Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 28 22:27:43 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uj0_26559/04_2023/7uj0_26559_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uj0_26559/04_2023/7uj0_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_26559/04_2023/7uj0_26559.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uj0_26559/04_2023/7uj0_26559.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uj0_26559/04_2023/7uj0_26559_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uj0_26559/04_2023/7uj0_26559_trim_updated.pdb" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned 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: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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: 24.06, per 1000 atoms: 0.32 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: 50.73 Conformation dependent library (CDL) restraints added in 5.1 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: 3.61 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: 31.87 Time building geometry restraints manager: 53.38 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: 29433 28.42 - 56.85: 799 56.85 - 85.27: 85 85.27 - 113.69: 12 113.69 - 142.12: 14 Dihedral angle restraints: 30343 sinusoidal: 14824 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 30340 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: 0.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.870 Extract box with map and model: 6.830 Check model and map are aligned: 0.850 Set scattering table: 0.500 Process input model: 189.850 Find NCS groups from input model: 3.450 Set up NCS constraints: 0.250 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: 0.020 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 205.620 ------------------------------------------------------------------------------- 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 : 14.196 142.116 14625 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 % 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 *********************** 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 : 4.633 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 outliers start: 0 outliers final: 0 residues processed: 1515 average time/residue: 1.1084 time to fit residues: 2607.1351 Evaluate side-chains 1280 residues out of total 4059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1280 time to evaluate : 4.495 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.9709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 405 optimal weight: 7.9990 chunk 363 optimal weight: 9.9990 chunk 201 optimal weight: 6.9990 chunk 124 optimal weight: 10.0000 chunk 245 optimal weight: 5.9990 chunk 194 optimal weight: 3.9990 chunk 376 optimal weight: 10.0000 chunk 145 optimal weight: 5.9990 chunk 228 optimal weight: 10.0000 chunk 280 optimal weight: 5.9990 chunk 435 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 672 GLN F 688 ASN F 711 ASN H 41 ASN I 41 ASN I 116 ASN I 131 GLN I 163 GLN J 150 ASN K 122 HIS L 41 ASN ** N 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.042 38586 Z= 0.320 Angle : 0.610 7.876 52137 Z= 0.322 Chirality : 0.041 0.175 5981 Planarity : 0.004 0.055 6728 Dihedral : 8.439 156.167 5334 Min Nonbonded Distance : 1.743 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer Outliers : 1.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.11), residues: 4795 helix: 0.65 (0.10), residues: 2408 sheet: -1.02 (0.20), residues: 591 loop : -0.80 (0.13), residues: 1796 *********************** 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 1430 residues out of total 4059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 1367 time to evaluate : 4.650 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 outliers start: 63 outliers final: 44 residues processed: 1384 average time/residue: 1.1462 time to fit residues: 2471.9394 Evaluate side-chains 1332 residues out of total 4059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 1288 time to evaluate : 4.573 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 2 residues processed: 44 average time/residue: 0.7318 time to fit residues: 65.5984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 242 optimal weight: 5.9990 chunk 135 optimal weight: 10.0000 chunk 362 optimal weight: 0.0970 chunk 296 optimal weight: 8.9990 chunk 120 optimal weight: 6.9990 chunk 436 optimal weight: 6.9990 chunk 471 optimal weight: 9.9990 chunk 388 optimal weight: 2.9990 chunk 433 optimal weight: 10.0000 chunk 148 optimal weight: 4.9990 chunk 350 optimal weight: 10.0000 overall best weight: 4.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 652 HIS A 711 ASN B 200 GLN C 177 ASN ** C 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 233 GLN F 390 ASN F 606 ASN F 747 GLN H 150 ASN I 159 GLN J 123 GLN K 122 HIS L 41 ASN M 138 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 38586 Z= 0.242 Angle : 0.543 6.987 52137 Z= 0.280 Chirality : 0.040 0.145 5981 Planarity : 0.004 0.050 6728 Dihedral : 8.226 155.290 5334 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer Outliers : 0.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.11), residues: 4795 helix: 0.79 (0.10), residues: 2444 sheet: -0.92 (0.21), residues: 579 loop : -0.65 (0.14), residues: 1772 *********************** 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 1364 residues out of total 4059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 1332 time to evaluate : 4.660 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 outliers start: 32 outliers final: 22 residues processed: 1342 average time/residue: 1.1170 time to fit residues: 2322.9793 Evaluate side-chains 1289 residues out of total 4059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 1267 time to evaluate : 4.686 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 22 outliers final: 1 residues processed: 22 average time/residue: 0.8771 time to fit residues: 40.3777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 431 optimal weight: 9.9990 chunk 328 optimal weight: 10.0000 chunk 226 optimal weight: 9.9990 chunk 48 optimal weight: 7.9990 chunk 208 optimal weight: 10.0000 chunk 293 optimal weight: 10.0000 chunk 438 optimal weight: 9.9990 chunk 463 optimal weight: 7.9990 chunk 228 optimal weight: 10.0000 chunk 415 optimal weight: 7.9990 chunk 125 optimal weight: 10.0000 overall best weight: 8.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 575 ASN ** D 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 556 HIS E 288 HIS ** E 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 558 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 747 GLN F 178 GLN ** F 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 583 ASN F 684 GLN F 688 ASN H 41 ASN ** H 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 159 GLN K 122 HIS M 41 ASN N 81 GLN N 129 GLN N 159 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.3261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.063 38586 Z= 0.438 Angle : 0.610 8.238 52137 Z= 0.322 Chirality : 0.043 0.166 5981 Planarity : 0.004 0.065 6728 Dihedral : 8.416 167.203 5334 Min Nonbonded Distance : 1.714 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer Outliers : 1.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.12), residues: 4795 helix: 0.58 (0.10), residues: 2463 sheet: -0.81 (0.21), residues: 554 loop : -0.82 (0.14), residues: 1778 *********************** 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 1402 residues out of total 4059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 1339 time to evaluate : 4.643 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 outliers start: 63 outliers final: 42 residues processed: 1360 average time/residue: 1.1556 time to fit residues: 2440.1776 Evaluate side-chains 1325 residues out of total 4059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 1283 time to evaluate : 4.570 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 42 outliers final: 1 residues processed: 42 average time/residue: 0.7895 time to fit residues: 65.0308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 386 optimal weight: 9.9990 chunk 263 optimal weight: 0.9980 chunk 6 optimal weight: 30.0000 chunk 345 optimal weight: 40.0000 chunk 191 optimal weight: 5.9990 chunk 395 optimal weight: 9.9990 chunk 320 optimal weight: 50.0000 chunk 0 optimal weight: 40.0000 chunk 236 optimal weight: 2.9990 chunk 416 optimal weight: 5.9990 chunk 117 optimal weight: 3.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 279 ASN C 369 HIS ** C 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 711 ASN ** D 325 GLN ** 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 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 672 GLN H 41 ASN I 34 GLN I 131 GLN J 123 GLN K 41 ASN K 122 HIS L 41 ASN M 123 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.3500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 38586 Z= 0.222 Angle : 0.536 7.401 52137 Z= 0.275 Chirality : 0.040 0.162 5981 Planarity : 0.003 0.052 6728 Dihedral : 8.186 167.344 5334 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer Outliers : 0.84 % 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: 0.00 (0.12), residues: 4795 helix: 0.80 (0.10), residues: 2449 sheet: -0.80 (0.21), residues: 580 loop : -0.72 (0.14), residues: 1766 *********************** 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 1344 residues out of total 4059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 1310 time to evaluate : 5.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 22 residues processed: 1321 average time/residue: 1.1338 time to fit residues: 2319.6117 Evaluate side-chains 1287 residues out of total 4059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 1265 time to evaluate : 4.576 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 22 outliers final: 1 residues processed: 22 average time/residue: 0.7311 time to fit residues: 35.3093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 156 optimal weight: 3.9990 chunk 417 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 272 optimal weight: 6.9990 chunk 114 optimal weight: 9.9990 chunk 464 optimal weight: 9.9990 chunk 385 optimal weight: 5.9990 chunk 215 optimal weight: 9.9990 chunk 38 optimal weight: 20.0000 chunk 153 optimal weight: 5.9990 chunk 243 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 556 HIS B 575 ASN ** C 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 325 GLN ** 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 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 41 ASN K 41 ASN K 122 HIS M 163 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.3710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 38586 Z= 0.285 Angle : 0.544 6.926 52137 Z= 0.281 Chirality : 0.040 0.164 5981 Planarity : 0.004 0.079 6728 Dihedral : 8.118 169.287 5334 Min Nonbonded Distance : 1.745 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer Outliers : 0.74 % 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: -0.00 (0.12), residues: 4795 helix: 0.82 (0.10), residues: 2460 sheet: -0.80 (0.21), residues: 593 loop : -0.76 (0.14), residues: 1742 *********************** 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 1324 residues out of total 4059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 1294 time to evaluate : 5.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 20 residues processed: 1302 average time/residue: 1.1343 time to fit residues: 2285.0976 Evaluate side-chains 1287 residues out of total 4059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 1267 time to evaluate : 4.738 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 20 outliers final: 1 residues processed: 20 average time/residue: 0.8874 time to fit residues: 37.3727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 447 optimal weight: 6.9990 chunk 52 optimal weight: 20.0000 chunk 264 optimal weight: 8.9990 chunk 339 optimal weight: 40.0000 chunk 262 optimal weight: 9.9990 chunk 390 optimal weight: 5.9990 chunk 259 optimal weight: 9.9990 chunk 462 optimal weight: 9.9990 chunk 289 optimal weight: 6.9990 chunk 282 optimal weight: 40.0000 chunk 213 optimal weight: 5.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- 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** ** C 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 325 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 558 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 122 HIS L 41 ASN M 123 GLN N 116 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.3939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.054 38586 Z= 0.350 Angle : 0.567 7.110 52137 Z= 0.295 Chirality : 0.041 0.164 5981 Planarity : 0.004 0.063 6728 Dihedral : 8.166 173.960 5334 Min Nonbonded Distance : 1.730 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer Outliers : 0.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.12), residues: 4795 helix: 0.75 (0.10), residues: 2462 sheet: -0.84 (0.20), residues: 608 loop : -0.88 (0.14), residues: 1725 *********************** 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 1357 residues out of total 4059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 1322 time to evaluate : 4.598 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 outliers start: 35 outliers final: 23 residues processed: 1334 average time/residue: 1.1458 time to fit residues: 2363.9586 Evaluate side-chains 1311 residues out of total 4059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 1288 time to evaluate : 4.605 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 23 outliers final: 1 residues processed: 23 average time/residue: 0.8125 time to fit residues: 38.8011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 286 optimal weight: 30.0000 chunk 184 optimal weight: 6.9990 chunk 276 optimal weight: 10.0000 chunk 139 optimal weight: 6.9990 chunk 90 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 294 optimal weight: 10.0000 chunk 315 optimal weight: 6.9990 chunk 228 optimal weight: 6.9990 chunk 43 optimal weight: 50.0000 chunk 363 optimal weight: 9.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 659 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** ** E 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 558 HIS E 747 GLN ** F 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 131 GLN K 122 HIS K 159 GLN M 123 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.4115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.053 38586 Z= 0.317 Angle : 0.560 6.932 52137 Z= 0.291 Chirality : 0.040 0.161 5981 Planarity : 0.004 0.062 6728 Dihedral : 8.138 173.281 5334 Min Nonbonded Distance : 1.751 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer Outliers : 0.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.12), residues: 4795 helix: 0.77 (0.10), residues: 2463 sheet: -0.85 (0.21), residues: 601 loop : -0.84 (0.14), residues: 1731 *********************** 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 1328 residues out of total 4059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 1306 time to evaluate : 5.723 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 outliers start: 22 outliers final: 15 residues processed: 1310 average time/residue: 1.1665 time to fit residues: 2368.8073 Evaluate side-chains 1299 residues out of total 4059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 1284 time to evaluate : 4.589 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 15 outliers final: 1 residues processed: 15 average time/residue: 0.8422 time to fit residues: 27.7366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 420 optimal weight: 0.0970 chunk 443 optimal weight: 5.9990 chunk 404 optimal weight: 8.9990 chunk 431 optimal weight: 1.9990 chunk 259 optimal weight: 10.0000 chunk 187 optimal weight: 0.7980 chunk 338 optimal weight: 20.0000 chunk 132 optimal weight: 10.0000 chunk 389 optimal weight: 3.9990 chunk 407 optimal weight: 4.9990 chunk 429 optimal weight: 5.9990 overall best weight: 2.3784 ------------------------------------------------------------------------------- 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** ** C 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 747 GLN ** F 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 122 HIS K 150 ASN L 41 ASN ** M 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 123 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.4138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 38586 Z= 0.183 Angle : 0.527 7.849 52137 Z= 0.269 Chirality : 0.039 0.152 5981 Planarity : 0.003 0.064 6728 Dihedral : 7.970 168.929 5334 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer Outliers : 0.30 % 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: 0.14 (0.12), residues: 4795 helix: 0.96 (0.10), residues: 2469 sheet: -0.75 (0.21), residues: 613 loop : -0.74 (0.14), residues: 1713 *********************** 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 1329 residues out of total 4059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 1317 time to evaluate : 4.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 8 residues processed: 1319 average time/residue: 1.1532 time to fit residues: 2358.7494 Evaluate side-chains 1291 residues out of total 4059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 1283 time to evaluate : 4.569 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 8 outliers final: 1 residues processed: 8 average time/residue: 0.7046 time to fit residues: 16.3650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 283 optimal weight: 40.0000 chunk 455 optimal weight: 7.9990 chunk 278 optimal weight: 3.9990 chunk 216 optimal weight: 7.9990 chunk 316 optimal weight: 4.9990 chunk 478 optimal weight: 9.9990 chunk 440 optimal weight: 9.9990 chunk 380 optimal weight: 9.9990 chunk 39 optimal weight: 20.0000 chunk 294 optimal weight: 10.0000 chunk 233 optimal weight: 9.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- 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** C 175 ASN ** C 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 747 GLN ** F 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 34 GLN K 122 HIS K 150 ASN ** M 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 123 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.4299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.051 38586 Z= 0.356 Angle : 0.573 7.582 52137 Z= 0.298 Chirality : 0.041 0.159 5981 Planarity : 0.004 0.067 6728 Dihedral : 8.109 172.689 5334 Min Nonbonded Distance : 1.713 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer Outliers : 0.39 % 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: 0.84 (0.10), residues: 2466 sheet: -0.83 (0.21), residues: 600 loop : -0.82 (0.14), residues: 1729 ********************** 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 1313 residues out of total 4059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 1297 time to evaluate : 4.630 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 outliers start: 16 outliers final: 14 residues processed: 1298 average time/residue: 1.1574 time to fit residues: 2322.1837 Evaluate side-chains 1312 residues out of total 4059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 1298 time to evaluate : 4.601 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 14 outliers final: 1 residues processed: 14 average time/residue: 0.8356 time to fit residues: 26.0918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 302 optimal weight: 20.0000 chunk 405 optimal weight: 3.9990 chunk 116 optimal weight: 10.0000 chunk 351 optimal weight: 0.9990 chunk 56 optimal weight: 30.0000 chunk 105 optimal weight: 6.9990 chunk 381 optimal weight: 9.9990 chunk 159 optimal weight: 8.9990 chunk 391 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 chunk 70 optimal weight: 20.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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** C 178 GLN ** C 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 709 GLN ** E 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 747 GLN ** F 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 41 ASN K 122 HIS K 150 ASN L 41 ASN ** M 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 123 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.155444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.108223 restraints weight = 155762.221| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.93 r_work: 0.3053 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.4371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 38586 Z= 0.263 Angle : 0.553 9.634 52137 Z= 0.285 Chirality : 0.040 0.158 5981 Planarity : 0.004 0.067 6728 Dihedral : 8.038 169.750 5334 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer Outliers : 0.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.12), residues: 4795 helix: 0.86 (0.10), residues: 2475 sheet: -0.87 (0.21), residues: 609 loop : -0.83 (0.14), residues: 1711 =============================================================================== Job complete usr+sys time: 30416.67 seconds wall clock time: 522 minutes 32.22 seconds (31352.22 seconds total)