 (tm-30) REVERT: N 146 LYS cc_start: 0.9022 (tttt) cc_final: 0.8513 (tttt) outliers start: 82 outliers final: 65 residues processed: 1353 average time/residue: 1.1546 time to fit residues: 2431.7030 Evaluate side-chains 1352 residues out of total 4059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 1284 time to evaluate : 4.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 491 PHE Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 710 ASP Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain B residue 523 GLU Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 642 ASN Chi-restraints excluded: chain B residue 727 ASP Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 391 ASP Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain C residue 585 THR Chi-restraints excluded: chain C residue 611 GLU Chi-restraints excluded: chain C residue 626 THR Chi-restraints excluded: chain C residue 637 THR Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain D residue 727 ASP Chi-restraints excluded: chain D residue 742 LEU Chi-restraints excluded: chain D residue 746 PHE Chi-restraints excluded: chain E residue 186 ASP Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 209 ASN Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 459 LEU Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain E residue 707 VAL Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 243 CYS Chi-restraints excluded: chain F residue 310 LEU Chi-restraints excluded: chain F residue 412 MET Chi-restraints excluded: chain F residue 558 HIS Chi-restraints excluded: chain F residue 570 HIS Chi-restraints excluded: chain F residue 676 LYS Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 58 ASP Chi-restraints excluded: chain I residue 116 ASN Chi-restraints excluded: chain I residue 117 SER Chi-restraints excluded: chain J residue 81 GLN Chi-restraints excluded: chain J residue 160 SER Chi-restraints excluded: chain J residue 189 LEU Chi-restraints excluded: chain K residue 16 SER Chi-restraints excluded: chain K residue 41 ASN Chi-restraints excluded: chain K residue 160 SER Chi-restraints excluded: chain K residue 187 SER Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain L residue 184 LEU Chi-restraints excluded: chain M residue 121 ILE Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 92 MET Chi-restraints excluded: chain N residue 117 SER Chi-restraints excluded: chain N residue 120 MET Chi-restraints excluded: chain N residue 182 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 156 optimal weight: 5.9990 chunk 417 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 272 optimal weight: 0.8980 chunk 114 optimal weight: 9.9990 chunk 464 optimal weight: 10.0000 chunk 385 optimal weight: 6.9990 chunk 215 optimal weight: 9.9990 chunk 38 optimal weight: 20.0000 chunk 153 optimal weight: 4.9990 chunk 243 optimal weight: 8.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 507 GLN A 556 HIS ** A 659 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 711 ASN ** E 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 558 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 747 GLN ** F 659 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 34 GLN ** K 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 122 HIS L 41 ASN M 123 GLN N 159 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.3541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 38586 Z= 0.256 Angle : 0.527 6.813 52137 Z= 0.271 Chirality : 0.039 0.148 5981 Planarity : 0.004 0.055 6728 Dihedral : 8.876 166.736 5411 Min Nonbonded Distance : 1.770 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.95 % Allowed : 15.77 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.12), residues: 4795 helix: 0.89 (0.10), residues: 2455 sheet: -0.77 (0.21), residues: 580 loop : -0.67 (0.14), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 229 HIS 0.010 0.001 HIS E 558 PHE 0.023 0.001 PHE F 172 TYR 0.019 0.001 TYR C 259 ARG 0.008 0.000 ARG E 592 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Evaluate side-chains 1384 residues out of total 4059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 1305 time to evaluate : 4.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 MET cc_start: 0.8185 (mmp) cc_final: 0.7863 (mmp) REVERT: A 335 ARG cc_start: 0.6304 (ttt-90) cc_final: 0.4647 (ttt90) REVERT: A 343 LYS cc_start: 0.8835 (tmmt) cc_final: 0.8273 (tmmt) REVERT: A 345 ASP cc_start: 0.7210 (p0) cc_final: 0.6943 (p0) REVERT: A 348 GLU cc_start: 0.8819 (pt0) cc_final: 0.8354 (tt0) REVERT: A 379 ARG cc_start: 0.8748 (ptm160) cc_final: 0.7886 (tpt90) REVERT: A 404 GLU cc_start: 0.7832 (mm-30) cc_final: 0.7377 (mm-30) REVERT: A 503 GLU cc_start: 0.8554 (mp0) cc_final: 0.7906 (tt0) REVERT: A 601 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8618 (tt) REVERT: B 247 SER cc_start: 0.8840 (t) cc_final: 0.8200 (p) REVERT: B 279 ASN cc_start: 0.7842 (t0) cc_final: 0.7374 (t0) REVERT: B 370 ASP cc_start: 0.8069 (t0) cc_final: 0.7765 (t0) REVERT: B 447 ASP cc_start: 0.7216 (t0) cc_final: 0.6950 (t0) REVERT: B 572 ASP cc_start: 0.8366 (m-30) cc_final: 0.8103 (m-30) REVERT: B 642 ASN cc_start: 0.8528 (OUTLIER) cc_final: 0.8120 (t0) REVERT: B 727 ASP cc_start: 0.7946 (OUTLIER) cc_final: 0.7701 (m-30) REVERT: D 329 ASN cc_start: 0.9053 (m110) cc_final: 0.8726 (m110) REVERT: D 503 GLU cc_start: 0.7339 (tp30) cc_final: 0.6942 (tp30) REVERT: E 258 LYS cc_start: 0.8788 (tmtt) cc_final: 0.8353 (tptt) REVERT: E 352 GLU cc_start: 0.7575 (mm-30) cc_final: 0.7196 (mm-30) REVERT: E 366 GLU cc_start: 0.7486 (mt-10) cc_final: 0.7047 (mt-10) REVERT: E 633 LYS cc_start: 0.8613 (mttt) cc_final: 0.8199 (mttp) REVERT: F 212 LEU cc_start: 0.8449 (mt) cc_final: 0.8113 (mp) REVERT: F 215 GLU cc_start: 0.7878 (mm-30) cc_final: 0.7622 (mm-30) REVERT: F 305 ASN cc_start: 0.7544 (m-40) cc_final: 0.7257 (m-40) REVERT: F 352 GLU cc_start: 0.7786 (mp0) cc_final: 0.7431 (mp0) REVERT: F 390 ASN cc_start: 0.7268 (p0) cc_final: 0.6609 (t0) REVERT: F 596 PHE cc_start: 0.8070 (m-80) cc_final: 0.7627 (m-10) REVERT: F 631 GLU cc_start: 0.8515 (mp0) cc_final: 0.7799 (pt0) REVERT: H 149 MET cc_start: 0.8716 (mmp) cc_final: 0.8197 (mmp) REVERT: I 136 GLU cc_start: 0.8375 (tm-30) cc_final: 0.7991 (tm-30) REVERT: I 144 LYS cc_start: 0.8683 (mttp) cc_final: 0.8370 (mttp) REVERT: I 169 GLU cc_start: 0.8020 (mm-30) cc_final: 0.7711 (mm-30) REVERT: J 60 TYR cc_start: 0.8394 (m-10) cc_final: 0.8168 (m-10) REVERT: J 123 GLN cc_start: 0.8556 (pt0) cc_final: 0.8043 (pt0) REVERT: J 172 ARG cc_start: 0.8094 (tpp80) cc_final: 0.7851 (tpt90) REVERT: K 144 LYS cc_start: 0.8665 (mmmt) cc_final: 0.8382 (mttp) REVERT: K 151 GLU cc_start: 0.7490 (mt-10) cc_final: 0.7206 (mt-10) REVERT: K 169 GLU cc_start: 0.8242 (tp30) cc_final: 0.7860 (tp30) REVERT: L 34 GLN cc_start: 0.8535 (tp40) cc_final: 0.8296 (tp40) REVERT: L 86 ASP cc_start: 0.7783 (m-30) cc_final: 0.7466 (t0) REVERT: L 141 GLU cc_start: 0.7654 (tm-30) cc_final: 0.7170 (tm-30) REVERT: M 120 MET cc_start: 0.8390 (tmm) cc_final: 0.8058 (tmm) REVERT: M 146 LYS cc_start: 0.7349 (mttt) cc_final: 0.6969 (mttp) REVERT: M 151 GLU cc_start: 0.7996 (tt0) cc_final: 0.7618 (tt0) REVERT: M 171 ASP cc_start: 0.8691 (m-30) cc_final: 0.8391 (m-30) REVERT: N 58 ASP cc_start: 0.8161 (p0) cc_final: 0.7813 (p0) REVERT: N 136 GLU cc_start: 0.8590 (tm-30) cc_final: 0.8364 (tm-30) REVERT: N 140 ARG cc_start: 0.8110 (mmm160) cc_final: 0.7848 (mtp85) outliers start: 79 outliers final: 65 residues processed: 1329 average time/residue: 1.1415 time to fit residues: 2359.7590 Evaluate side-chains 1349 residues out of total 4059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 1281 time to evaluate : 4.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 491 PHE Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 710 ASP Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 642 ASN Chi-restraints excluded: chain B residue 727 ASP Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 391 ASP Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain C residue 585 THR Chi-restraints excluded: chain C residue 611 GLU Chi-restraints excluded: chain C residue 637 THR Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 531 SER Chi-restraints excluded: chain D residue 564 ASP Chi-restraints excluded: chain D residue 727 ASP Chi-restraints excluded: chain D residue 735 LEU Chi-restraints excluded: chain D residue 742 LEU Chi-restraints excluded: chain D residue 746 PHE Chi-restraints excluded: chain E residue 209 ASN Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 302 ASP Chi-restraints excluded: chain E residue 459 LEU Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain E residue 707 VAL Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 243 CYS Chi-restraints excluded: chain F residue 310 LEU Chi-restraints excluded: chain F residue 558 HIS Chi-restraints excluded: chain F residue 570 HIS Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 172 ARG Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 58 ASP Chi-restraints excluded: chain I residue 116 ASN Chi-restraints excluded: chain I residue 117 SER Chi-restraints excluded: chain I residue 175 SER Chi-restraints excluded: chain J residue 81 GLN Chi-restraints excluded: chain K residue 16 SER Chi-restraints excluded: chain K residue 41 ASN Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain L residue 152 LEU Chi-restraints excluded: chain L residue 160 SER Chi-restraints excluded: chain L residue 184 LEU Chi-restraints excluded: chain L residue 188 ILE Chi-restraints excluded: chain M residue 121 ILE Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 63 ILE Chi-restraints excluded: chain N residue 117 SER Chi-restraints excluded: chain N residue 120 MET Chi-restraints excluded: chain N residue 182 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 447 optimal weight: 9.9990 chunk 52 optimal weight: 40.0000 chunk 264 optimal weight: 10.0000 chunk 339 optimal weight: 50.0000 chunk 262 optimal weight: 10.0000 chunk 390 optimal weight: 7.9990 chunk 259 optimal weight: 10.0000 chunk 462 optimal weight: 10.0000 chunk 289 optimal weight: 10.0000 chunk 282 optimal weight: 8.9990 chunk 213 optimal weight: 5.9990 overall best weight: 8.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 507 GLN ** A 659 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 558 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 747 GLN F 507 GLN ** F 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 122 HIS M 123 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.3874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 38586 Z= 0.431 Angle : 0.595 7.428 52137 Z= 0.312 Chirality : 0.042 0.167 5981 Planarity : 0.004 0.068 6728 Dihedral : 9.077 175.243 5411 Min Nonbonded Distance : 1.685 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.24 % Allowed : 15.84 % Favored : 81.92 % 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: -0.20 (0.12), residues: 4795 helix: 0.67 (0.10), residues: 2460 sheet: -0.89 (0.20), residues: 612 loop : -0.88 (0.14), residues: 1723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 689 HIS 0.009 0.001 HIS E 558 PHE 0.023 0.002 PHE M 17 TYR 0.027 0.002 TYR C 259 ARG 0.009 0.001 ARG E 592 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Evaluate side-chains 1422 residues out of total 4059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 1331 time to evaluate : 4.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 MET cc_start: 0.8249 (mmp) cc_final: 0.7944 (mmp) REVERT: A 343 LYS cc_start: 0.8830 (tmmt) cc_final: 0.8303 (ttpp) REVERT: A 348 GLU cc_start: 0.8851 (pt0) cc_final: 0.8482 (tt0) REVERT: A 379 ARG cc_start: 0.8774 (ptm160) cc_final: 0.7913 (tpt90) REVERT: A 404 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7430 (mm-30) REVERT: A 503 GLU cc_start: 0.8573 (mp0) cc_final: 0.7916 (tt0) REVERT: A 601 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8631 (tt) REVERT: B 204 ARG cc_start: 0.8406 (ptm160) cc_final: 0.8185 (ptm160) REVERT: B 247 SER cc_start: 0.8870 (t) cc_final: 0.8261 (p) REVERT: B 279 ASN cc_start: 0.7947 (t0) cc_final: 0.7509 (t0) REVERT: B 370 ASP cc_start: 0.8139 (t0) cc_final: 0.7847 (t0) REVERT: B 447 ASP cc_start: 0.7359 (t0) cc_final: 0.7125 (t0) REVERT: B 572 ASP cc_start: 0.8417 (m-30) cc_final: 0.8125 (m-30) REVERT: B 642 ASN cc_start: 0.8574 (OUTLIER) cc_final: 0.8152 (t0) REVERT: B 722 PHE cc_start: 0.9125 (OUTLIER) cc_final: 0.7310 (p90) REVERT: B 727 ASP cc_start: 0.8176 (OUTLIER) cc_final: 0.7958 (m-30) REVERT: D 503 GLU cc_start: 0.7442 (tp30) cc_final: 0.7046 (tp30) REVERT: D 696 ASP cc_start: 0.8334 (t0) cc_final: 0.8061 (t0) REVERT: E 258 LYS cc_start: 0.8792 (tmtt) cc_final: 0.8359 (tptt) REVERT: E 366 GLU cc_start: 0.7544 (mt-10) cc_final: 0.7128 (mt-10) REVERT: E 551 ASP cc_start: 0.7115 (m-30) cc_final: 0.6680 (m-30) REVERT: E 633 LYS cc_start: 0.8768 (mttt) cc_final: 0.8341 (mttp) REVERT: F 212 LEU cc_start: 0.8582 (mt) cc_final: 0.8256 (mp) REVERT: F 215 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7501 (mm-30) REVERT: F 352 GLU cc_start: 0.7833 (mp0) cc_final: 0.7492 (mp0) REVERT: F 390 ASN cc_start: 0.7342 (p0) cc_final: 0.6652 (t0) REVERT: F 631 GLU cc_start: 0.8526 (mp0) cc_final: 0.8309 (mp0) REVERT: H 149 MET cc_start: 0.8686 (mmp) cc_final: 0.8223 (mmp) REVERT: I 136 GLU cc_start: 0.8389 (tm-30) cc_final: 0.7989 (tm-30) REVERT: I 149 MET cc_start: 0.8626 (mmp) cc_final: 0.8308 (mmp) REVERT: I 169 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7757 (mm-30) REVERT: J 60 TYR cc_start: 0.8524 (m-10) cc_final: 0.8281 (m-10) REVERT: J 84 LYS cc_start: 0.8400 (tttp) cc_final: 0.8194 (tttp) REVERT: J 123 GLN cc_start: 0.8649 (pt0) cc_final: 0.8140 (pt0) REVERT: J 172 ARG cc_start: 0.8148 (tpp80) cc_final: 0.7794 (tpt90) REVERT: K 144 LYS cc_start: 0.8714 (mmmt) cc_final: 0.8411 (mttp) REVERT: K 151 GLU cc_start: 0.7458 (mt-10) cc_final: 0.7184 (mt-10) REVERT: L 34 GLN cc_start: 0.8555 (tp40) cc_final: 0.8307 (tp40) REVERT: L 86 ASP cc_start: 0.7879 (m-30) cc_final: 0.7558 (t0) REVERT: L 141 GLU cc_start: 0.7775 (tm-30) cc_final: 0.7290 (tm-30) REVERT: M 151 GLU cc_start: 0.8026 (tt0) cc_final: 0.7642 (tt0) REVERT: M 171 ASP cc_start: 0.8719 (m-30) cc_final: 0.8443 (m-30) REVERT: N 58 ASP cc_start: 0.8241 (p0) cc_final: 0.7925 (p0) REVERT: N 146 LYS cc_start: 0.8929 (tttt) cc_final: 0.8595 (tttt) REVERT: N 151 GLU cc_start: 0.7554 (mt-10) cc_final: 0.7322 (mt-10) REVERT: N 178 GLU cc_start: 0.8325 (mt-10) cc_final: 0.7947 (mt-10) outliers start: 91 outliers final: 77 residues processed: 1364 average time/residue: 1.1182 time to fit residues: 2369.0064 Evaluate side-chains 1384 residues out of total 4059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 1303 time to evaluate : 4.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 491 PHE Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 652 HIS Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 710 ASP Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 642 ASN Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain B residue 727 ASP Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 391 ASP Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 585 THR Chi-restraints excluded: chain C residue 611 GLU Chi-restraints excluded: chain C residue 637 THR Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain D residue 531 SER Chi-restraints excluded: chain D residue 564 ASP Chi-restraints excluded: chain D residue 727 ASP Chi-restraints excluded: chain D residue 746 PHE Chi-restraints excluded: chain E residue 186 ASP Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 459 LEU Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain E residue 606 ASN Chi-restraints excluded: chain E residue 707 VAL Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 243 CYS Chi-restraints excluded: chain F residue 310 LEU Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 525 MET Chi-restraints excluded: chain F residue 558 HIS Chi-restraints excluded: chain F residue 570 HIS Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 172 ARG Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 58 ASP Chi-restraints excluded: chain I residue 116 ASN Chi-restraints excluded: chain I residue 117 SER Chi-restraints excluded: chain I residue 171 ASP Chi-restraints excluded: chain I residue 175 SER Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain I residue 187 SER Chi-restraints excluded: chain J residue 81 GLN Chi-restraints excluded: chain J residue 160 SER Chi-restraints excluded: chain K residue 16 SER Chi-restraints excluded: chain K residue 86 ASP Chi-restraints excluded: chain K residue 187 SER Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain L residue 160 SER Chi-restraints excluded: chain L residue 184 LEU Chi-restraints excluded: chain L residue 188 ILE Chi-restraints excluded: chain M residue 121 ILE Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 63 ILE Chi-restraints excluded: chain N residue 92 MET Chi-restraints excluded: chain N residue 117 SER Chi-restraints excluded: chain N residue 120 MET Chi-restraints excluded: chain N residue 182 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 286 optimal weight: 30.0000 chunk 184 optimal weight: 5.9990 chunk 276 optimal weight: 7.9990 chunk 139 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 294 optimal weight: 9.9990 chunk 315 optimal weight: 6.9990 chunk 228 optimal weight: 10.0000 chunk 43 optimal weight: 40.0000 chunk 363 optimal weight: 8.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 507 GLN ** A 659 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 558 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 747 GLN F 672 GLN ** F 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 34 GLN I 131 GLN L 41 ASN M 81 GLN M 123 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.3991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 38586 Z= 0.220 Angle : 0.531 6.590 52137 Z= 0.273 Chirality : 0.039 0.152 5981 Planarity : 0.004 0.059 6728 Dihedral : 8.836 170.726 5411 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.82 % Allowed : 17.00 % Favored : 81.18 % 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: 0.03 (0.12), residues: 4795 helix: 0.87 (0.10), residues: 2466 sheet: -0.83 (0.21), residues: 600 loop : -0.77 (0.14), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 649 HIS 0.008 0.001 HIS E 558 PHE 0.015 0.001 PHE M 17 TYR 0.029 0.001 TYR A 324 ARG 0.009 0.000 ARG J 140 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Evaluate side-chains 1414 residues out of total 4059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 1340 time to evaluate : 5.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 MET cc_start: 0.8230 (mmp) cc_final: 0.7918 (mmp) REVERT: A 343 LYS cc_start: 0.8833 (tmmt) cc_final: 0.8134 (tmmt) REVERT: A 348 GLU cc_start: 0.8849 (pt0) cc_final: 0.8497 (tt0) REVERT: A 379 ARG cc_start: 0.8746 (ptm160) cc_final: 0.7876 (tpt90) REVERT: A 404 GLU cc_start: 0.7869 (mm-30) cc_final: 0.7406 (mm-30) REVERT: A 427 GLU cc_start: 0.8743 (mt-10) cc_final: 0.8512 (mt-10) REVERT: A 503 GLU cc_start: 0.8597 (mp0) cc_final: 0.7926 (tt0) REVERT: A 577 LEU cc_start: 0.8614 (mt) cc_final: 0.8348 (mp) REVERT: A 601 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8604 (tt) REVERT: A 721 LEU cc_start: 0.9253 (mt) cc_final: 0.9019 (mt) REVERT: B 204 ARG cc_start: 0.8371 (ptm160) cc_final: 0.8136 (ptm160) REVERT: B 247 SER cc_start: 0.8845 (t) cc_final: 0.8216 (p) REVERT: B 279 ASN cc_start: 0.7961 (t0) cc_final: 0.7567 (t0) REVERT: B 370 ASP cc_start: 0.8110 (t0) cc_final: 0.7817 (t0) REVERT: B 408 ARG cc_start: 0.8246 (ttm-80) cc_final: 0.8029 (ttm170) REVERT: B 447 ASP cc_start: 0.7234 (t0) cc_final: 0.7029 (t0) REVERT: B 572 ASP cc_start: 0.8404 (m-30) cc_final: 0.8134 (m-30) REVERT: B 642 ASN cc_start: 0.8564 (OUTLIER) cc_final: 0.8162 (t0) REVERT: B 722 PHE cc_start: 0.9060 (OUTLIER) cc_final: 0.7255 (p90) REVERT: B 727 ASP cc_start: 0.8013 (OUTLIER) cc_final: 0.7778 (m-30) REVERT: C 273 GLN cc_start: 0.8374 (mt0) cc_final: 0.8143 (mt0) REVERT: D 329 ASN cc_start: 0.9063 (m110) cc_final: 0.8774 (m-40) REVERT: D 697 ARG cc_start: 0.8431 (mtp-110) cc_final: 0.8035 (mmm160) REVERT: E 258 LYS cc_start: 0.8802 (tmtt) cc_final: 0.8348 (tptt) REVERT: E 366 GLU cc_start: 0.7496 (mt-10) cc_final: 0.7089 (mt-10) REVERT: E 432 ARG cc_start: 0.8388 (ptm-80) cc_final: 0.8011 (tmm-80) REVERT: E 551 ASP cc_start: 0.7045 (m-30) cc_final: 0.6619 (m-30) REVERT: E 633 LYS cc_start: 0.8661 (mttt) cc_final: 0.8249 (mttp) REVERT: F 212 LEU cc_start: 0.8535 (mt) cc_final: 0.8208 (mp) REVERT: F 215 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7386 (mm-30) REVERT: F 220 LYS cc_start: 0.8050 (pttm) cc_final: 0.7699 (ptpp) REVERT: F 343 LYS cc_start: 0.8691 (ttpt) cc_final: 0.8405 (ttpp) REVERT: F 352 GLU cc_start: 0.7783 (mp0) cc_final: 0.7448 (mp0) REVERT: F 390 ASN cc_start: 0.7315 (p0) cc_final: 0.6603 (t0) REVERT: F 631 GLU cc_start: 0.8545 (mp0) cc_final: 0.7856 (pt0) REVERT: H 149 MET cc_start: 0.8677 (mmp) cc_final: 0.8231 (mmp) REVERT: I 136 GLU cc_start: 0.8386 (tm-30) cc_final: 0.7991 (tm-30) REVERT: I 169 GLU cc_start: 0.8049 (mm-30) cc_final: 0.7736 (mm-30) REVERT: J 60 TYR cc_start: 0.8393 (m-10) cc_final: 0.8176 (m-10) REVERT: J 84 LYS cc_start: 0.8392 (tttp) cc_final: 0.8172 (tttp) REVERT: J 123 GLN cc_start: 0.8659 (pt0) cc_final: 0.8127 (pt0) REVERT: J 172 ARG cc_start: 0.8113 (tpp80) cc_final: 0.7774 (tpt90) REVERT: K 144 LYS cc_start: 0.8704 (mmmt) cc_final: 0.8374 (mttp) REVERT: K 169 GLU cc_start: 0.8329 (tp30) cc_final: 0.7933 (tp30) REVERT: L 34 GLN cc_start: 0.8499 (tp40) cc_final: 0.8257 (tp40) REVERT: L 86 ASP cc_start: 0.7792 (m-30) cc_final: 0.7495 (t0) REVERT: M 120 MET cc_start: 0.8398 (tmm) cc_final: 0.8093 (tmm) REVERT: M 151 GLU cc_start: 0.7973 (tt0) cc_final: 0.7594 (tt0) REVERT: N 57 LYS cc_start: 0.8357 (mtpp) cc_final: 0.8112 (mtpp) REVERT: N 58 ASP cc_start: 0.8208 (p0) cc_final: 0.7858 (p0) REVERT: N 146 LYS cc_start: 0.8901 (tttt) cc_final: 0.8572 (tttt) outliers start: 74 outliers final: 58 residues processed: 1365 average time/residue: 1.1151 time to fit residues: 2362.7919 Evaluate side-chains 1381 residues out of total 4059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 1319 time to evaluate : 4.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 491 PHE Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 652 HIS Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 642 ASN Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain B residue 727 ASP Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain C residue 585 THR Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain D residue 531 SER Chi-restraints excluded: chain D residue 742 LEU Chi-restraints excluded: chain D residue 746 PHE Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 459 LEU Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain E residue 707 VAL Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 243 CYS Chi-restraints excluded: chain F residue 310 LEU Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 558 HIS Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 172 ARG Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 58 ASP Chi-restraints excluded: chain I residue 116 ASN Chi-restraints excluded: chain I residue 117 SER Chi-restraints excluded: chain I residue 175 SER Chi-restraints excluded: chain J residue 81 GLN Chi-restraints excluded: chain K residue 16 SER Chi-restraints excluded: chain K residue 187 SER Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain L residue 160 SER Chi-restraints excluded: chain L residue 181 GLU Chi-restraints excluded: chain L residue 184 LEU Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 117 SER Chi-restraints excluded: chain N residue 120 MET Chi-restraints excluded: chain N residue 182 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 420 optimal weight: 9.9990 chunk 443 optimal weight: 7.9990 chunk 404 optimal weight: 2.9990 chunk 431 optimal weight: 7.9990 chunk 259 optimal weight: 10.0000 chunk 187 optimal weight: 2.9990 chunk 338 optimal weight: 10.0000 chunk 132 optimal weight: 5.9990 chunk 389 optimal weight: 4.9990 chunk 407 optimal weight: 10.0000 chunk 429 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 507 GLN ** A 659 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 558 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 747 GLN ** F 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 123 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.4087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 38586 Z= 0.269 Angle : 0.542 8.370 52137 Z= 0.278 Chirality : 0.040 0.157 5981 Planarity : 0.004 0.062 6728 Dihedral : 8.777 170.919 5411 Min Nonbonded Distance : 1.744 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.72 % Allowed : 17.39 % Favored : 80.88 % 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: 0.07 (0.12), residues: 4795 helix: 0.92 (0.10), residues: 2465 sheet: -0.82 (0.20), residues: 600 loop : -0.78 (0.14), residues: 1730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 649 HIS 0.006 0.001 HIS E 558 PHE 0.022 0.001 PHE N 173 TYR 0.026 0.001 TYR M 77 ARG 0.010 0.000 ARG L 140 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Evaluate side-chains 1397 residues out of total 4059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 1327 time to evaluate : 4.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 MET cc_start: 0.8177 (mmp) cc_final: 0.7870 (mmp) REVERT: A 343 LYS cc_start: 0.8829 (tmmt) cc_final: 0.8292 (ttpp) REVERT: A 348 GLU cc_start: 0.8843 (pt0) cc_final: 0.8489 (tt0) REVERT: A 372 ARG cc_start: 0.7615 (ptt-90) cc_final: 0.7389 (ptt-90) REVERT: A 379 ARG cc_start: 0.8739 (ptm160) cc_final: 0.7878 (tpt90) REVERT: A 503 GLU cc_start: 0.8597 (mp0) cc_final: 0.7946 (tt0) REVERT: A 577 LEU cc_start: 0.8626 (mt) cc_final: 0.8357 (mp) REVERT: A 601 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8671 (tt) REVERT: A 721 LEU cc_start: 0.9242 (mt) cc_final: 0.9004 (mt) REVERT: B 247 SER cc_start: 0.8868 (t) cc_final: 0.8242 (p) REVERT: B 279 ASN cc_start: 0.8014 (t0) cc_final: 0.7561 (t0) REVERT: B 370 ASP cc_start: 0.8145 (t0) cc_final: 0.7893 (t0) REVERT: B 408 ARG cc_start: 0.8261 (ttm-80) cc_final: 0.8038 (ttm170) REVERT: B 447 ASP cc_start: 0.7251 (t0) cc_final: 0.7050 (t0) REVERT: B 572 ASP cc_start: 0.8408 (m-30) cc_final: 0.8129 (m-30) REVERT: B 642 ASN cc_start: 0.8557 (OUTLIER) cc_final: 0.8139 (t0) REVERT: B 722 PHE cc_start: 0.9064 (OUTLIER) cc_final: 0.7210 (p90) REVERT: B 727 ASP cc_start: 0.8022 (OUTLIER) cc_final: 0.7597 (m-30) REVERT: C 273 GLN cc_start: 0.8392 (mt0) cc_final: 0.8166 (mt0) REVERT: D 329 ASN cc_start: 0.9044 (m110) cc_final: 0.8762 (m-40) REVERT: D 696 ASP cc_start: 0.8368 (t0) cc_final: 0.8080 (t0) REVERT: D 697 ARG cc_start: 0.8438 (mtp-110) cc_final: 0.8120 (mmm160) REVERT: E 258 LYS cc_start: 0.8783 (tmtt) cc_final: 0.8334 (tptt) REVERT: E 366 GLU cc_start: 0.7513 (mt-10) cc_final: 0.7116 (mt-10) REVERT: E 432 ARG cc_start: 0.8412 (ptm-80) cc_final: 0.8029 (tmm-80) REVERT: E 551 ASP cc_start: 0.7112 (m-30) cc_final: 0.6680 (m-30) REVERT: E 633 LYS cc_start: 0.8669 (mttt) cc_final: 0.8263 (mttp) REVERT: E 695 TYR cc_start: 0.7497 (t80) cc_final: 0.7236 (t80) REVERT: F 212 LEU cc_start: 0.8559 (mt) cc_final: 0.8239 (mp) REVERT: F 215 GLU cc_start: 0.7891 (mm-30) cc_final: 0.7410 (mm-30) REVERT: F 220 LYS cc_start: 0.8096 (pttm) cc_final: 0.7716 (ptpp) REVERT: F 352 GLU cc_start: 0.7794 (mp0) cc_final: 0.7461 (mp0) REVERT: F 390 ASN cc_start: 0.7322 (p0) cc_final: 0.6615 (t0) REVERT: F 631 GLU cc_start: 0.8553 (mp0) cc_final: 0.7855 (pt0) REVERT: H 149 MET cc_start: 0.8684 (mmp) cc_final: 0.8243 (mmp) REVERT: I 136 GLU cc_start: 0.8381 (tm-30) cc_final: 0.8010 (tm-30) REVERT: I 169 GLU cc_start: 0.8048 (mm-30) cc_final: 0.7732 (mm-30) REVERT: J 60 TYR cc_start: 0.8421 (m-10) cc_final: 0.8200 (m-10) REVERT: J 123 GLN cc_start: 0.8671 (pt0) cc_final: 0.8130 (pt0) REVERT: J 172 ARG cc_start: 0.8110 (tpp80) cc_final: 0.7852 (tpt90) REVERT: K 144 LYS cc_start: 0.8713 (mmmt) cc_final: 0.8399 (mttp) REVERT: K 151 GLU cc_start: 0.7399 (mt-10) cc_final: 0.7076 (mt-10) REVERT: K 169 GLU cc_start: 0.8324 (tp30) cc_final: 0.7920 (tp30) REVERT: L 34 GLN cc_start: 0.8513 (tp40) cc_final: 0.8273 (tp40) REVERT: L 86 ASP cc_start: 0.7796 (m-30) cc_final: 0.7471 (t0) REVERT: M 120 MET cc_start: 0.8311 (tmm) cc_final: 0.8029 (tmm) REVERT: M 151 GLU cc_start: 0.8002 (tt0) cc_final: 0.7617 (tt0) REVERT: N 57 LYS cc_start: 0.8322 (mtpp) cc_final: 0.8080 (mtpp) REVERT: N 58 ASP cc_start: 0.8199 (p0) cc_final: 0.7852 (p0) REVERT: N 140 ARG cc_start: 0.8056 (mmm160) cc_final: 0.7703 (mtp85) outliers start: 70 outliers final: 64 residues processed: 1351 average time/residue: 1.1201 time to fit residues: 2351.0620 Evaluate side-chains 1384 residues out of total 4059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 1316 time to evaluate : 4.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 491 PHE Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 652 HIS Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 642 ASN Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain B residue 727 ASP Chi-restraints excluded: chain B residue 748 SER Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 585 THR Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain D residue 531 SER Chi-restraints excluded: chain D residue 727 ASP Chi-restraints excluded: chain D residue 735 LEU Chi-restraints excluded: chain D residue 742 LEU Chi-restraints excluded: chain D residue 746 PHE Chi-restraints excluded: chain E residue 209 ASN Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 459 LEU Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain E residue 707 VAL Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 243 CYS Chi-restraints excluded: chain F residue 310 LEU Chi-restraints excluded: chain F residue 558 HIS Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 172 ARG Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 58 ASP Chi-restraints excluded: chain I residue 116 ASN Chi-restraints excluded: chain I residue 117 SER Chi-restraints excluded: chain I residue 175 SER Chi-restraints excluded: chain I residue 187 SER Chi-restraints excluded: chain J residue 81 GLN Chi-restraints excluded: chain K residue 16 SER Chi-restraints excluded: chain K residue 187 SER Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain L residue 160 SER Chi-restraints excluded: chain L residue 181 GLU Chi-restraints excluded: chain L residue 184 LEU Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 63 ILE Chi-restraints excluded: chain N residue 117 SER Chi-restraints excluded: chain N residue 120 MET Chi-restraints excluded: chain N residue 182 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 283 optimal weight: 40.0000 chunk 455 optimal weight: 7.9990 chunk 278 optimal weight: 2.9990 chunk 216 optimal weight: 6.9990 chunk 316 optimal weight: 9.9990 chunk 478 optimal weight: 10.0000 chunk 440 optimal weight: 9.9990 chunk 380 optimal weight: 9.9990 chunk 39 optimal weight: 30.0000 chunk 294 optimal weight: 9.9990 chunk 233 optimal weight: 9.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 507 GLN ** A 659 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 558 HIS E 747 GLN ** F 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.4246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 38586 Z= 0.381 Angle : 0.582 8.655 52137 Z= 0.303 Chirality : 0.041 0.157 5981 Planarity : 0.004 0.070 6728 Dihedral : 8.903 174.139 5411 Min Nonbonded Distance : 1.710 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.97 % Allowed : 17.59 % Favored : 80.44 % 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: -0.10 (0.12), residues: 4795 helix: 0.79 (0.10), residues: 2465 sheet: -0.90 (0.20), residues: 599 loop : -0.89 (0.14), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 649 HIS 0.006 0.001 HIS C 393 PHE 0.020 0.001 PHE M 17 TYR 0.024 0.001 TYR C 259 ARG 0.011 0.000 ARG E 592 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9590 Ramachandran restraints generated. 4795 Oldfield, 0 Emsley, 4795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Evaluate side-chains 1395 residues out of total 4059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 1315 time to evaluate : 4.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 MET cc_start: 0.8210 (mmp) cc_final: 0.7914 (mmp) REVERT: A 343 LYS cc_start: 0.8865 (tmmt) cc_final: 0.8324 (ttpp) REVERT: A 348 GLU cc_start: 0.8868 (pt0) cc_final: 0.8496 (tt0) REVERT: A 379 ARG cc_start: 0.8760 (ptm160) cc_final: 0.7887 (tpt90) REVERT: A 404 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7437 (mm-30) REVERT: A 410 ARG cc_start: 0.7605 (ptm160) cc_final: 0.7266 (ptm160) REVERT: A 503 GLU cc_start: 0.8616 (mp0) cc_final: 0.7968 (tt0) REVERT: A 577 LEU cc_start: 0.8672 (mt) cc_final: 0.8421 (mp) REVERT: A 601 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8686 (tt) REVERT: A 721 LEU cc_start: 0.9236 (mt) cc_final: 0.9009 (mt) REVERT: B 247 SER cc_start: 0.8850 (t) cc_final: 0.8252 (p) REVERT: B 279 ASN cc_start: 0.8079 (t0) cc_final: 0.7651 (t0) REVERT: B 370 ASP cc_start: 0.8191 (t0) cc_final: 0.7942 (t0) REVERT: B 408 ARG cc_start: 0.8305 (ttm-80) cc_final: 0.8067 (ttm170) REVERT: B 572 ASP cc_start: 0.8411 (m-30) cc_final: 0.8119 (m-30) REVERT: B 642 ASN cc_start: 0.8578 (OUTLIER) cc_final: 0.8149 (t0) REVERT: B 722 PHE cc_start: 0.9082 (OUTLIER) cc_final: 0.7319 (p90) REVERT: B 727 ASP cc_start: 0.8168 (OUTLIER) cc_final: 0.7774 (m-30) REVERT: C 273 GLN cc_start: 0.8419 (mt0) cc_final: 0.8199 (mt0) REVERT: C 325 GLN cc_start: 0.7927 (mt0) cc_final: 0.7685 (mt0) REVERT: C 730 GLN cc_start: 0.7756 (pm20) cc_final: 0.7436 (pm20) REVERT: D 696 ASP cc_start: 0.8409 (t0) cc_final: 0.8107 (t0) REVERT: D 697 ARG cc_start: 0.8460 (mtp-110) cc_final: 0.8156 (mmm160) REVERT: E 258 LYS cc_start: 0.8806 (tmtt) cc_final: 0.8356 (tptt) REVERT: E 366 GLU cc_start: 0.7556 (mt-10) cc_final: 0.7166 (mt-10) REVERT: E 468 GLU cc_start: 0.7937 (pp20) cc_final: 0.7564 (pp20) REVERT: E 551 ASP cc_start: 0.7205 (m-30) cc_final: 0.6763 (m-30) REVERT: E 633 LYS cc_start: 0.8754 (mttt) cc_final: 0.8343 (mttp) REVERT: E 695 TYR cc_start: 0.7526 (t80) cc_final: 0.7277 (t80) REVERT: F 212 LEU cc_start: 0.8597 (mt) cc_final: 0.8281 (mp) REVERT: F 305 ASN cc_start: 0.7486 (m-40) cc_final: 0.7177 (m-40) REVERT: F 343 LYS cc_start: 0.8795 (ttpt) cc_final: 0.8525 (ttpp) REVERT: F 352 GLU cc_start: 0.7804 (mp0) cc_final: 0.7473 (mp0) REVERT: F 390 ASN cc_start: 0.7332 (p0) cc_final: 0.6607 (t0) REVERT: H 108 LYS cc_start: 0.8703 (mtmt) cc_final: 0.8462 (ttmt) REVERT: H 149 MET cc_start: 0.8710 (mmp) cc_final: 0.8242 (mmp) REVERT: I 136 GLU cc_start: 0.8405 (tm-30) cc_final: 0.8023 (tm-30) REVERT: I 169 GLU cc_start: 0.8070 (mm-30) cc_final: 0.7741 (mm-30) REVERT: J 60 TYR cc_start: 0.8495 (m-10) cc_final: 0.8259 (m-10) REVERT: J 118 ARG cc_start: 0.8059 (mmm-85) cc_final: 0.7838 (mmm-85) REVERT: J 123 GLN cc_start: 0.8681 (pt0) cc_final: 0.8151 (pt0) REVERT: J 172 ARG cc_start: 0.8102 (tpp80) cc_final: 0.7805 (tpt90) REVERT: K 144 LYS cc_start: 0.8732 (mmmt) cc_final: 0.8412 (mttp) REVERT: K 151 GLU cc_start: 0.7484 (mt-10) cc_final: 0.7154 (mt-10) REVERT: L 34 GLN cc_start: 0.8536 (tp40) cc_final: 0.8290 (tp40) REVERT: L 86 ASP cc_start: 0.7832 (m-30) cc_final: 0.7511 (t0) REVERT: M 120 MET cc_start: 0.8281 (tmm) cc_final: 0.8069 (tmm) REVERT: M 144 LYS cc_start: 0.8444 (mttp) cc_final: 0.8194 (mttp) REVERT: M 151 GLU cc_start: 0.8024 (tt0) cc_final: 0.7633 (tt0) REVERT: N 57 LYS cc_start: 0.8287 (mtpp) cc_final: 0.8048 (mtpp) REVERT: N 58 ASP cc_start: 0.8220 (p0) cc_final: 0.7893 (p0) REVERT: N 140 ARG cc_start: 0.8053 (mmm160) cc_final: 0.7703 (mtp85) REVERT: N 146 LYS cc_start: 0.8908 (tttt) cc_final: 0.8615 (tttt) REVERT: N 151 GLU cc_start: 0.7542 (mt-10) cc_final: 0.7292 (mt-10) outliers start: 80 outliers final: 70 residues processed: 1343 average time/residue: 1.1146 time to fit residues: 2320.7292 Evaluate side-chains 1376 residues out of total 4059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 1302 time to evaluate : 4.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 331 PHE Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 491 PHE Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 652 HIS Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 642 ASN Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain B residue 727 ASP Chi-restraints excluded: chain B residue 748 SER Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain C residue 585 THR Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 531 SER Chi-restraints excluded: chain D residue 666 ILE Chi-restraints excluded: chain D residue 722 PHE Chi-restraints excluded: chain D residue 727 ASP Chi-restraints excluded: chain D residue 742 LEU Chi-restraints excluded: chain D residue 746 PHE Chi-restraints excluded: chain E residue 186 ASP Chi-restraints excluded: chain E residue 209 ASN Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 459 LEU Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain E residue 707 VAL Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 243 CYS Chi-restraints excluded: chain F residue 310 LEU Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 525 MET Chi-restraints excluded: chain F residue 558 HIS Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 172 ARG Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 58 ASP Chi-restraints excluded: chain I residue 116 ASN Chi-restraints excluded: chain I residue 117 SER Chi-restraints excluded: chain I residue 171 ASP Chi-restraints excluded: chain I residue 175 SER Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain I residue 187 SER Chi-restraints excluded: chain J residue 81 GLN Chi-restraints excluded: chain K residue 16 SER Chi-restraints excluded: chain K residue 86 ASP Chi-restraints excluded: chain K residue 187 SER Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain L residue 160 SER Chi-restraints excluded: chain L residue 181 GLU Chi-restraints excluded: chain L residue 184 LEU Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 63 ILE Chi-restraints excluded: chain N residue 117 SER Chi-restraints excluded: chain N residue 120 MET Chi-restraints excluded: chain N residue 182 TYR 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: 5.9990 chunk 116 optimal weight: 8.9990 chunk 351 optimal weight: 5.9990 chunk 56 optimal weight: 10.0000 chunk 105 optimal weight: 5.9990 chunk 381 optimal weight: 8.9990 chunk 159 optimal weight: 9.9990 chunk 391 optimal weight: 1.9990 chunk 48 optimal weight: 10.0000 chunk 70 optimal weight: 3.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 659 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 747 GLN ** F 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.154259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.109579 restraints weight = 157016.226| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 3.16 r_work: 0.3047 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.4288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 38586 Z= 0.271 Angle : 0.550 7.532 52137 Z= 0.284 Chirality : 0.040 0.155 5981 Planarity : 0.004 0.067 6728 Dihedral : 8.771 171.332 5411 Min Nonbonded Distance : 1.751 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.72 % Allowed : 18.18 % Favored : 80.09 % 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: -0.01 (0.12), residues: 4795 helix: 0.87 (0.10), residues: 2470 sheet: -0.89 (0.20), residues: 598 loop : -0.84 (0.14), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 649 HIS 0.005 0.001 HIS K 122 PHE 0.016 0.001 PHE N 173 TYR 0.020 0.001 TYR C 259 ARG 0.012 0.000 ARG E 592 =============================================================================== Job complete usr+sys time: 30957.64 seconds wall clock time: 531 minutes 36.52 seconds (31896.52 seconds total)