Starting phenix.real_space_refine on Sun Mar 17 01:49:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uiz_26558/03_2024/7uiz_26558_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uiz_26558/03_2024/7uiz_26558.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uiz_26558/03_2024/7uiz_26558.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uiz_26558/03_2024/7uiz_26558.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uiz_26558/03_2024/7uiz_26558_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uiz_26558/03_2024/7uiz_26558_trim_updated.pdb" } resolution = 3.24 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 33 5.49 5 Mg 10 5.21 5 S 171 5.16 5 C 23909 2.51 5 N 6743 2.21 5 O 7265 1.98 5 H 38390 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 186": "OD1" <-> "OD2" Residue "A GLU 225": "OE1" <-> "OE2" Residue "A ASP 235": "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 ASP 262": "OD1" <-> "OD2" Residue "A GLU 264": "OE1" <-> "OE2" Residue "A PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 334": "OD1" <-> "OD2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 373": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 383": "OE1" <-> "OE2" Residue "A ASP 445": "OD1" <-> "OD2" Residue "A ASP 447": "OD1" <-> "OD2" Residue "A ASP 454": "OD1" <-> "OD2" Residue "A PHE 461": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 484": "OE1" <-> "OE2" Residue "A GLU 503": "OE1" <-> "OE2" Residue "A TYR 524": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 588": "OD1" <-> "OD2" Residue "A ASP 595": "OD1" <-> "OD2" Residue "A GLU 611": "OE1" <-> "OE2" Residue "A ASP 627": "OD1" <-> "OD2" Residue "A GLU 630": "OE1" <-> "OE2" Residue "A GLU 631": "OE1" <-> "OE2" Residue "A PHE 636": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 650": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 656": "OD1" <-> "OD2" Residue "A ASP 674": "OD1" <-> "OD2" Residue "A ASP 736": "OD1" <-> "OD2" Residue "B ASP 235": "OD1" <-> "OD2" Residue "B GLU 238": "OE1" <-> "OE2" Residue "B TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 249": "OD1" <-> "OD2" 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 ASP 334": "OD1" <-> "OD2" Residue "B TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 373": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 388": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 447": "OD1" <-> "OD2" Residue "B PHE 461": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 631": "OE1" <-> "OE2" Residue "B PHE 636": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 640": "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 692": "OE1" <-> "OE2" Residue "C GLU 170": "OE1" <-> "OE2" Residue "C ASP 186": "OD1" <-> "OD2" Residue "C GLU 196": "OE1" <-> "OE2" Residue "C ASP 235": "OD1" <-> "OD2" Residue "C ASP 242": "OD1" <-> "OD2" Residue "C TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 249": "OD1" <-> "OD2" Residue "C TYR 259": "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 GLU 427": "OE1" <-> "OE2" Residue "C ASP 447": "OD1" <-> "OD2" Residue "C TYR 540": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 588": "OD1" <-> "OD2" Residue "C PHE 636": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 665": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 746": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 170": "OE1" <-> "OE2" Residue "D GLU 238": "OE1" <-> "OE2" Residue "D ASP 242": "OD1" <-> "OD2" Residue "D ASP 262": "OD1" <-> "OD2" Residue "D GLU 264": "OE1" <-> "OE2" Residue "D GLU 286": "OE1" <-> "OE2" Residue "D PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 370": "OD1" <-> "OD2" Residue "D TYR 373": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 388": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 391": "OD1" <-> "OD2" Residue "D ASP 400": "OD1" <-> "OD2" Residue "D GLU 438": "OE1" <-> "OE2" 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 GLU 613": "OE1" <-> "OE2" Residue "D GLU 630": "OE1" <-> "OE2" Residue "D PHE 636": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 238": "OE1" <-> "OE2" Residue "E TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 262": "OD1" <-> "OD2" Residue "E ASP 302": "OD1" <-> "OD2" Residue "E TYR 324": "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 ASP 396": "OD1" <-> "OD2" Residue "E PHE 461": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 503": "OE1" <-> "OE2" Residue "E TYR 524": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 565": "OE1" <-> "OE2" Residue "E PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 595": "OD1" <-> "OD2" Residue "E PHE 596": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 611": "OE1" <-> "OE2" 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 PHE 650": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 668": "OE1" <-> "OE2" Residue "E ASP 674": "OD1" <-> "OD2" Residue "E GLU 681": "OE1" <-> "OE2" Residue "E ASP 736": "OD1" <-> "OD2" Residue "E GLU 738": "OE1" <-> "OE2" Residue "F TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 249": "OD1" <-> "OD2" Residue "F PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 285": "OD1" <-> "OD2" Residue "F ASP 302": "OD1" <-> "OD2" Residue "F ASP 334": "OD1" <-> "OD2" Residue "F GLU 352": "OE1" <-> "OE2" Residue "F GLU 353": "OE1" <-> "OE2" Residue "F TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 388": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 396": "OD1" <-> "OD2" Residue "F ASP 447": "OD1" <-> "OD2" Residue "F PHE 461": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 464": "OD1" <-> "OD2" Residue "F GLU 472": "OE1" <-> "OE2" Residue "F GLU 484": "OE1" <-> "OE2" Residue "F PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 503": "OE1" <-> "OE2" Residue "F GLU 515": "OE1" <-> "OE2" Residue "F ASP 520": "OD1" <-> "OD2" Residue "F TYR 524": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 526": "OE1" <-> "OE2" Residue "F ASP 544": "OD1" <-> "OD2" Residue "F ASP 551": "OD1" <-> "OD2" Residue "F ASP 564": "OD1" <-> "OD2" Residue "F PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 595": "OD1" <-> "OD2" Residue "F PHE 596": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 627": "OD1" <-> "OD2" Residue "F PHE 636": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 639": "OE1" <-> "OE2" Residue "F PHE 640": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 651": "OD1" <-> "OD2" Residue "F ASP 663": "OD1" <-> "OD2" Residue "F PHE 665": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 668": "OE1" <-> "OE2" Residue "F ASP 674": "OD1" <-> "OD2" Residue "F GLU 681": "OE1" <-> "OE2" Residue "F GLU 692": "OE1" <-> "OE2" Residue "F TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 710": "OD1" <-> "OD2" Residue "F ASP 727": "OD1" <-> "OD2" Residue "F GLU 738": "OE1" <-> "OE2" Residue "S PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S GLU 15": "OE1" <-> "OE2" Residue "H ARG 12": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ASP 37": "OD1" <-> "OD2" Residue "H GLU 51": "OE1" <-> "OE2" Residue "H TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 78": "OD1" <-> "OD2" Residue "H PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ARG 118": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ASP 134": "OD1" <-> "OD2" Residue "H GLU 136": "OE1" <-> "OE2" Residue "H GLU 141": "OE1" <-> "OE2" Residue "H ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H GLU 151": "OE1" <-> "OE2" Residue "H ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H GLU 169": "OE1" <-> "OE2" Residue "H ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I ARG 12": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I GLU 56": "OE1" <-> "OE2" Residue "I PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I ASP 134": "OD1" <-> "OD2" Residue "I GLU 141": "OE1" <-> "OE2" Residue "I ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I GLU 181": "OE1" <-> "OE2" 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 TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ASP 167": "OD1" <-> "OD2" Residue "J ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J GLU 181": "OE1" <-> "OE2" Residue "J ASP 186": "OD1" <-> "OD2" 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 ASP 134": "OD1" <-> "OD2" Residue "K GLU 136": "OE1" <-> "OE2" Residue "K ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K GLU 151": "OE1" <-> "OE2" Residue "K ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ASP 171": "OD1" <-> "OD2" 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 TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ASP 78": "OD1" <-> "OD2" Residue "L PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ASP 86": "OD1" <-> "OD2" Residue "L PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ARG 118": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ASP 134": "OD1" <-> "OD2" Residue "L GLU 136": "OE1" <-> "OE2" 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 "L GLU 181": "OE1" <-> "OE2" Residue "L TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M GLU 8": "OE1" <-> "OE2" Residue "M ARG 12": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M GLU 14": "OE1" <-> "OE2" Residue "M PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ASP 58": "OD1" <-> "OD2" Residue "M TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M ASP 134": "OD1" <-> "OD2" Residue "M GLU 136": "OE1" <-> "OE2" Residue "M ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M GLU 151": "OE1" <-> "OE2" 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 PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N ARG 12": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N GLU 14": "OE1" <-> "OE2" Residue "N PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N ASP 37": "OD1" <-> "OD2" Residue "N TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N ASP 134": "OD1" <-> "OD2" Residue "N ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ASP 171": "OD1" <-> "OD2" Residue "N PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 76521 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 9098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 9098 Classifications: {'peptide': 577} Link IDs: {'PTRANS': 18, 'TRANS': 558} Chain: "B" Number of atoms: 9141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 580, 9141 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: 9144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 580, 9144 Classifications: {'peptide': 580} Link IDs: {'PTRANS': 18, 'TRANS': 561} Chain: "E" Number of atoms: 9138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 580, 9138 Classifications: {'peptide': 580} Link IDs: {'PTRANS': 18, 'TRANS': 561} Chain: "F" Number of atoms: 9122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 9122 Classifications: {'peptide': 579} Link IDs: {'PTRANS': 18, 'TRANS': 560} Chain: "S" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 396 Classifications: {'peptide': 25} Link IDs: {'PTRANS': 2, 'TRANS': 22} Chain: "H" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 3001 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 7, 'TRANS': 183} Chain: "I" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 3001 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 7, 'TRANS': 183} Chain: "J" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 3001 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 7, 'TRANS': 183} Chain: "K" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 3001 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 7, 'TRANS': 183} Chain: "L" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 3001 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 7, 'TRANS': 183} Chain: "M" Number of atoms: 2977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 2977 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: 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: "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: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 25.49, per 1000 atoms: 0.33 Number of scatterers: 76521 At special positions: 0 Unit cell: (147.9, 152.25, 166.17, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 171 16.00 P 33 15.00 Mg 10 11.99 O 7265 8.00 N 6743 7.00 C 23909 6.00 H 38390 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: 51.00 Conformation dependent library (CDL) restraints added in 6.0 seconds 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8934 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 224 helices and 45 sheets defined 48.3% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.06 Creating SS restraints... Processing helix chain 'A' and resid 176 through 182 Processing helix chain 'A' and resid 192 through 202 Processing helix chain 'A' and resid 220 through 233 removed outlier: 3.901A pdb=" N ALA A 228 " --> pdb=" O ALA A 224 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TRP A 229 " --> pdb=" O GLU A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 255 Processing helix chain 'A' and resid 262 through 274 Processing helix chain 'A' and resid 288 through 291 No H-bonds generated for 'chain 'A' and resid 288 through 291' Processing helix chain 'A' and resid 303 through 313 Proline residue: A 309 - end of helix Processing helix chain 'A' and resid 324 through 333 removed outlier: 3.665A pdb=" N GLU A 332 " --> pdb=" O SER A 328 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LYS A 333 " --> pdb=" O ASN A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 340 Processing helix chain 'A' and resid 351 through 369 removed outlier: 3.608A pdb=" N GLN A 356 " --> pdb=" O GLU A 352 " (cutoff:3.500A) Proline residue: A 363 - end of helix Processing helix chain 'A' and resid 375 through 388 removed outlier: 3.569A pdb=" N ARG A 379 " --> pdb=" O ALA A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 411 removed outlier: 3.702A pdb=" N ILE A 399 " --> pdb=" O PRO A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 434 removed outlier: 3.638A pdb=" N SER A 428 " --> pdb=" O ALA A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 450 Processing helix chain 'A' and resid 452 through 459 Processing helix chain 'A' and resid 464 through 479 removed outlier: 3.531A pdb=" N ALA A 477 " --> pdb=" O ALA A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 512 removed outlier: 3.528A pdb=" N SER A 509 " --> pdb=" O THR A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 533 removed outlier: 4.113A pdb=" N ARG A 532 " --> pdb=" O HIS A 528 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N LEU A 533 " --> pdb=" O THR A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 555 Processing helix chain 'A' and resid 566 through 568 No H-bonds generated for 'chain 'A' and resid 566 through 568' Processing helix chain 'A' and resid 571 through 583 removed outlier: 3.506A pdb=" N LEU A 578 " --> pdb=" O ASN A 575 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N MET A 581 " --> pdb=" O LEU A 578 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN A 583 " --> pdb=" O VAL A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 609 No H-bonds generated for 'chain 'A' and resid 607 through 609' Processing helix chain 'A' and resid 630 through 635 removed outlier: 3.927A 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 676 removed outlier: 3.726A pdb=" N HIS A 659 " --> pdb=" O THR A 655 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLN A 660 " --> pdb=" O ASP A 656 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLN A 675 " --> pdb=" O VAL A 671 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LYS A 676 " --> pdb=" O GLN A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 684 through 694 removed outlier: 3.563A pdb=" N GLY A 694 " --> pdb=" O LEU A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 711 removed outlier: 3.553A pdb=" N ARG A 706 " --> pdb=" O ARG A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 721 Processing helix chain 'A' and resid 724 through 726 No H-bonds generated for 'chain 'A' and resid 724 through 726' Processing helix chain 'B' and resid 176 through 182 removed outlier: 3.887A 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: 4.178A pdb=" N ALA B 228 " --> pdb=" O ALA B 224 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TRP B 229 " --> pdb=" O GLU B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 253 No H-bonds generated for 'chain 'B' and resid 250 through 253' Processing helix chain 'B' and resid 262 through 277 removed outlier: 3.569A pdb=" N GLN B 273 " --> pdb=" O ALA B 269 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASP B 277 " --> pdb=" O GLN B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 292 Processing helix chain 'B' and resid 303 through 313 Proline residue: B 309 - end of helix Processing helix chain 'B' and resid 324 through 329 Processing helix chain 'B' and resid 335 through 340 removed outlier: 3.659A pdb=" N ARG B 340 " --> pdb=" O ALA B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 369 removed outlier: 4.089A 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: 3.622A pdb=" N ARG B 379 " --> pdb=" O ALA B 375 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N VAL B 386 " --> pdb=" O VAL B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 410 Processing helix chain 'B' and resid 423 through 434 Processing helix chain 'B' and resid 443 through 451 removed outlier: 3.734A pdb=" N THR B 448 " --> pdb=" O SER B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 459 removed outlier: 3.534A pdb=" N LEU B 459 " --> pdb=" O ARG B 455 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 455 through 459' Processing helix chain 'B' and resid 464 through 479 Processing helix chain 'B' and resid 503 through 512 removed outlier: 3.552A pdb=" N SER B 509 " --> pdb=" O THR B 505 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS B 510 " --> pdb=" O VAL B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 524 Processing helix chain 'B' and resid 527 through 534 removed outlier: 3.516A pdb=" N SER B 531 " --> pdb=" O HIS B 528 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ILE B 534 " --> pdb=" O SER B 531 " (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 582 removed outlier: 3.873A pdb=" N GLN B 579 " --> pdb=" O ASN B 575 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL B 580 " --> pdb=" O ILE B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 613 Processing helix chain 'B' and resid 625 through 635 Processing helix chain 'B' and resid 638 through 642 Processing helix chain 'B' and resid 655 through 676 removed outlier: 3.513A pdb=" N HIS B 659 " --> pdb=" O THR B 655 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN B 660 " --> pdb=" O ASP B 656 " (cutoff:3.500A) removed outlier: 3.723A 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: 3.533A pdb=" N VAL B 707 " --> pdb=" O MET B 704 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE B 708 " --> pdb=" O ALA B 705 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN B 711 " --> pdb=" O ILE B 708 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 721 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: 3.885A pdb=" N ALA C 228 " --> pdb=" O ALA C 224 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TRP C 229 " --> pdb=" O GLU C 225 " (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 removed outlier: 3.589A pdb=" N LEU C 274 " --> pdb=" O LEU C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 291 removed outlier: 3.578A pdb=" N ILE C 291 " --> pdb=" O HIS C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 311 Proline residue: C 309 - end of helix Processing helix chain 'C' and resid 324 through 329 Processing helix chain 'C' and resid 331 through 333 No H-bonds generated for 'chain 'C' and resid 331 through 333' Processing helix chain 'C' and resid 335 through 340 Processing helix chain 'C' and resid 351 through 369 removed outlier: 3.647A pdb=" N GLN C 356 " --> pdb=" O GLU C 352 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE C 357 " --> pdb=" O GLU C 353 " (cutoff:3.500A) Proline residue: C 363 - end of helix removed outlier: 3.511A pdb=" N ALA C 367 " --> pdb=" O PRO C 363 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N HIS C 368 " --> pdb=" O LYS C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 388 removed outlier: 3.524A pdb=" N ARG C 379 " --> pdb=" O ALA C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 411 removed outlier: 3.502A pdb=" N VAL C 401 " --> pdb=" O LYS C 397 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA C 409 " --> pdb=" O ALA C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 423 through 434 Processing helix chain 'C' and resid 443 through 450 removed outlier: 3.568A pdb=" N THR C 448 " --> pdb=" O SER C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 458 Processing helix chain 'C' and resid 464 through 479 Processing helix chain 'C' and resid 503 through 512 removed outlier: 3.627A pdb=" N SER C 509 " --> pdb=" O THR C 505 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LYS C 510 " --> pdb=" O VAL C 506 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA C 511 " --> pdb=" O GLN C 507 " (cutoff:3.500A) Processing helix chain 'C' and resid 527 through 534 removed outlier: 3.823A pdb=" N ILE C 534 " --> pdb=" O SER C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 543 No H-bonds generated for 'chain 'C' and resid 541 through 543' Processing helix chain 'C' and resid 548 through 555 Processing helix chain 'C' and resid 571 through 582 removed outlier: 3.969A pdb=" N GLN C 579 " --> pdb=" O ILE C 576 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N MET C 581 " --> pdb=" O LEU C 578 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASP C 582 " --> pdb=" O GLN C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 609 through 613 Processing helix chain 'C' and resid 624 through 635 removed outlier: 3.593A pdb=" N ALA C 628 " --> pdb=" O SER C 625 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N MET C 629 " --> pdb=" O THR C 626 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE C 635 " --> pdb=" O ILE C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 638 through 643 removed outlier: 3.645A pdb=" N ARG C 643 " --> pdb=" O GLU C 639 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 676 removed outlier: 3.673A pdb=" N HIS C 659 " --> pdb=" O THR C 655 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLN C 660 " --> pdb=" O ASP C 656 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS C 676 " --> pdb=" O GLN C 672 " (cutoff:3.500A) Processing helix chain 'C' and resid 684 through 693 Processing helix chain 'C' and resid 703 through 711 removed outlier: 3.599A pdb=" N VAL C 707 " --> pdb=" O MET C 704 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ILE C 708 " --> pdb=" O ALA C 705 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ASP C 710 " --> pdb=" O VAL C 707 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN C 711 " --> pdb=" O ILE C 708 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 721 Processing helix chain 'C' and resid 724 through 726 No H-bonds generated for 'chain 'C' and resid 724 through 726' Processing helix chain 'D' and resid 176 through 182 removed outlier: 3.641A pdb=" N ARG D 181 " --> pdb=" O ASN D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 202 Processing helix chain 'D' and resid 220 through 233 removed outlier: 4.047A pdb=" N ALA D 228 " --> pdb=" O ALA D 224 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TRP D 229 " --> pdb=" O GLU D 225 " (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: 3.576A pdb=" N LYS D 272 " --> pdb=" O LYS D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 289 No H-bonds generated for 'chain 'D' and resid 287 through 289' Processing helix chain 'D' and resid 303 through 313 Proline residue: D 309 - end of helix removed outlier: 3.543A pdb=" N SER D 312 " --> pdb=" O LYS D 308 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER D 313 " --> pdb=" O PRO D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 329 Processing helix chain 'D' and resid 335 through 340 removed outlier: 3.663A pdb=" N ARG D 340 " --> pdb=" O ALA D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 369 removed outlier: 3.966A pdb=" N GLN D 356 " --> pdb=" O GLU D 352 " (cutoff:3.500A) Proline residue: D 363 - end of helix removed outlier: 3.510A pdb=" N HIS D 368 " --> pdb=" O LYS D 364 " (cutoff:3.500A) 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 444 through 459 removed outlier: 4.089A pdb=" N GLY D 453 " --> pdb=" O LYS D 450 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG D 455 " --> pdb=" O LEU D 452 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU D 456 " --> pdb=" O GLY D 453 " (cutoff:3.500A) Processing helix chain 'D' and resid 464 through 479 Processing helix chain 'D' and resid 504 through 512 removed outlier: 3.740A pdb=" N LYS D 510 " --> pdb=" O VAL D 506 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA D 511 " --> pdb=" O GLN D 507 " (cutoff:3.500A) Processing helix chain 'D' and resid 527 through 534 Processing helix chain 'D' and resid 548 through 555 Processing helix chain 'D' and resid 566 through 568 No H-bonds generated for 'chain 'D' and resid 566 through 568' Processing helix chain 'D' and resid 571 through 582 removed outlier: 3.546A pdb=" N ASN D 575 " --> pdb=" O ASP D 572 " (cutoff:3.500A) removed outlier: 4.057A 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 626 through 635 removed outlier: 3.787A pdb=" N GLU D 630 " --> pdb=" O ASP D 627 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU D 631 " --> pdb=" O ALA D 628 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS D 633 " --> pdb=" O GLU D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 638 through 643 removed outlier: 3.681A pdb=" N ARG D 643 " --> pdb=" O GLU D 639 " (cutoff:3.500A) Processing helix chain 'D' and resid 655 through 676 removed outlier: 3.617A pdb=" N GLN D 660 " --> pdb=" O ASP D 656 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN D 675 " --> pdb=" O VAL D 671 " (cutoff:3.500A) removed outlier: 4.010A 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: 3.670A pdb=" N VAL D 707 " --> pdb=" O MET D 704 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASN D 711 " --> pdb=" O ILE D 708 " (cutoff:3.500A) Processing helix chain 'D' and resid 713 through 721 removed outlier: 3.699A pdb=" N ASN D 718 " --> pdb=" O LYS D 714 " (cutoff:3.500A) removed outlier: 3.732A 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: 3.536A 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 222 through 233 removed outlier: 3.676A pdb=" N ALA E 228 " --> pdb=" O ALA E 224 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 240 No H-bonds generated for 'chain 'E' and resid 238 through 240' Processing helix chain 'E' and resid 250 through 254 Processing helix chain 'E' and resid 262 through 276 Processing helix chain 'E' and resid 287 through 293 removed outlier: 3.511A pdb=" N ILE E 291 " --> pdb=" O HIS E 288 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA E 293 " --> pdb=" O ILE E 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 312 removed outlier: 3.535A pdb=" N ILE E 307 " --> pdb=" O ALA E 303 " (cutoff:3.500A) Proline residue: E 309 - end of helix Processing helix chain 'E' and resid 324 through 328 Processing helix chain 'E' and resid 335 through 340 removed outlier: 3.582A pdb=" N ARG E 340 " --> pdb=" O ALA E 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 369 removed outlier: 3.592A 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: 3.522A pdb=" N VAL E 382 " --> pdb=" O VAL E 378 " (cutoff:3.500A) Processing helix chain 'E' and resid 394 through 411 removed outlier: 3.579A pdb=" N GLY E 406 " --> pdb=" O ILE E 402 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU E 411 " --> pdb=" O ALA E 407 " (cutoff:3.500A) Processing helix chain 'E' and resid 423 through 434 removed outlier: 3.528A pdb=" N SER E 428 " --> pdb=" O ALA E 424 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL E 429 " --> pdb=" O ASP E 425 " (cutoff:3.500A) 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: 3.663A pdb=" N LEU E 470 " --> pdb=" O ALA E 466 " (cutoff:3.500A) Processing helix chain 'E' and resid 503 through 512 Processing helix chain 'E' and resid 527 through 534 removed outlier: 3.966A pdb=" N VAL E 530 " --> pdb=" O ARG E 527 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER E 531 " --> pdb=" O HIS E 528 " (cutoff:3.500A) Processing helix chain 'E' and resid 548 through 555 Processing helix chain 'E' and resid 566 through 568 No H-bonds generated for 'chain 'E' and resid 566 through 568' Processing helix chain 'E' and resid 571 through 583 removed outlier: 3.549A pdb=" N ILE E 576 " --> pdb=" O ASP E 572 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLN E 579 " --> pdb=" O ASN E 575 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL E 580 " --> pdb=" O ILE E 576 " (cutoff:3.500A) Processing helix chain 'E' and resid 609 through 613 Processing helix chain 'E' and resid 627 through 635 removed outlier: 3.595A pdb=" N ILE E 632 " --> pdb=" O ALA E 628 " (cutoff:3.500A) Processing helix chain 'E' and resid 638 through 643 Processing helix chain 'E' and resid 655 through 674 removed outlier: 3.700A pdb=" N HIS E 659 " --> pdb=" O THR E 655 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASP E 663 " --> pdb=" O HIS E 659 " (cutoff:3.500A) Processing helix chain 'E' and resid 684 through 694 removed outlier: 3.531A pdb=" N GLU E 692 " --> pdb=" O ASN E 688 " (cutoff:3.500A) Processing helix chain 'E' and resid 702 through 711 removed outlier: 3.575A pdb=" N ALA E 705 " --> pdb=" O ARG E 702 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL E 707 " --> pdb=" O MET E 704 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE E 708 " --> pdb=" O ALA E 705 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASN E 711 " --> pdb=" O ILE E 708 " (cutoff:3.500A) Processing helix chain 'E' and resid 713 through 721 removed outlier: 3.519A pdb=" N ASN E 718 " --> pdb=" O LYS E 714 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU E 721 " --> pdb=" O ALA E 717 " (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 Processing helix chain 'F' and resid 192 through 202 removed outlier: 3.543A pdb=" N ARG F 197 " --> pdb=" O LYS F 193 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA F 198 " --> pdb=" O GLU F 194 " (cutoff:3.500A) Processing helix chain 'F' and resid 220 through 233 Processing helix chain 'F' and resid 250 through 254 Processing helix chain 'F' and resid 262 through 276 Processing helix chain 'F' and resid 287 through 289 No H-bonds generated for 'chain 'F' and resid 287 through 289' Processing helix chain 'F' and resid 305 through 313 Proline residue: F 309 - end of helix Processing helix chain 'F' and resid 324 through 327 No H-bonds generated for 'chain 'F' and resid 324 through 327' Processing helix chain 'F' and resid 330 through 333 No H-bonds generated for 'chain 'F' and resid 330 through 333' Processing helix chain 'F' and resid 335 through 340 Processing helix chain 'F' and resid 351 through 369 removed outlier: 3.568A pdb=" N GLN F 356 " --> pdb=" O GLU F 352 " (cutoff:3.500A) Proline residue: F 363 - end of helix Processing helix chain 'F' and resid 375 through 388 removed outlier: 3.679A pdb=" N VAL F 382 " --> pdb=" O VAL F 378 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU F 383 " --> pdb=" O ARG F 379 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS F 387 " --> pdb=" O GLU F 383 " (cutoff:3.500A) Processing helix chain 'F' and resid 394 through 411 Processing helix chain 'F' and resid 423 through 434 removed outlier: 3.762A pdb=" N SER F 428 " --> pdb=" O ALA F 424 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N VAL F 429 " --> pdb=" O ASP F 425 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG F 432 " --> pdb=" O SER F 428 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE F 433 " --> pdb=" O VAL F 429 " (cutoff:3.500A) Processing helix chain 'F' and resid 438 through 441 No H-bonds generated for 'chain 'F' and resid 438 through 441' Processing helix chain 'F' and resid 445 through 450 Processing helix chain 'F' and resid 452 through 459 Processing helix chain 'F' and resid 464 through 478 removed outlier: 3.542A pdb=" N GLU F 472 " --> pdb=" O GLU F 468 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA F 477 " --> pdb=" O ALA F 473 " (cutoff:3.500A) Processing helix chain 'F' and resid 501 through 512 removed outlier: 4.007A pdb=" N THR F 505 " --> pdb=" O LYS F 501 " (cutoff:3.500A) Processing helix chain 'F' and resid 527 through 534 removed outlier: 3.998A pdb=" N SER F 531 " --> pdb=" O ARG F 527 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ARG F 532 " --> pdb=" O HIS F 528 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU F 533 " --> pdb=" O THR F 529 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ILE F 534 " --> pdb=" O VAL F 530 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 527 through 534' Processing helix chain 'F' and resid 548 through 555 Processing helix chain 'F' and resid 571 through 583 removed outlier: 3.656A pdb=" N ASN F 575 " --> pdb=" O PRO F 571 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE F 576 " --> pdb=" O ASP F 572 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU F 577 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL F 580 " --> pdb=" O ILE F 576 " (cutoff:3.500A) Processing helix chain 'F' and resid 609 through 613 Processing helix chain 'F' and resid 628 through 635 Processing helix chain 'F' and resid 638 through 643 Processing helix chain 'F' and resid 655 through 674 removed outlier: 3.595A pdb=" N HIS F 659 " --> pdb=" O THR F 655 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLN F 660 " --> pdb=" O ASP F 656 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL F 661 " --> pdb=" O VAL F 657 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE F 665 " --> pdb=" O VAL F 661 " (cutoff:3.500A) Processing helix chain 'F' and resid 684 through 694 removed outlier: 3.686A pdb=" N ASN F 688 " --> pdb=" O GLN F 684 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TRP F 689 " --> pdb=" O GLU F 685 " (cutoff:3.500A) Processing helix chain 'F' and resid 700 through 721 Proline residue: F 703 - end of helix removed outlier: 3.702A pdb=" N ILE F 708 " --> pdb=" O ALA F 705 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASP F 710 " --> pdb=" O VAL F 707 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASN F 711 " --> pdb=" O ILE F 708 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU F 712 " --> pdb=" O GLN F 709 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N LYS F 713 " --> pdb=" O ASP F 710 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N LYS F 714 " --> pdb=" O ASN F 711 " (cutoff:3.500A) Proline residue: F 715 - end of helix removed outlier: 3.535A pdb=" N LEU F 721 " --> pdb=" O ASN F 718 " (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: 3.611A pdb=" N GLU H 26 " --> pdb=" O ARG H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 53 Processing helix chain 'H' and resid 70 through 82 removed outlier: 3.937A pdb=" N SER H 75 " --> pdb=" O THR H 71 " (cutoff:3.500A) removed outlier: 3.659A 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: 3.555A pdb=" N LEU H 143 " --> pdb=" O ALA H 139 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS H 144 " --> pdb=" O ARG H 140 " (cutoff:3.500A) Processing helix chain 'H' and resid 161 through 168 Processing helix chain 'H' and resid 176 through 182 removed outlier: 3.745A pdb=" N VAL H 180 " --> pdb=" O ALA H 176 " (cutoff:3.500A) Processing helix chain 'I' and resid 19 through 25 Processing helix chain 'I' and resid 37 through 53 removed outlier: 3.715A pdb=" N ALA I 52 " --> pdb=" O LEU I 48 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU I 53 " --> pdb=" O PHE I 49 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 82 removed outlier: 3.776A pdb=" N SER I 75 " --> pdb=" O THR I 71 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE I 76 " --> pdb=" O ALA I 72 " (cutoff:3.500A) Processing helix chain 'I' and resid 97 through 104 Processing helix chain 'I' and resid 132 through 157 removed outlier: 3.520A pdb=" N LEU I 155 " --> pdb=" O GLU I 151 " (cutoff:3.500A) Processing helix chain 'I' and resid 161 through 169 Processing helix chain 'I' and resid 176 through 182 removed outlier: 3.502A pdb=" N GLU I 181 " --> pdb=" O PRO I 177 " (cutoff:3.500A) Processing helix chain 'J' and resid 19 through 26 removed outlier: 3.782A pdb=" N GLU J 26 " --> pdb=" O ARG J 22 " (cutoff:3.500A) Processing helix chain 'J' and resid 37 through 53 removed outlier: 3.700A pdb=" N LEU J 42 " --> pdb=" O HIS J 38 " (cutoff:3.500A) Processing helix chain 'J' and resid 70 through 82 removed outlier: 3.939A pdb=" N SER J 75 " --> pdb=" O THR J 71 " (cutoff:3.500A) removed outlier: 4.241A 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 169 Processing helix chain 'J' and resid 176 through 181 Processing helix chain 'K' and resid 19 through 26 removed outlier: 3.597A pdb=" N LEU K 23 " --> pdb=" O ILE K 19 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU K 26 " --> pdb=" O ARG K 22 " (cutoff:3.500A) Processing helix chain 'K' and resid 37 through 53 removed outlier: 3.531A pdb=" N LEU K 42 " --> pdb=" O HIS K 38 " (cutoff:3.500A) Processing helix chain 'K' and resid 70 through 82 removed outlier: 3.620A pdb=" N SER K 75 " --> pdb=" O THR K 71 " (cutoff:3.500A) Processing helix chain 'K' and resid 100 through 105 Processing helix chain 'K' and resid 132 through 157 removed outlier: 3.701A pdb=" N ILE K 137 " --> pdb=" O THR K 133 " (cutoff:3.500A) Processing helix chain 'K' and resid 161 through 168 Processing helix chain 'K' and resid 176 through 182 removed outlier: 3.906A pdb=" N VAL K 180 " --> pdb=" O ALA K 176 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLU K 181 " --> pdb=" O PRO K 177 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 26 removed outlier: 3.649A 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: 4.016A pdb=" N SER L 75 " --> pdb=" O THR L 71 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ILE L 76 " --> pdb=" O ALA L 72 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR L 77 " --> pdb=" O GLY L 73 " (cutoff:3.500A) Processing helix chain 'L' and resid 97 through 104 Processing helix chain 'L' and resid 132 through 157 removed outlier: 3.540A pdb=" N ILE L 137 " --> pdb=" O THR L 133 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU L 141 " --> pdb=" O ILE L 137 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE L 142 " --> pdb=" O HIS L 138 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASN L 150 " --> pdb=" O LYS L 146 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N HIS L 156 " --> pdb=" O LEU L 152 " (cutoff:3.500A) Processing helix chain 'L' and resid 161 through 168 Processing helix chain 'L' and resid 176 through 182 Processing helix chain 'M' and resid 19 through 25 Processing helix chain 'M' and resid 37 through 53 removed outlier: 3.875A pdb=" N ASN M 41 " --> pdb=" O ASP M 37 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU M 42 " --> pdb=" O HIS M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 70 through 81 removed outlier: 3.567A pdb=" N SER M 75 " --> pdb=" O THR M 71 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ILE M 76 " --> pdb=" O ALA M 72 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLN M 81 " --> pdb=" O TYR M 77 " (cutoff:3.500A) Processing helix chain 'M' and resid 97 through 103 Processing helix chain 'M' and resid 132 through 157 removed outlier: 3.625A pdb=" N LEU M 143 " --> pdb=" O ALA M 139 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS M 144 " --> pdb=" O ARG M 140 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N HIS M 156 " --> pdb=" O LEU M 152 " (cutoff:3.500A) Processing helix chain 'M' and resid 161 through 168 Processing helix chain 'M' and resid 176 through 182 Processing helix chain 'N' and resid 19 through 26 removed outlier: 3.500A pdb=" N LYS N 25 " --> pdb=" O SER N 21 " (cutoff:3.500A) removed outlier: 3.771A 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: 3.926A pdb=" N SER N 75 " --> pdb=" O THR N 71 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ILE N 76 " --> pdb=" O ALA N 72 " (cutoff:3.500A) Processing helix chain 'N' and resid 97 through 104 Processing helix chain 'N' and resid 132 through 157 Processing helix chain 'N' and resid 161 through 169 removed outlier: 3.661A pdb=" N GLU N 169 " --> pdb=" O GLU N 165 " (cutoff:3.500A) Processing helix chain 'N' and resid 176 through 182 removed outlier: 3.709A pdb=" N VAL N 180 " --> pdb=" O ALA N 176 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU N 181 " --> pdb=" O PRO N 177 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 173 through 175 Processing sheet with id= B, first strand: chain 'A' and resid 209 through 211 Processing sheet with id= C, first strand: chain 'A' and resid 646 through 650 removed outlier: 3.724A pdb=" N ASN A 646 " --> pdb=" O SER A 490 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU A 492 " --> pdb=" O ASN A 646 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA A 494 " --> pdb=" O ILE A 648 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N LEU A 601 " --> pdb=" O PHE A 491 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N PHE A 493 " --> pdb=" O LEU A 601 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N MET A 603 " --> pdb=" O PHE A 493 " (cutoff:3.500A) removed outlier: 8.930A pdb=" N GLY A 495 " --> pdb=" O MET A 603 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N THR A 605 " --> pdb=" O GLY A 495 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N GLU A 515 " --> pdb=" O VAL A 560 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N LEU A 562 " --> pdb=" O GLU A 515 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LEU A 517 " --> pdb=" O LEU A 562 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N ASP A 564 " --> pdb=" O LEU A 517 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N PHE A 519 " --> pdb=" O ASP A 564 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 585 through 587 Processing sheet with id= E, first strand: chain 'A' and resid 679 through 682 Processing sheet with id= F, first strand: chain 'B' and resid 341 through 345 removed outlier: 7.067A pdb=" N ASN B 209 " --> pdb=" O GLN B 342 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N ILE B 344 " --> pdb=" O ASN B 209 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N LEU B 211 " --> pdb=" O ILE B 344 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N VAL B 318 " --> pdb=" O PRO B 210 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N LEU B 212 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N GLY B 320 " --> pdb=" O LEU B 212 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LEU B 282 " --> pdb=" O ILE B 319 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N SER B 321 " --> pdb=" O LEU B 282 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N ILE B 284 " --> pdb=" O SER B 321 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 646 through 650 removed outlier: 3.670A pdb=" N ALA B 494 " --> pdb=" O ILE B 648 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU B 601 " --> pdb=" O PHE B 491 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N PHE B 493 " --> pdb=" O LEU B 601 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N MET B 603 " --> pdb=" O PHE B 493 " (cutoff:3.500A) removed outlier: 8.617A pdb=" N GLY B 495 " --> pdb=" O MET B 603 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 585 through 587 removed outlier: 3.597A pdb=" N LEU B 586 " --> pdb=" O ALA B 594 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 680 through 682 removed outlier: 6.438A pdb=" N VAL B 731 " --> pdb=" O GLU B 681 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLU B 741 " --> pdb=" O ASP B 736 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 173 through 175 removed outlier: 4.878A pdb=" N ASP C 285 " --> pdb=" O LEU C 248 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ARG C 317 " --> pdb=" O LEU C 282 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N ILE C 284 " --> pdb=" O ARG C 317 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ILE C 319 " --> pdb=" O ILE C 284 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N GLN C 342 " --> pdb=" O LEU C 211 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL C 213 " --> pdb=" O GLN C 342 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ILE C 344 " --> pdb=" O VAL C 213 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 489 through 494 removed outlier: 4.261A pdb=" N GLY C 489 " --> pdb=" O VAL C 599 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N ALA C 559 " --> pdb=" O VAL C 600 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N VAL C 602 " --> pdb=" O ALA C 559 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N LEU C 561 " --> pdb=" O VAL C 602 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N THR C 604 " --> pdb=" O LEU C 561 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU C 563 " --> pdb=" O THR C 604 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N GLU C 515 " --> pdb=" O VAL C 560 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N LEU C 562 " --> pdb=" O GLU C 515 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU C 517 " --> pdb=" O LEU C 562 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N ASP C 564 " --> pdb=" O LEU C 517 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N PHE C 519 " --> pdb=" O ASP C 564 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 585 through 587 Processing sheet with id= M, first strand: chain 'C' and resid 679 through 682 removed outlier: 3.733A pdb=" N GLU C 741 " --> pdb=" O ASP C 736 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 173 through 175 removed outlier: 4.806A pdb=" N ASP D 285 " --> pdb=" O LEU D 248 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER D 321 " --> pdb=" O ILE D 284 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N GLN D 342 " --> pdb=" O LEU D 211 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL D 213 " --> pdb=" O GLN D 342 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N ILE D 344 " --> pdb=" O VAL D 213 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 489 through 494 removed outlier: 4.229A pdb=" N GLY D 489 " --> pdb=" O VAL D 599 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ALA D 559 " --> pdb=" O VAL D 600 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N VAL D 602 " --> pdb=" O ALA D 559 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LEU D 561 " --> pdb=" O VAL D 602 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N THR D 604 " --> pdb=" O LEU D 561 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N LEU D 563 " --> pdb=" O THR D 604 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N GLU D 515 " --> pdb=" O VAL D 560 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N LEU D 562 " --> pdb=" O GLU D 515 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU D 517 " --> pdb=" O LEU D 562 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N ASP D 564 " --> pdb=" O LEU D 517 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N PHE D 519 " --> pdb=" O ASP D 564 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 680 through 682 removed outlier: 6.316A pdb=" N VAL D 731 " --> pdb=" O GLU D 681 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASP D 736 " --> pdb=" O GLU D 741 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLU D 741 " --> pdb=" O ASP D 736 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 173 through 175 removed outlier: 7.011A pdb=" N ILE E 281 " --> pdb=" O TYR E 246 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N LEU E 248 " --> pdb=" O ILE E 281 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N PHE E 283 " --> pdb=" O LEU E 248 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ARG E 317 " --> pdb=" O LEU E 282 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N ILE E 284 " --> pdb=" O ARG E 317 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ILE E 319 " --> pdb=" O ILE E 284 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N GLN E 342 " --> pdb=" O LEU E 211 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N VAL E 213 " --> pdb=" O GLN E 342 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N ILE E 344 " --> pdb=" O VAL E 213 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 646 through 649 removed outlier: 3.520A pdb=" N ASN E 646 " --> pdb=" O SER E 490 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU E 492 " --> pdb=" O ASN E 646 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU E 601 " --> pdb=" O PHE E 491 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N PHE E 493 " --> pdb=" O LEU E 601 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N MET E 603 " --> pdb=" O PHE E 493 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL E 600 " --> pdb=" O ALA E 559 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N GLU E 515 " --> pdb=" O VAL E 560 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N LEU E 562 " --> pdb=" O GLU E 515 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU E 517 " --> pdb=" O LEU E 562 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N ASP E 564 " --> pdb=" O LEU E 517 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N PHE E 519 " --> pdb=" O ASP E 564 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 585 through 587 removed outlier: 3.564A pdb=" N LEU E 586 " --> pdb=" O ALA E 594 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'F' and resid 210 through 213 removed outlier: 5.975A pdb=" N GLN F 342 " --> pdb=" O LEU F 211 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL F 213 " --> pdb=" O GLN F 342 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N ILE F 344 " --> pdb=" O VAL F 213 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'F' and resid 244 through 248 removed outlier: 6.815A pdb=" N ARG F 317 " --> pdb=" O LEU F 282 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N ILE F 284 " --> pdb=" O ARG F 317 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N ILE F 319 " --> pdb=" O ILE F 284 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'F' and resid 646 through 650 removed outlier: 4.014A pdb=" N LEU F 492 " --> pdb=" O ASN F 646 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE F 650 " --> pdb=" O ALA F 494 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE F 491 " --> pdb=" O LEU F 601 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY F 495 " --> pdb=" O THR F 605 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N VAL F 602 " --> pdb=" O ALA F 559 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N LEU F 561 " --> pdb=" O VAL F 602 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N THR F 604 " --> pdb=" O LEU F 561 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N LEU F 563 " --> pdb=" O THR F 604 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N GLU F 515 " --> pdb=" O VAL F 560 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N LEU F 562 " --> pdb=" O GLU F 515 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N LEU F 517 " --> pdb=" O LEU F 562 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N ASP F 564 " --> pdb=" O LEU F 517 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N PHE F 519 " --> pdb=" O ASP F 564 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'F' and resid 585 through 587 removed outlier: 3.553A pdb=" N ALA F 594 " --> pdb=" O LEU F 586 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'F' and resid 732 through 735 removed outlier: 3.506A pdb=" N THR F 732 " --> pdb=" O GLY F 745 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'H' and resid 5 through 8 removed outlier: 3.573A pdb=" N ARG H 15 " --> pdb=" O GLU H 8 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'H' and resid 28 through 32 removed outlier: 6.350A pdb=" N TYR H 60 " --> pdb=" O ILE H 29 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N LEU H 31 " --> pdb=" O TYR H 60 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N TYR H 62 " --> pdb=" O LEU H 31 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'H' and resid 118 through 121 Processing sheet with id= AB, first strand: chain 'I' and resid 5 through 9 Processing sheet with id= AC, first strand: chain 'I' and resid 28 through 32 removed outlier: 6.510A pdb=" N TYR I 60 " --> pdb=" O ILE I 29 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N LEU I 31 " --> pdb=" O TYR I 60 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N TYR I 62 " --> pdb=" O LEU I 31 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'I' and resid 118 through 121 Processing sheet with id= AE, first strand: chain 'J' and resid 5 through 9 Processing sheet with id= AF, first strand: chain 'J' and resid 28 through 32 removed outlier: 6.499A pdb=" N TYR J 60 " --> pdb=" O ILE J 29 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N LEU J 31 " --> pdb=" O TYR J 60 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N TYR J 62 " --> pdb=" O LEU J 31 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N SER J 88 " --> pdb=" O LEU J 61 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N ILE J 63 " --> pdb=" O SER J 88 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ILE J 90 " --> pdb=" O ILE J 63 " (cutoff:3.500A) No H-bonds generated for sheet with id= AF Processing sheet with id= AG, first strand: chain 'J' and resid 119 through 121 Processing sheet with id= AH, first strand: chain 'K' and resid 5 through 9 Processing sheet with id= AI, first strand: chain 'K' and resid 28 through 32 removed outlier: 6.499A pdb=" N TYR K 60 " --> pdb=" O ILE K 29 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N LEU K 31 " --> pdb=" O TYR K 60 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N TYR K 62 " --> pdb=" O LEU K 31 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N CYS K 91 " --> pdb=" O PHE K 112 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'K' and resid 118 through 121 removed outlier: 3.531A pdb=" N ILE K 121 " --> pdb=" O ARG K 172 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'L' and resid 5 through 9 Processing sheet with id= AL, first strand: chain 'L' and resid 28 through 31 removed outlier: 6.833A pdb=" N TYR L 60 " --> pdb=" O ILE L 29 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N LEU L 31 " --> pdb=" O TYR L 60 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N TYR L 62 " --> pdb=" O LEU L 31 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'L' and resid 118 through 121 Processing sheet with id= AN, first strand: chain 'M' and resid 5 through 9 Processing sheet with id= AO, first strand: chain 'M' and resid 28 through 32 removed outlier: 6.221A pdb=" N TYR M 60 " --> pdb=" O ILE M 29 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N LEU M 31 " --> pdb=" O TYR M 60 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N TYR M 62 " --> pdb=" O LEU M 31 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'M' and resid 118 through 121 Processing sheet with id= AQ, first strand: chain 'N' and resid 5 through 8 removed outlier: 3.524A pdb=" N ARG N 15 " --> pdb=" O GLU N 8 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'N' and resid 59 through 63 Processing sheet with id= AS, first strand: chain 'N' and resid 119 through 121 1403 hydrogen bonds defined for protein. 3918 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: 28.21 Time building geometry restraints manager: 53.58 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: 38364 1.06 - 1.28: 6563 1.28 - 1.50: 15559 1.50 - 1.73: 16310 1.73 - 1.95: 307 Bond restraints: 77103 Sorted by residual: bond pdb=" C4 ADP F 802 " pdb=" C5 ADP F 802 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.96e+01 bond pdb=" C4 ADP E 802 " pdb=" C5 ADP E 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 E 801 " pdb=" C5 ADP E 801 " ideal model delta sigma weight residual 1.490 1.382 0.108 2.00e-02 2.50e+03 2.93e+01 bond pdb=" C5 ADP E 802 " pdb=" C6 ADP E 802 " ideal model delta sigma weight residual 1.490 1.407 0.083 2.00e-02 2.50e+03 1.74e+01 bond pdb=" C5 ADP E 801 " pdb=" C6 ADP E 801 " ideal model delta sigma weight residual 1.490 1.407 0.083 2.00e-02 2.50e+03 1.70e+01 ... (remaining 77098 not shown) Histogram of bond angle deviations from ideal: 78.42 - 89.53: 11 89.53 - 100.63: 40 100.63 - 111.74: 89508 111.74 - 122.84: 41240 122.84 - 133.95: 8939 Bond angle restraints: 139738 Sorted by residual: angle pdb="HG22 THR D 626 " pdb=" CG2 THR D 626 " pdb="HG23 THR D 626 " ideal model delta sigma weight residual 109.00 78.42 30.58 3.00e+00 1.11e-01 1.04e+02 angle pdb="HG21 THR D 626 " pdb=" CG2 THR D 626 " pdb="HG22 THR D 626 " ideal model delta sigma weight residual 109.00 78.80 30.20 3.00e+00 1.11e-01 1.01e+02 angle pdb="HD11 ILE A 620 " pdb=" CD1 ILE A 620 " pdb="HD13 ILE A 620 " ideal model delta sigma weight residual 110.00 79.99 30.01 3.00e+00 1.11e-01 1.00e+02 angle pdb="HD11 ILE A 620 " pdb=" CD1 ILE A 620 " pdb="HD12 ILE A 620 " ideal model delta sigma weight residual 110.00 80.30 29.70 3.00e+00 1.11e-01 9.80e+01 angle pdb=" CG1 ILE A 620 " pdb=" CD1 ILE A 620 " pdb="HD13 ILE A 620 " ideal model delta sigma weight residual 109.00 80.45 28.55 3.00e+00 1.11e-01 9.06e+01 ... (remaining 139733 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.51: 34489 30.51 - 61.03: 1152 61.03 - 91.54: 60 91.54 - 122.05: 13 122.05 - 152.57: 7 Dihedral angle restraints: 35721 sinusoidal: 20151 harmonic: 15570 Sorted by residual: dihedral pdb=" O2A ADP F 802 " pdb=" O3A ADP F 802 " pdb=" PA ADP F 802 " pdb=" PB ADP F 802 " ideal model delta sinusoidal sigma weight residual 300.00 171.56 128.45 1 2.00e+01 2.50e-03 3.89e+01 dihedral pdb=" O1B ADP E 801 " pdb=" O3A ADP E 801 " pdb=" PB ADP E 801 " pdb=" PA ADP E 801 " ideal model delta sinusoidal sigma weight residual -60.00 61.48 -121.48 1 2.00e+01 2.50e-03 3.65e+01 dihedral pdb=" O1B ADP F 802 " pdb=" O3A ADP F 802 " pdb=" PB ADP F 802 " pdb=" PA ADP F 802 " ideal model delta sinusoidal sigma weight residual -60.00 54.81 -114.82 1 2.00e+01 2.50e-03 3.41e+01 ... (remaining 35718 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.342: 6000 0.342 - 0.684: 0 0.684 - 1.026: 0 1.026 - 1.367: 0 1.367 - 1.709: 1 Chirality restraints: 6001 Sorted by residual: chirality pdb=" CG LEU E 725 " pdb=" CB LEU E 725 " pdb=" CD1 LEU E 725 " pdb=" CD2 LEU E 725 " both_signs ideal model delta sigma weight residual False -2.59 -0.88 -1.71 2.00e-01 2.50e+01 7.30e+01 chirality pdb=" C3' ADP E 802 " pdb=" C2' ADP E 802 " pdb=" C4' ADP E 802 " pdb=" O3' ADP E 802 " both_signs ideal model delta sigma weight residual False -2.51 -2.71 0.20 2.00e-01 2.50e+01 9.94e-01 chirality pdb=" CA ILE F 436 " pdb=" N ILE F 436 " pdb=" C ILE F 436 " pdb=" CB ILE F 436 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 9.18e-01 ... (remaining 5998 not shown) Planarity restraints: 11404 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG C 702 " 0.034 5.00e-02 4.00e+02 5.14e-02 4.23e+00 pdb=" N PRO C 703 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO C 703 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 703 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS J 84 " -0.034 5.00e-02 4.00e+02 5.10e-02 4.16e+00 pdb=" N PRO J 85 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO J 85 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO J 85 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET E 412 " 0.034 5.00e-02 4.00e+02 5.02e-02 4.04e+00 pdb=" N PRO E 413 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO E 413 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO E 413 " 0.028 5.00e-02 4.00e+02 ... (remaining 11401 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.26: 8913 2.26 - 2.84: 177135 2.84 - 3.43: 199020 3.43 - 4.01: 276653 4.01 - 4.60: 427291 Nonbonded interactions: 1089012 Sorted by model distance: nonbonded pdb=" H PHE E 493 " pdb=" O MET E 603 " model vdw 1.670 1.850 nonbonded pdb=" HG1 THR D 502 " pdb="MG MG D 804 " model vdw 1.674 1.700 nonbonded pdb=" O ALA H 96 " pdb=" H ALA H 100 " model vdw 1.684 1.850 nonbonded pdb=" HG1 THR B 221 " pdb="MG MG B 803 " model vdw 1.684 1.700 nonbonded pdb=" OE1 GLU E 484 " pdb=" H GLU E 484 " model vdw 1.690 1.850 ... (remaining 1089007 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 347 or (resid 348 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name OE1 or name OE2 or name \ HA or name HB2 or name HB3 or name HG2 or name HG3)) or resid 349 through 352 or \ (resid 353 and (name N or name CA or name C or name O or name CB or name CG or \ name CD or name OE1 or name OE2 or name HA or name HB2 or name HB3 or name HG2 o \ r name HG3)) or resid 354 through 462 or (resid 463 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name OE1 or name NE2 or name \ H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HE21)) or r \ esid 464 through 474 or (resid 475 and (name N or name CA or name C or name O or \ name CB or name CG or name CD or name CE or name NZ or name H or name HA or nam \ e HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE2 or \ name HE3)) or resid 476 through 496 or (resid 497 and (name N or name CA or nam \ e 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 498 through 597 or (resid 598 \ and (name N or name CA or name C or name O or name CB or name CG or name OD1 or \ name ND2 or name H or name HA or name HB2 or name HB3)) or resid 599 through 60 \ 0 or (resid 601 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 HA or name HB2 or name HB3 or name HG or name H \ D11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23)) or resid \ 602 through 622 or (resid 623 and (name N or name CA or name C or name O or name \ CB or name CG or name OD1 or name OD2 or name HA or name HB2 or name HB3)) or r \ esid 624 through 696 or (resid 697 and (name N or name CA or name C or name O or \ name CB or name CG or name CD or name NE or name CZ or name NH1 or name NH2 or \ name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or \ name HD3 or name HE or name HH21)) or resid 698 through 729 or (resid 730 and ( \ name N or name CA or name C or name O or name CB or name CG or name CD or name O \ E1 or name NE2 or name H or name HA or name HB2 or name HB3 or name HG2 or name \ HG3)) or resid 731 through 748 or resid 803)) 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 347 or (resid 348 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name OE1 or name OE2 or name HA or \ name HB2 or name HB3 or name HG2 or name HG3)) or resid 349 through 352 or (res \ id 353 and (name N or name CA or name C or name O or name CB or name CG or name \ CD or name OE1 or name OE2 or name HA or name HB2 or name HB3 or name HG2 or nam \ e HG3)) or resid 354 through 431 or (resid 432 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2 or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or \ name HD2 or name HD3 or name HE or name HH11 or name HH21)) or resid 433 throug \ h 454 or (resid 455 and (name N or name CA or name C or name O or name CB or nam \ e CG or name CD or name NE or name CZ or name NH1 or name NH2 or name H or name \ HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or na \ me HE or name HH11 or name HH12 or name HH22)) or resid 456 through 462 or (resi \ d 463 and (name N or name CA or name C or name O or name CB or name CG or name C \ D or name OE1 or name NE2 or name H or name HA or name HB2 or name HB3 or name H \ G2 or name HG3 or name HE21)) or resid 464 through 474 or (resid 475 and (name N \ or name CA or name C or name O or name CB or name CG or name CD or name CE or n \ ame NZ or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or n \ ame HD2 or name HD3 or name HE2 or name HE3)) or resid 476 through 496 or (resid \ 497 and (name N or name CA or name C or name O or name CB or name OG1 or name C \ G2 or name H or name HA or name HB or name HG21 or name HG22 or name HG23)) or r \ esid 498 through 597 or (resid 598 and (name N or name CA or name C or name O or \ name CB or name CG or name OD1 or name ND2 or name H or name HA or name HB2 or \ name HB3)) or resid 599 through 600 or (resid 601 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 HA or name HB \ 2 or name HB3 or name HG or name HD11 or name HD12 or name HD13 or name HD21 or \ name HD22 or name HD23)) or resid 602 through 622 or (resid 623 and (name N or n \ ame CA or name C or name O or name CB or name CG or name OD1 or name OD2 or name \ HA or name HB2 or name HB3)) or resid 624 through 696 or (resid 697 and (name N \ or name CA or name C or name O or name CB or name CG or name CD or name NE or n \ ame CZ or name NH1 or name NH2 or name H or name HA or name HB2 or name HB3 or n \ ame HG2 or name HG3 or name HD2 or name HD3 or name HE or name HH21)) or resid 6 \ 98 through 729 or (resid 730 and (name N or name CA or name C or name O or name \ CB or name CG or name CD or name OE1 or name NE2 or name H or name HA or name HB \ 2 or name HB3 or name HG2 or name HG3)) or resid 731 through 748 or resid 803)) 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 347 or (resid 348 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name OE1 or name OE2 or name HA or \ name HB2 or name HB3 or name HG2 or name HG3)) or resid 349 through 352 or (res \ id 353 and (name N or name CA or name C or name O or name CB or name CG or name \ CD or name OE1 or name OE2 or name HA or name HB2 or name HB3 or name HG2 or nam \ e HG3)) or resid 354 through 431 or (resid 432 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2 or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or \ name HD2 or name HD3 or name HE or name HH11 or name HH21)) or resid 433 throug \ h 454 or (resid 455 and (name N or name CA or name C or name O or name CB or nam \ e CG or name CD or name NE or name CZ or name NH1 or name NH2 or name H or name \ HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or na \ me HE or name HH11 or name HH12 or name HH22)) or resid 456 through 462 or (resi \ d 463 and (name N or name CA or name C or name O or name CB or name CG or name C \ D or name OE1 or name NE2 or name H or name HA or name HB2 or name HB3 or name H \ G2 or name HG3 or name HE21)) or resid 464 through 474 or (resid 475 and (name N \ or name CA or name C or name O or name CB or name CG or name CD or name CE or n \ ame NZ or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or n \ ame HD2 or name HD3 or name HE2 or name HE3)) or resid 476 through 496 or (resid \ 497 and (name N or name CA or name C or name O or name CB or name OG1 or name C \ G2 or name H or name HA or name HB or name HG21 or name HG22 or name HG23)) or r \ esid 498 through 597 or (resid 598 and (name N or name CA or name C or name O or \ name CB or name CG or name OD1 or name ND2 or name H or name HA or name HB2 or \ name HB3)) or resid 599 through 600 or (resid 601 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 HA or name HB \ 2 or name HB3 or name HG or name HD11 or name HD12 or name HD13 or name HD21 or \ name HD22 or name HD23)) or resid 602 through 622 or (resid 623 and (name N or n \ ame CA or name C or name O or name CB or name CG or name OD1 or name OD2 or name \ HA or name HB2 or name HB3)) or resid 624 through 696 or (resid 697 and (name N \ or name CA or name C or name O or name CB or name CG or name CD or name NE or n \ ame CZ or name NH1 or name NH2 or name H or name HA or name HB2 or name HB3 or n \ ame HG2 or name HG3 or name HD2 or name HD3 or name HE or name HH21)) or resid 6 \ 98 through 748 or resid 803)) 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 347 or (resid 348 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name OE1 or name OE2 or name HA or \ name HB2 or name HB3 or name HG2 or name HG3)) or resid 349 through 352 or (res \ id 353 and (name N or name CA or name C or name O or name CB or name CG or name \ CD or name OE1 or name OE2 or name HA or name HB2 or name HB3 or name HG2 or nam \ e HG3)) or resid 354 through 431 or (resid 432 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2 or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or \ name HD2 or name HD3 or name HE or name HH11 or name HH21)) or resid 433 throug \ h 454 or (resid 455 and (name N or name CA or name C or name O or name CB or nam \ e CG or name CD or name NE or name CZ or name NH1 or name NH2 or name H or name \ HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or na \ me HE or name HH11 or name HH12 or name HH22)) or resid 456 through 462 or (resi \ d 463 and (name N or name CA or name C or name O or name CB or name CG or name C \ D or name OE1 or name NE2 or name H or name HA or name HB2 or name HB3 or name H \ G2 or name HG3 or name HE21)) or resid 464 through 474 or (resid 475 and (name N \ or name CA or name C or name O or name CB or name CG or name CD or name CE or n \ ame NZ or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or n \ ame HD2 or name HD3 or name HE2 or name HE3)) or resid 476 through 496 or (resid \ 497 and (name N or name CA or name C or name O or name CB or name OG1 or name C \ G2 or name H or name HA or name HB or name HG21 or name HG22 or name HG23)) or r \ esid 498 through 597 or (resid 598 and (name N or name CA or name C or name O or \ name CB or name CG or name OD1 or name ND2 or name H or name HA or name HB2 or \ name HB3)) or resid 599 through 600 or (resid 601 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 HA or name HB \ 2 or name HB3 or name HG or name HD11 or name HD12 or name HD13 or name HD21 or \ name HD22 or name HD23)) or resid 602 through 622 or (resid 623 and (name N or n \ ame CA or name C or name O or name CB or name CG or name OD1 or name OD2 or name \ HA or name HB2 or name HB3)) or resid 624 through 696 or (resid 697 and (name N \ or name CA or name C or name O or name CB or name CG or name CD or name NE or n \ ame CZ or name NH1 or name NH2 or name H or name HA or name HB2 or name HB3 or n \ ame HG2 or name HG3 or name HD2 or name HD3 or name HE or name HH21)) or resid 6 \ 98 through 729 or (resid 730 and (name N or name CA or name C or name O or name \ CB or name CG or name CD or name OE1 or name NE2 or name H or name HA or name HB \ 2 or name HB3 or name HG2 or name HG3)) or resid 731 through 748 or resid 803)) 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 431 or (resid 432 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2 or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or \ name HD2 or name HD3 or name HE or name HH11 or name HH21)) or resid 433 throug \ h 454 or (resid 455 and (name N or name CA or name C or name O or name CB or nam \ e CG or name CD or name NE or name CZ or name NH1 or name NH2 or name H or name \ HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or na \ me HE or name HH11 or name HH12 or name HH22)) or resid 456 through 462 or (resi \ d 463 and (name N or name CA or name C or name O or name CB or name CG or name C \ D or name OE1 or name NE2 or name H or name HA or name HB2 or name HB3 or name H \ G2 or name HG3 or name HE21)) or resid 464 through 474 or (resid 475 and (name N \ or name CA or name C or name O or name CB or name CG or name CD or name CE or n \ ame NZ or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or n \ ame HD2 or name HD3 or name HE2 or name HE3)) or resid 476 through 597 or (resid \ 598 and (name N or name CA or name C or name O or name CB or name CG or name OD \ 1 or name ND2 or name H or name HA or name HB2 or name HB3)) or resid 599 throug \ h 600 or (resid 601 and (name N or name CA or name C or name O or name CB or nam \ e CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name HG or na \ me HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23)) or re \ sid 602 through 622 or (resid 623 and (name N or name CA or name C or name O or \ name CB or name CG or name OD1 or name OD2 or name HA or name HB2 or name HB3)) \ or resid 624 through 729 or (resid 730 and (name N or name CA or name C or name \ O or name CB or name CG or name CD or name OE1 or name NE2 or name H or name HA \ or name HB2 or name HB3 or name HG2 or name HG3)) or resid 731 through 748 or re \ sid 803)) 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 347 or (resid 348 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name OE1 or name OE2 or name HA or \ name HB2 or name HB3 or name HG2 or name HG3)) or resid 349 through 352 or (res \ id 353 and (name N or name CA or name C or name O or name CB or name CG or name \ CD or name OE1 or name OE2 or name HA or name HB2 or name HB3 or name HG2 or nam \ e HG3)) or resid 354 through 431 or (resid 432 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2 or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or \ name HD2 or name HD3 or name HE or name HH11 or name HH21)) or resid 433 throug \ h 454 or (resid 455 and (name N or name CA or name C or name O or name CB or nam \ e CG or name CD or name NE or name CZ or name NH1 or name NH2 or name H or name \ HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or na \ me HE or name HH11 or name HH12 or name HH22)) or resid 456 through 496 or (resi \ d 497 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 498 through 696 or (resid 697 and (name N or name CA or name C or name O o \ r name CB or name CG or name CD or name NE or name CZ or name NH1 or name NH2 or \ name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 o \ r name HD3 or name HE or name HH21)) or resid 698 through 729 or (resid 730 and \ (name N or name CA or name C or name O or name CB or name CG or name CD or name \ OE1 or name NE2 or name H or name HA or name HB2 or name HB3 or name HG2 or name \ HG3)) or resid 731 through 748 or resid 803)) } 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' and (resid 2 through 186 or (resid 187 and (name N or name CA or name \ C or name O or name CB or name OG or name HA or name HB2 or name HB3 or name HG \ )) or resid 188 through 191)) } 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: 0.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.840 Extract box with map and model: 5.020 Check model and map are aligned: 0.860 Set scattering table: 0.550 Process input model: 193.670 Find NCS groups from input model: 3.570 Set up NCS constraints: 0.230 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 207.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.109 38713 Z= 0.271 Angle : 0.749 13.518 52313 Z= 0.367 Chirality : 0.047 1.709 6001 Planarity : 0.004 0.051 6750 Dihedral : 13.793 152.566 14761 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Rotamer: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % 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: -1.03 (0.11), residues: 4809 helix: -0.43 (0.09), residues: 2332 sheet: -0.72 (0.19), residues: 696 loop : -0.75 (0.13), residues: 1781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 229 HIS 0.008 0.001 HIS D 393 PHE 0.029 0.001 PHE M 82 TYR 0.021 0.001 TYR F 540 ARG 0.004 0.000 ARG F 532 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 497 is missing expected H atoms. Skipping. Residue LYS 475 is missing expected H atoms. Skipping. Evaluate side-chains 1556 residues out of total 4071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1556 time to evaluate : 5.261 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: A 266 ARG cc_start: 0.8129 (mtt180) cc_final: 0.7925 (tpt-90) REVERT: A 288 HIS cc_start: 0.8262 (p90) cc_final: 0.7839 (p90) REVERT: A 570 HIS cc_start: 0.7880 (t-90) cc_final: 0.7619 (t-90) REVERT: A 572 ASP cc_start: 0.7991 (m-30) cc_final: 0.7745 (m-30) REVERT: A 684 GLN cc_start: 0.7853 (tp40) cc_final: 0.7617 (tp-100) REVERT: A 693 LYS cc_start: 0.7864 (tttp) cc_final: 0.7516 (tttm) REVERT: A 731 VAL cc_start: 0.7974 (m) cc_final: 0.7510 (p) REVERT: B 194 GLU cc_start: 0.8177 (mp0) cc_final: 0.7775 (mp0) REVERT: B 258 LYS cc_start: 0.7870 (tttt) cc_final: 0.7640 (tttm) REVERT: B 343 LYS cc_start: 0.8978 (ttpp) cc_final: 0.8773 (ttmt) REVERT: B 450 LYS cc_start: 0.8777 (ttpt) cc_final: 0.8529 (tttp) REVERT: C 637 THR cc_start: 0.8882 (t) cc_final: 0.8591 (p) REVERT: D 317 ARG cc_start: 0.8152 (mtm180) cc_final: 0.7710 (mtm180) REVERT: D 366 GLU cc_start: 0.8352 (mt-10) cc_final: 0.8125 (mt-10) REVERT: D 372 ARG cc_start: 0.7503 (ttp80) cc_final: 0.7216 (ttt90) REVERT: D 526 GLU cc_start: 0.7111 (mp0) cc_final: 0.6789 (mp0) REVERT: E 194 GLU cc_start: 0.8370 (mp0) cc_final: 0.7907 (mp0) REVERT: E 530 VAL cc_start: 0.9363 (p) cc_final: 0.9155 (p) REVERT: E 611 GLU cc_start: 0.7579 (mm-30) cc_final: 0.7353 (mm-30) REVERT: F 317 ARG cc_start: 0.6907 (ptp-170) cc_final: 0.5787 (ptt180) REVERT: F 357 ILE cc_start: 0.8586 (mt) cc_final: 0.8382 (mt) REVERT: F 362 LYS cc_start: 0.8597 (tttt) cc_final: 0.8211 (ttpt) REVERT: F 464 ASP cc_start: 0.8435 (m-30) cc_final: 0.8127 (m-30) REVERT: F 468 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7956 (mt-10) REVERT: F 633 LYS cc_start: 0.7974 (mtmt) cc_final: 0.7499 (mttp) REVERT: F 636 PHE cc_start: 0.8112 (m-80) cc_final: 0.7790 (m-80) REVERT: F 639 GLU cc_start: 0.8926 (mt-10) cc_final: 0.8693 (pt0) REVERT: F 659 HIS cc_start: 0.8816 (m-70) cc_final: 0.8521 (m-70) REVERT: F 699 MET cc_start: 0.7534 (mmm) cc_final: 0.7326 (mmm) REVERT: F 711 ASN cc_start: 0.7930 (m110) cc_final: 0.7514 (m110) REVERT: F 713 LYS cc_start: 0.7649 (mtpt) cc_final: 0.7321 (mtpp) REVERT: F 740 ASN cc_start: 0.8183 (m-40) cc_final: 0.7902 (p0) REVERT: H 58 ASP cc_start: 0.7755 (m-30) cc_final: 0.7478 (m-30) REVERT: H 71 THR cc_start: 0.8967 (p) cc_final: 0.8759 (p) REVERT: H 78 ASP cc_start: 0.8468 (m-30) cc_final: 0.8038 (m-30) REVERT: H 110 LYS cc_start: 0.8265 (mttt) cc_final: 0.8028 (mttt) REVERT: H 136 GLU cc_start: 0.8147 (tm-30) cc_final: 0.7527 (tm-30) REVERT: H 141 GLU cc_start: 0.8096 (tp30) cc_final: 0.7868 (tp30) REVERT: I 141 GLU cc_start: 0.7303 (tt0) cc_final: 0.7030 (tt0) REVERT: I 161 LEU cc_start: 0.7188 (pp) cc_final: 0.6987 (tp) REVERT: I 185 VAL cc_start: 0.8813 (t) cc_final: 0.8575 (m) REVERT: J 25 LYS cc_start: 0.8869 (tttm) cc_final: 0.8414 (ttmm) REVERT: J 110 LYS cc_start: 0.7848 (mttp) cc_final: 0.7253 (mttp) REVERT: J 125 LEU cc_start: 0.7147 (tp) cc_final: 0.6888 (tp) REVERT: K 18 ASP cc_start: 0.7512 (p0) cc_final: 0.7248 (p0) REVERT: K 35 VAL cc_start: 0.8893 (t) cc_final: 0.8657 (t) REVERT: K 78 ASP cc_start: 0.8499 (m-30) cc_final: 0.8082 (m-30) REVERT: K 138 HIS cc_start: 0.8589 (m-70) cc_final: 0.8365 (m-70) REVERT: K 155 LEU cc_start: 0.8370 (tp) cc_final: 0.8131 (tt) REVERT: M 144 LYS cc_start: 0.8064 (ttmm) cc_final: 0.7737 (mtpp) REVERT: M 146 LYS cc_start: 0.8254 (ttpt) cc_final: 0.7972 (ttmt) REVERT: N 8 GLU cc_start: 0.6842 (tt0) cc_final: 0.6636 (tt0) REVERT: N 110 LYS cc_start: 0.7739 (mttt) cc_final: 0.7477 (mttp) REVERT: N 136 GLU cc_start: 0.8219 (tm-30) cc_final: 0.7758 (tm-30) REVERT: N 141 GLU cc_start: 0.8250 (tp30) cc_final: 0.8048 (tp30) outliers start: 0 outliers final: 0 residues processed: 1556 average time/residue: 1.1466 time to fit residues: 2770.2014 Evaluate side-chains 1254 residues out of total 4071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1254 time to evaluate : 4.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 406 optimal weight: 7.9990 chunk 364 optimal weight: 20.0000 chunk 202 optimal weight: 9.9990 chunk 124 optimal weight: 9.9990 chunk 245 optimal weight: 5.9990 chunk 194 optimal weight: 3.9990 chunk 377 optimal weight: 9.9990 chunk 145 optimal weight: 5.9990 chunk 229 optimal weight: 10.0000 chunk 280 optimal weight: 0.9990 chunk 436 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 590 ASN A 622 GLN A 624 ASN B 209 ASN B 579 GLN B 606 ASN C 233 GLN C 305 ASN C 606 ASN ** D 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 300 GLN E 579 GLN E 660 GLN ** E 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 178 GLN F 279 ASN F 356 GLN ** F 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 672 GLN I 41 ASN I 156 HIS K 116 ASN ** K 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 41 ASN L 116 ASN M 116 ASN N 116 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 38713 Z= 0.295 Angle : 0.584 9.817 52313 Z= 0.306 Chirality : 0.046 1.704 6001 Planarity : 0.004 0.057 6750 Dihedral : 9.961 174.896 5443 Min Nonbonded Distance : 1.637 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.11 % Allowed : 10.66 % Favored : 88.23 % 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: -0.19 (0.11), residues: 4809 helix: 0.45 (0.10), residues: 2442 sheet: -0.59 (0.20), residues: 623 loop : -0.59 (0.13), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 229 HIS 0.010 0.001 HIS F 570 PHE 0.017 0.001 PHE E 596 TYR 0.015 0.001 TYR I 128 ARG 0.009 0.001 ARG E 455 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 497 is missing expected H atoms. Skipping. Residue LYS 475 is missing expected H atoms. Skipping. Evaluate side-chains 1377 residues out of total 4071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 1332 time to evaluate : 4.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 ARG cc_start: 0.8275 (mtt180) cc_final: 0.7993 (mmm-85) REVERT: A 359 ASN cc_start: 0.8807 (m-40) cc_final: 0.8579 (m110) REVERT: A 423 VAL cc_start: 0.8633 (t) cc_final: 0.8423 (p) REVERT: A 668 GLU cc_start: 0.7324 (mt-10) cc_final: 0.7107 (mt-10) REVERT: A 681 GLU cc_start: 0.6748 (mp0) cc_final: 0.6247 (mp0) REVERT: A 684 GLN cc_start: 0.7535 (tp40) cc_final: 0.7292 (tp-100) REVERT: A 730 GLN cc_start: 0.7572 (pm20) cc_final: 0.7369 (pm20) REVERT: A 731 VAL cc_start: 0.7924 (m) cc_final: 0.7223 (p) REVERT: A 741 GLU cc_start: 0.7818 (mm-30) cc_final: 0.7572 (mm-30) REVERT: B 194 GLU cc_start: 0.8321 (mp0) cc_final: 0.7771 (mp0) REVERT: B 258 LYS cc_start: 0.8023 (tttt) cc_final: 0.7776 (tttm) REVERT: B 450 LYS cc_start: 0.8811 (ttpt) cc_final: 0.8604 (tttp) REVERT: B 451 ASN cc_start: 0.7675 (m-40) cc_final: 0.7100 (m110) REVERT: C 527 ARG cc_start: 0.8478 (mtp-110) cc_final: 0.8276 (mtp-110) REVERT: D 317 ARG cc_start: 0.8251 (mtm180) cc_final: 0.7804 (mtm180) REVERT: D 372 ARG cc_start: 0.7518 (ttp80) cc_final: 0.7234 (ttt90) REVERT: D 408 ARG cc_start: 0.8431 (ttp80) cc_final: 0.8230 (ttp80) REVERT: D 605 THR cc_start: 0.8616 (t) cc_final: 0.8332 (t) REVERT: D 606 ASN cc_start: 0.7783 (p0) cc_final: 0.7511 (p0) REVERT: D 614 ARG cc_start: 0.7299 (ptm-80) cc_final: 0.6917 (ptm-80) REVERT: D 684 GLN cc_start: 0.8196 (tp40) cc_final: 0.7930 (tp-100) REVERT: D 693 LYS cc_start: 0.8593 (tptp) cc_final: 0.8338 (tptt) REVERT: E 194 GLU cc_start: 0.8377 (mp0) cc_final: 0.8108 (mp0) REVERT: E 370 ASP cc_start: 0.7946 (t0) cc_final: 0.7659 (t0) REVERT: E 525 MET cc_start: 0.8309 (mmm) cc_final: 0.7964 (mmm) REVERT: F 229 TRP cc_start: 0.8050 (t60) cc_final: 0.7379 (t60) REVERT: F 259 TYR cc_start: 0.6884 (OUTLIER) cc_final: 0.6507 (t80) REVERT: F 464 ASP cc_start: 0.8483 (m-30) cc_final: 0.8199 (m-30) REVERT: F 465 LYS cc_start: 0.9145 (tppt) cc_final: 0.8718 (mmmm) REVERT: F 639 GLU cc_start: 0.9015 (mt-10) cc_final: 0.8682 (pm20) REVERT: F 668 GLU cc_start: 0.8381 (tm-30) cc_final: 0.8073 (tm-30) REVERT: F 709 GLN cc_start: 0.7962 (tt0) cc_final: 0.7754 (tt0) REVERT: F 711 ASN cc_start: 0.7942 (m110) cc_final: 0.7490 (m110) REVERT: F 719 GLU cc_start: 0.7983 (tp30) cc_final: 0.7503 (tp30) REVERT: H 17 PHE cc_start: 0.7686 (m-80) cc_final: 0.7416 (m-80) REVERT: H 58 ASP cc_start: 0.7805 (m-30) cc_final: 0.7514 (m-30) REVERT: H 78 ASP cc_start: 0.8527 (m-30) cc_final: 0.8103 (m-30) REVERT: H 84 LYS cc_start: 0.8098 (mtpt) cc_final: 0.7880 (mtmm) REVERT: H 110 LYS cc_start: 0.8299 (mttt) cc_final: 0.8029 (mttt) REVERT: H 136 GLU cc_start: 0.8272 (tm-30) cc_final: 0.7627 (tm-30) REVERT: H 141 GLU cc_start: 0.8279 (tp30) cc_final: 0.8075 (tp30) REVERT: I 22 ARG cc_start: 0.8865 (tpt-90) cc_final: 0.8605 (tpt90) REVERT: I 140 ARG cc_start: 0.8304 (mtm110) cc_final: 0.8092 (mtm110) REVERT: I 171 ASP cc_start: 0.7500 (p0) cc_final: 0.7230 (p0) REVERT: J 98 MET cc_start: 0.8626 (tpp) cc_final: 0.8405 (tpp) REVERT: J 125 LEU cc_start: 0.7192 (tp) cc_final: 0.6908 (tp) REVERT: J 172 ARG cc_start: 0.7965 (mmm-85) cc_final: 0.7721 (mmm-85) REVERT: K 78 ASP cc_start: 0.8696 (m-30) cc_final: 0.8132 (m-30) REVERT: K 138 HIS cc_start: 0.8679 (m-70) cc_final: 0.8309 (m-70) REVERT: K 140 ARG cc_start: 0.8006 (ttm-80) cc_final: 0.7723 (ttm110) REVERT: K 141 GLU cc_start: 0.7959 (tp30) cc_final: 0.7736 (tp30) REVERT: K 155 LEU cc_start: 0.8517 (tp) cc_final: 0.8237 (tt) REVERT: L 116 ASN cc_start: 0.8693 (m-40) cc_final: 0.8317 (m-40) REVERT: L 140 ARG cc_start: 0.8321 (mmm-85) cc_final: 0.8075 (mmm-85) REVERT: L 161 LEU cc_start: 0.8376 (mt) cc_final: 0.8011 (tp) REVERT: M 144 LYS cc_start: 0.8029 (ttmm) cc_final: 0.7673 (mtpp) REVERT: M 146 LYS cc_start: 0.8418 (ttpt) cc_final: 0.7989 (ttmt) REVERT: N 8 GLU cc_start: 0.6979 (tt0) cc_final: 0.6699 (tt0) REVERT: N 136 GLU cc_start: 0.8555 (tm-30) cc_final: 0.7995 (tm-30) REVERT: N 170 ARG cc_start: 0.8232 (tpp-160) cc_final: 0.7888 (tpp80) outliers start: 45 outliers final: 31 residues processed: 1348 average time/residue: 1.1582 time to fit residues: 2429.7610 Evaluate side-chains 1282 residues out of total 4071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 1250 time to evaluate : 4.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 GLN Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 564 ASP Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 370 ASP Chi-restraints excluded: chain B residue 383 GLU Chi-restraints excluded: chain C residue 193 LYS Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain C residue 534 ILE Chi-restraints excluded: chain D residue 321 SER Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 690 LEU Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 321 SER Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 332 GLU Chi-restraints excluded: chain E residue 564 ASP Chi-restraints excluded: chain F residue 194 GLU Chi-restraints excluded: chain F residue 196 GLU Chi-restraints excluded: chain F residue 259 TYR Chi-restraints excluded: chain F residue 370 ASP Chi-restraints excluded: chain F residue 447 ASP Chi-restraints excluded: chain F residue 583 ASN Chi-restraints excluded: chain H residue 174 LEU Chi-restraints excluded: chain J residue 75 SER Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain N residue 16 SER Chi-restraints excluded: chain N residue 74 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 242 optimal weight: 8.9990 chunk 135 optimal weight: 7.9990 chunk 363 optimal weight: 20.0000 chunk 297 optimal weight: 9.9990 chunk 120 optimal weight: 3.9990 chunk 437 optimal weight: 20.0000 chunk 472 optimal weight: 9.9990 chunk 389 optimal weight: 8.9990 chunk 433 optimal weight: 10.0000 chunk 149 optimal weight: 3.9990 chunk 351 optimal weight: 6.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 558 HIS ** A 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 675 GLN ** D 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 579 GLN ** E 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 659 HIS ** H 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 46 GLN ** N 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 159 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 38713 Z= 0.347 Angle : 0.566 9.803 52313 Z= 0.294 Chirality : 0.047 1.710 6001 Planarity : 0.004 0.070 6750 Dihedral : 9.895 178.540 5443 Min Nonbonded Distance : 1.697 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.87 % Allowed : 12.21 % Favored : 85.92 % 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: -0.18 (0.12), residues: 4809 helix: 0.44 (0.10), residues: 2465 sheet: -0.54 (0.20), residues: 620 loop : -0.59 (0.14), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 229 HIS 0.007 0.001 HIS D 393 PHE 0.028 0.002 PHE E 596 TYR 0.021 0.002 TYR I 77 ARG 0.006 0.001 ARG M 166 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 497 is missing expected H atoms. Skipping. Residue LYS 475 is missing expected H atoms. Skipping. Evaluate side-chains 1421 residues out of total 4071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 1345 time to evaluate : 4.596 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: A 266 ARG cc_start: 0.8272 (mtt180) cc_final: 0.8034 (mmm-85) REVERT: A 359 ASN cc_start: 0.8728 (m-40) cc_final: 0.8460 (m110) REVERT: A 663 ASP cc_start: 0.8033 (m-30) cc_final: 0.7818 (m-30) REVERT: A 684 GLN cc_start: 0.7664 (tp40) cc_final: 0.7179 (tp-100) REVERT: A 741 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7589 (mm-30) REVERT: B 194 GLU cc_start: 0.8396 (mp0) cc_final: 0.7756 (mp0) REVERT: B 258 LYS cc_start: 0.8150 (tttt) cc_final: 0.7810 (tttm) REVERT: B 265 LYS cc_start: 0.8444 (mtmt) cc_final: 0.8243 (mtmt) REVERT: B 447 ASP cc_start: 0.7432 (m-30) cc_final: 0.6667 (m-30) REVERT: B 450 LYS cc_start: 0.8877 (ttpt) cc_final: 0.8658 (tttp) REVERT: B 451 ASN cc_start: 0.7713 (m-40) cc_final: 0.7189 (m110) REVERT: B 727 ASP cc_start: 0.6804 (OUTLIER) cc_final: 0.6170 (p0) REVERT: D 372 ARG cc_start: 0.7524 (ttp80) cc_final: 0.7219 (ttt90) REVERT: D 671 VAL cc_start: 0.8895 (t) cc_final: 0.8634 (t) REVERT: D 684 GLN cc_start: 0.8281 (tp40) cc_final: 0.8047 (tp-100) REVERT: D 693 LYS cc_start: 0.8721 (tptp) cc_final: 0.8456 (tppt) REVERT: D 719 GLU cc_start: 0.7538 (mm-30) cc_final: 0.7012 (mm-30) REVERT: E 651 ASP cc_start: 0.7207 (p0) cc_final: 0.6824 (p0) REVERT: F 259 TYR cc_start: 0.7124 (OUTLIER) cc_final: 0.6697 (t80) REVERT: F 340 ARG cc_start: 0.7578 (mmt180) cc_final: 0.7059 (mmm160) REVERT: F 465 LYS cc_start: 0.9146 (tppt) cc_final: 0.8755 (mmmm) REVERT: F 639 GLU cc_start: 0.8973 (mt-10) cc_final: 0.8701 (pm20) REVERT: F 659 HIS cc_start: 0.8709 (m-70) cc_final: 0.8208 (m90) REVERT: F 711 ASN cc_start: 0.8020 (m110) cc_final: 0.7641 (m110) REVERT: F 719 GLU cc_start: 0.7995 (tp30) cc_final: 0.7335 (tp30) REVERT: F 740 ASN cc_start: 0.8405 (m-40) cc_final: 0.8115 (p0) REVERT: H 17 PHE cc_start: 0.8068 (m-80) cc_final: 0.7783 (m-10) REVERT: H 36 GLU cc_start: 0.7037 (OUTLIER) cc_final: 0.6673 (mp0) REVERT: H 84 LYS cc_start: 0.8103 (mtpt) cc_final: 0.7889 (mtmm) REVERT: H 136 GLU cc_start: 0.8281 (tm-30) cc_final: 0.7665 (tm-30) REVERT: H 145 VAL cc_start: 0.9193 (t) cc_final: 0.8891 (t) REVERT: I 51 GLU cc_start: 0.7792 (tt0) cc_final: 0.7477 (tt0) REVERT: I 64 ASN cc_start: 0.9113 (t0) cc_final: 0.8906 (t0) REVERT: I 140 ARG cc_start: 0.8275 (mtm110) cc_final: 0.8032 (mtm110) REVERT: J 125 LEU cc_start: 0.7169 (tp) cc_final: 0.6844 (tp) REVERT: J 165 GLU cc_start: 0.6293 (tm-30) cc_final: 0.6081 (tm-30) REVERT: J 167 ASP cc_start: 0.7658 (m-30) cc_final: 0.7345 (m-30) REVERT: J 169 GLU cc_start: 0.6826 (mm-30) cc_final: 0.6618 (mm-30) REVERT: J 173 PHE cc_start: 0.8651 (m-80) cc_final: 0.8196 (m-80) REVERT: K 18 ASP cc_start: 0.7869 (p0) cc_final: 0.7630 (p0) REVERT: K 78 ASP cc_start: 0.8788 (m-30) cc_final: 0.8374 (m-30) REVERT: K 138 HIS cc_start: 0.8678 (m-70) cc_final: 0.8205 (m-70) REVERT: K 140 ARG cc_start: 0.7986 (ttm-80) cc_final: 0.7668 (ttm110) REVERT: K 141 GLU cc_start: 0.8035 (tp30) cc_final: 0.7632 (tp30) REVERT: K 155 LEU cc_start: 0.8611 (tp) cc_final: 0.8317 (tt) REVERT: L 161 LEU cc_start: 0.8392 (mt) cc_final: 0.8033 (tp) REVERT: M 26 GLU cc_start: 0.7656 (mp0) cc_final: 0.5879 (mp0) REVERT: M 146 LYS cc_start: 0.8349 (ttpt) cc_final: 0.8056 (ttmt) REVERT: M 172 ARG cc_start: 0.7361 (tpt-90) cc_final: 0.6981 (tpp80) REVERT: M 178 GLU cc_start: 0.8017 (mp0) cc_final: 0.7780 (mp0) REVERT: N 136 GLU cc_start: 0.8576 (tm-30) cc_final: 0.7892 (tm-30) REVERT: N 170 ARG cc_start: 0.8277 (tpp-160) cc_final: 0.7948 (tpp80) outliers start: 76 outliers final: 58 residues processed: 1368 average time/residue: 1.1281 time to fit residues: 2397.8439 Evaluate side-chains 1324 residues out of total 4071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 1263 time to evaluate : 4.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 634 LYS Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 383 GLU Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 531 SER Chi-restraints excluded: chain B residue 616 SER Chi-restraints excluded: chain B residue 642 ASN Chi-restraints excluded: chain B residue 674 ASP Chi-restraints excluded: chain B residue 727 ASP Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 617 ILE Chi-restraints excluded: chain D residue 321 SER Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 445 ASP Chi-restraints excluded: chain D residue 637 THR Chi-restraints excluded: chain D residue 679 SER Chi-restraints excluded: chain D residue 690 LEU Chi-restraints excluded: chain D residue 743 THR Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 321 SER Chi-restraints excluded: chain E residue 564 ASP Chi-restraints excluded: chain F residue 194 GLU Chi-restraints excluded: chain F residue 196 GLU Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 259 TYR Chi-restraints excluded: chain F residue 370 ASP Chi-restraints excluded: chain F residue 426 ILE Chi-restraints excluded: chain F residue 447 ASP Chi-restraints excluded: chain F residue 583 ASN Chi-restraints excluded: chain F residue 623 ASP Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 174 LEU Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 94 GLN Chi-restraints excluded: chain I residue 123 GLN Chi-restraints excluded: chain I residue 157 THR Chi-restraints excluded: chain J residue 75 SER Chi-restraints excluded: chain J residue 117 SER Chi-restraints excluded: chain K residue 58 ASP Chi-restraints excluded: chain L residue 18 ASP Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain M residue 57 LYS Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain M residue 174 LEU Chi-restraints excluded: chain N residue 6 VAL Chi-restraints excluded: chain N residue 16 SER Chi-restraints excluded: chain N residue 39 MET Chi-restraints excluded: chain N residue 119 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 432 optimal weight: 10.0000 chunk 328 optimal weight: 20.0000 chunk 227 optimal weight: 0.8980 chunk 48 optimal weight: 8.9990 chunk 208 optimal weight: 10.0000 chunk 293 optimal weight: 9.9990 chunk 439 optimal weight: 20.0000 chunk 464 optimal weight: 9.9990 chunk 229 optimal weight: 10.0000 chunk 416 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 overall best weight: 5.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 356 GLN ** A 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 675 GLN ** D 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 730 GLN ** E 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 443 GLN ** F 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 558 HIS I 9 GLN K 41 ASN K 129 GLN N 81 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.4134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 38713 Z= 0.305 Angle : 0.537 9.832 52313 Z= 0.278 Chirality : 0.045 1.710 6001 Planarity : 0.004 0.061 6750 Dihedral : 9.685 172.784 5443 Min Nonbonded Distance : 1.746 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.11 % Allowed : 14.00 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.12), residues: 4809 helix: 0.51 (0.10), residues: 2467 sheet: -0.60 (0.20), residues: 622 loop : -0.49 (0.14), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 229 HIS 0.006 0.001 HIS I 122 PHE 0.026 0.001 PHE E 596 TYR 0.018 0.001 TYR I 77 ARG 0.012 0.000 ARG N 140 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 497 is missing expected H atoms. Skipping. Residue LYS 475 is missing expected H atoms. Skipping. Evaluate side-chains 1383 residues out of total 4071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 1297 time to evaluate : 4.663 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: A 266 ARG cc_start: 0.8303 (mtt180) cc_final: 0.8089 (mmm-85) REVERT: A 359 ASN cc_start: 0.8681 (m-40) cc_final: 0.8436 (m110) REVERT: A 548 LEU cc_start: 0.7286 (mt) cc_final: 0.6941 (mt) REVERT: A 663 ASP cc_start: 0.8024 (m-30) cc_final: 0.7817 (m-30) REVERT: A 692 GLU cc_start: 0.7204 (OUTLIER) cc_final: 0.6890 (pm20) REVERT: A 741 GLU cc_start: 0.7861 (mm-30) cc_final: 0.7613 (mm-30) REVERT: B 194 GLU cc_start: 0.8444 (mp0) cc_final: 0.7744 (mp0) REVERT: B 258 LYS cc_start: 0.8157 (tttt) cc_final: 0.7885 (tttm) REVERT: B 265 LYS cc_start: 0.8525 (mtmt) cc_final: 0.8309 (mtmt) REVERT: B 335 ARG cc_start: 0.6921 (mmp80) cc_final: 0.6718 (mmp80) REVERT: B 447 ASP cc_start: 0.7498 (m-30) cc_final: 0.6818 (m-30) REVERT: B 450 LYS cc_start: 0.8908 (ttpt) cc_final: 0.8654 (tttp) REVERT: B 451 ASN cc_start: 0.7807 (m-40) cc_final: 0.7265 (m-40) REVERT: B 674 ASP cc_start: 0.8182 (OUTLIER) cc_final: 0.7911 (t0) REVERT: B 727 ASP cc_start: 0.7090 (OUTLIER) cc_final: 0.6107 (p0) REVERT: D 372 ARG cc_start: 0.7517 (ttp80) cc_final: 0.7216 (ttt90) REVERT: D 684 GLN cc_start: 0.8340 (tp40) cc_final: 0.8052 (tp-100) REVERT: D 719 GLU cc_start: 0.7597 (mm-30) cc_final: 0.6999 (mm-30) REVERT: E 392 ARG cc_start: 0.7883 (mpp80) cc_final: 0.7673 (mtp85) REVERT: E 672 GLN cc_start: 0.8809 (tt0) cc_final: 0.8478 (tt0) REVERT: F 229 TRP cc_start: 0.8117 (t60) cc_final: 0.7416 (t60) REVERT: F 365 TYR cc_start: 0.8106 (m-80) cc_final: 0.7871 (m-80) REVERT: F 427 GLU cc_start: 0.7136 (tt0) cc_final: 0.6647 (tt0) REVERT: F 465 LYS cc_start: 0.9142 (tppt) cc_final: 0.8815 (mmmm) REVERT: F 556 HIS cc_start: 0.7920 (m90) cc_final: 0.7650 (m170) REVERT: F 639 GLU cc_start: 0.8954 (mt-10) cc_final: 0.8691 (pm20) REVERT: F 659 HIS cc_start: 0.8666 (m-70) cc_final: 0.8210 (m90) REVERT: F 719 GLU cc_start: 0.7974 (tp30) cc_final: 0.7352 (tp30) REVERT: F 740 ASN cc_start: 0.8392 (m-40) cc_final: 0.8118 (p0) REVERT: H 36 GLU cc_start: 0.7078 (OUTLIER) cc_final: 0.6766 (mp0) REVERT: H 64 ASN cc_start: 0.9211 (t0) cc_final: 0.9004 (t0) REVERT: H 78 ASP cc_start: 0.8522 (m-30) cc_final: 0.7919 (m-30) REVERT: H 136 GLU cc_start: 0.8228 (tm-30) cc_final: 0.7658 (tm-30) REVERT: I 64 ASN cc_start: 0.9170 (t0) cc_final: 0.8929 (t0) REVERT: I 116 ASN cc_start: 0.8272 (m110) cc_final: 0.8021 (m110) REVERT: J 125 LEU cc_start: 0.7174 (tp) cc_final: 0.6835 (tp) REVERT: J 167 ASP cc_start: 0.7561 (m-30) cc_final: 0.7341 (m-30) REVERT: K 18 ASP cc_start: 0.7943 (p0) cc_final: 0.7673 (p0) REVERT: K 78 ASP cc_start: 0.8813 (m-30) cc_final: 0.8511 (m-30) REVERT: K 140 ARG cc_start: 0.7985 (ttm-80) cc_final: 0.7658 (ttm110) REVERT: K 141 GLU cc_start: 0.7963 (tp30) cc_final: 0.7484 (tp30) REVERT: K 145 VAL cc_start: 0.9347 (t) cc_final: 0.8939 (m) REVERT: K 155 LEU cc_start: 0.8616 (tp) cc_final: 0.8373 (tt) REVERT: L 161 LEU cc_start: 0.8383 (mt) cc_final: 0.8032 (tp) REVERT: M 26 GLU cc_start: 0.7622 (mp0) cc_final: 0.6127 (mp0) REVERT: M 146 LYS cc_start: 0.8371 (ttpt) cc_final: 0.8095 (ttmt) REVERT: M 178 GLU cc_start: 0.8063 (mp0) cc_final: 0.7661 (mp0) REVERT: N 32 THR cc_start: 0.9130 (t) cc_final: 0.8807 (m) REVERT: N 136 GLU cc_start: 0.8689 (tm-30) cc_final: 0.8239 (tm-30) REVERT: N 170 ARG cc_start: 0.8356 (tpp-160) cc_final: 0.8047 (tpp80) outliers start: 86 outliers final: 65 residues processed: 1321 average time/residue: 1.1450 time to fit residues: 2356.7765 Evaluate side-chains 1330 residues out of total 4071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 1261 time to evaluate : 4.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 634 LYS Chi-restraints excluded: chain A residue 692 GLU Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 383 GLU Chi-restraints excluded: chain B residue 531 SER Chi-restraints excluded: chain B residue 613 GLU Chi-restraints excluded: chain B residue 642 ASN Chi-restraints excluded: chain B residue 674 ASP Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain B residue 727 ASP Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 617 ILE Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 321 SER Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 612 THR Chi-restraints excluded: chain D residue 637 THR Chi-restraints excluded: chain D residue 679 SER Chi-restraints excluded: chain D residue 690 LEU Chi-restraints excluded: chain D residue 722 PHE Chi-restraints excluded: chain D residue 743 THR Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 249 ASP Chi-restraints excluded: chain E residue 321 SER Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 564 ASP Chi-restraints excluded: chain F residue 194 GLU Chi-restraints excluded: chain F residue 196 GLU Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 259 TYR Chi-restraints excluded: chain F residue 362 LYS Chi-restraints excluded: chain F residue 370 ASP Chi-restraints excluded: chain F residue 426 ILE Chi-restraints excluded: chain F residue 447 ASP Chi-restraints excluded: chain F residue 583 ASN Chi-restraints excluded: chain F residue 621 HIS Chi-restraints excluded: chain F residue 623 ASP Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 181 GLU Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 58 ASP Chi-restraints excluded: chain I residue 94 GLN Chi-restraints excluded: chain I residue 123 GLN Chi-restraints excluded: chain I residue 157 THR Chi-restraints excluded: chain J residue 75 SER Chi-restraints excluded: chain J residue 117 SER Chi-restraints excluded: chain J residue 134 ASP Chi-restraints excluded: chain K residue 8 GLU Chi-restraints excluded: chain K residue 58 ASP Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain M residue 79 THR Chi-restraints excluded: chain M residue 117 SER Chi-restraints excluded: chain M residue 174 LEU Chi-restraints excluded: chain N residue 16 SER Chi-restraints excluded: chain N residue 18 ASP Chi-restraints excluded: chain N residue 119 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 387 optimal weight: 7.9990 chunk 263 optimal weight: 10.0000 chunk 6 optimal weight: 20.0000 chunk 346 optimal weight: 30.0000 chunk 191 optimal weight: 6.9990 chunk 396 optimal weight: 10.0000 chunk 321 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 chunk 237 optimal weight: 2.9990 chunk 417 optimal weight: 8.9990 chunk 117 optimal weight: 5.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 659 HIS C 305 ASN D 200 GLN D 305 ASN ** D 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 558 HIS ** H 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.4538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 38713 Z= 0.360 Angle : 0.558 9.813 52313 Z= 0.289 Chirality : 0.046 1.705 6001 Planarity : 0.004 0.075 6750 Dihedral : 9.650 169.346 5443 Min Nonbonded Distance : 1.711 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.26 % Allowed : 15.03 % Favored : 82.71 % 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: -0.15 (0.12), residues: 4809 helix: 0.50 (0.10), residues: 2454 sheet: -0.74 (0.20), residues: 637 loop : -0.52 (0.14), residues: 1718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 229 HIS 0.007 0.001 HIS I 122 PHE 0.031 0.002 PHE E 596 TYR 0.018 0.001 TYR I 128 ARG 0.008 0.000 ARG E 455 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 497 is missing expected H atoms. Skipping. Residue LYS 475 is missing expected H atoms. Skipping. Evaluate side-chains 1395 residues out of total 4071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 1303 time to evaluate : 4.740 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: A 266 ARG cc_start: 0.8347 (mtt180) cc_final: 0.7824 (mmm-85) REVERT: A 359 ASN cc_start: 0.8597 (m-40) cc_final: 0.8360 (m110) REVERT: A 548 LEU cc_start: 0.7339 (mt) cc_final: 0.7105 (mp) REVERT: A 655 THR cc_start: 0.8689 (m) cc_final: 0.8478 (p) REVERT: A 663 ASP cc_start: 0.8100 (m-30) cc_final: 0.7879 (m-30) REVERT: A 681 GLU cc_start: 0.7122 (mp0) cc_final: 0.6816 (mp0) REVERT: A 692 GLU cc_start: 0.7157 (OUTLIER) cc_final: 0.6802 (pm20) REVERT: A 741 GLU cc_start: 0.7843 (mm-30) cc_final: 0.7615 (mm-30) REVERT: B 194 GLU cc_start: 0.8469 (mp0) cc_final: 0.7715 (mp0) REVERT: B 207 LYS cc_start: 0.8272 (mmtm) cc_final: 0.7942 (mmtm) REVERT: B 258 LYS cc_start: 0.8194 (tttt) cc_final: 0.7880 (tttm) REVERT: B 343 LYS cc_start: 0.9057 (ttpp) cc_final: 0.8781 (ttmt) REVERT: B 447 ASP cc_start: 0.7576 (m-30) cc_final: 0.7031 (m-30) REVERT: B 450 LYS cc_start: 0.8923 (ttpt) cc_final: 0.8663 (tttp) REVERT: B 451 ASN cc_start: 0.7876 (m-40) cc_final: 0.7385 (m-40) REVERT: B 674 ASP cc_start: 0.8206 (OUTLIER) cc_final: 0.7923 (t0) REVERT: B 727 ASP cc_start: 0.7501 (OUTLIER) cc_final: 0.6444 (p0) REVERT: C 215 GLU cc_start: 0.8260 (mm-30) cc_final: 0.7961 (mm-30) REVERT: C 503 GLU cc_start: 0.8248 (tp30) cc_final: 0.7973 (tp30) REVERT: D 186 ASP cc_start: 0.8189 (OUTLIER) cc_final: 0.7793 (m-30) REVERT: D 372 ARG cc_start: 0.7513 (ttp80) cc_final: 0.7212 (ttt90) REVERT: D 684 GLN cc_start: 0.8438 (tp40) cc_final: 0.8135 (tp-100) REVERT: D 719 GLU cc_start: 0.7674 (mm-30) cc_final: 0.7037 (mm-30) REVERT: E 651 ASP cc_start: 0.7654 (p0) cc_final: 0.7275 (p0) REVERT: F 340 ARG cc_start: 0.7473 (mmt180) cc_final: 0.7003 (mmm160) REVERT: F 365 TYR cc_start: 0.8170 (m-80) cc_final: 0.7941 (m-80) REVERT: F 427 GLU cc_start: 0.7249 (mt-10) cc_final: 0.6899 (tt0) REVERT: F 465 LYS cc_start: 0.9133 (tppt) cc_final: 0.8848 (mmmm) REVERT: F 639 GLU cc_start: 0.8917 (mt-10) cc_final: 0.8660 (pm20) REVERT: F 659 HIS cc_start: 0.8705 (m-70) cc_final: 0.8079 (m90) REVERT: F 687 ARG cc_start: 0.7836 (mtt90) cc_final: 0.7590 (mpt180) REVERT: F 719 GLU cc_start: 0.7940 (tp30) cc_final: 0.7729 (tp30) REVERT: H 36 GLU cc_start: 0.7110 (OUTLIER) cc_final: 0.6751 (mp0) REVERT: H 78 ASP cc_start: 0.8535 (m-30) cc_final: 0.7897 (m-30) REVERT: H 136 GLU cc_start: 0.8267 (tm-30) cc_final: 0.7749 (tm-30) REVERT: I 64 ASN cc_start: 0.9223 (t0) cc_final: 0.8984 (t0) REVERT: I 116 ASN cc_start: 0.8358 (m110) cc_final: 0.8053 (m110) REVERT: J 34 GLN cc_start: 0.7614 (mt0) cc_final: 0.7381 (mm-40) REVERT: J 125 LEU cc_start: 0.7188 (tp) cc_final: 0.6842 (tp) REVERT: K 18 ASP cc_start: 0.8032 (p0) cc_final: 0.7704 (p0) REVERT: K 78 ASP cc_start: 0.8815 (m-30) cc_final: 0.8561 (m-30) REVERT: K 141 GLU cc_start: 0.7949 (tp30) cc_final: 0.7479 (tp30) REVERT: K 145 VAL cc_start: 0.9324 (t) cc_final: 0.8818 (m) REVERT: K 151 GLU cc_start: 0.7832 (mt-10) cc_final: 0.7608 (mt-10) REVERT: K 155 LEU cc_start: 0.8694 (tp) cc_final: 0.8443 (tt) REVERT: L 155 LEU cc_start: 0.8743 (tt) cc_final: 0.8480 (mm) REVERT: L 161 LEU cc_start: 0.8381 (mt) cc_final: 0.8036 (tp) REVERT: L 173 PHE cc_start: 0.8806 (m-80) cc_final: 0.8407 (m-10) REVERT: M 20 TYR cc_start: 0.8501 (m-10) cc_final: 0.8285 (m-10) REVERT: M 26 GLU cc_start: 0.7754 (mp0) cc_final: 0.6296 (mp0) REVERT: M 146 LYS cc_start: 0.8369 (ttpt) cc_final: 0.8081 (ttmt) REVERT: M 178 GLU cc_start: 0.8070 (mp0) cc_final: 0.7679 (mp0) REVERT: N 26 GLU cc_start: 0.8702 (mm-30) cc_final: 0.8210 (mp0) REVERT: N 32 THR cc_start: 0.9151 (t) cc_final: 0.8821 (m) REVERT: N 136 GLU cc_start: 0.8699 (tm-30) cc_final: 0.8202 (tm-30) REVERT: N 170 ARG cc_start: 0.8345 (tpp-160) cc_final: 0.8052 (tpp80) outliers start: 92 outliers final: 75 residues processed: 1333 average time/residue: 1.1507 time to fit residues: 2383.4782 Evaluate side-chains 1350 residues out of total 4071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 1270 time to evaluate : 4.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 634 LYS Chi-restraints excluded: chain A residue 692 GLU Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 531 SER Chi-restraints excluded: chain B residue 613 GLU Chi-restraints excluded: chain B residue 616 SER Chi-restraints excluded: chain B residue 639 GLU Chi-restraints excluded: chain B residue 642 ASN Chi-restraints excluded: chain B residue 674 ASP Chi-restraints excluded: chain B residue 727 ASP Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 321 SER Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 612 THR Chi-restraints excluded: chain D residue 637 THR Chi-restraints excluded: chain D residue 679 SER Chi-restraints excluded: chain D residue 690 LEU Chi-restraints excluded: chain D residue 722 PHE Chi-restraints excluded: chain D residue 743 THR Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 249 ASP Chi-restraints excluded: chain E residue 321 SER Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 490 SER Chi-restraints excluded: chain E residue 564 ASP Chi-restraints excluded: chain F residue 194 GLU Chi-restraints excluded: chain F residue 196 GLU Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 259 TYR Chi-restraints excluded: chain F residue 362 LYS Chi-restraints excluded: chain F residue 370 ASP Chi-restraints excluded: chain F residue 426 ILE Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 447 ASP Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 583 ASN Chi-restraints excluded: chain F residue 621 HIS Chi-restraints excluded: chain F residue 623 ASP Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 58 ASP Chi-restraints excluded: chain I residue 123 GLN Chi-restraints excluded: chain I residue 157 THR Chi-restraints excluded: chain J residue 75 SER Chi-restraints excluded: chain J residue 117 SER Chi-restraints excluded: chain J residue 134 ASP Chi-restraints excluded: chain K residue 8 GLU Chi-restraints excluded: chain K residue 58 ASP Chi-restraints excluded: chain K residue 175 SER Chi-restraints excluded: chain L residue 18 ASP Chi-restraints excluded: chain L residue 41 ASN Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain L residue 157 THR Chi-restraints excluded: chain M residue 16 SER Chi-restraints excluded: chain M residue 57 LYS Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain M residue 94 GLN Chi-restraints excluded: chain M residue 117 SER Chi-restraints excluded: chain M residue 174 LEU Chi-restraints excluded: chain N residue 7 ILE Chi-restraints excluded: chain N residue 16 SER Chi-restraints excluded: chain N residue 18 ASP Chi-restraints excluded: chain N residue 71 THR Chi-restraints excluded: chain N residue 119 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 156 optimal weight: 6.9990 chunk 418 optimal weight: 0.0040 chunk 91 optimal weight: 4.9990 chunk 272 optimal weight: 8.9990 chunk 114 optimal weight: 9.9990 chunk 465 optimal weight: 9.9990 chunk 386 optimal weight: 9.9990 chunk 215 optimal weight: 6.9990 chunk 38 optimal weight: 10.0000 chunk 153 optimal weight: 0.9990 chunk 244 optimal weight: 10.0000 overall best weight: 4.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 558 HIS ** H 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.4692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 38713 Z= 0.229 Angle : 0.511 9.869 52313 Z= 0.261 Chirality : 0.045 1.702 6001 Planarity : 0.004 0.069 6750 Dihedral : 9.396 166.615 5443 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.04 % Allowed : 16.14 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.12), residues: 4809 helix: 0.68 (0.11), residues: 2447 sheet: -0.74 (0.20), residues: 637 loop : -0.42 (0.14), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 229 HIS 0.006 0.001 HIS I 122 PHE 0.024 0.001 PHE E 596 TYR 0.016 0.001 TYR I 128 ARG 0.008 0.000 ARG E 455 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 497 is missing expected H atoms. Skipping. Residue LYS 475 is missing expected H atoms. Skipping. Evaluate side-chains 1379 residues out of total 4071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 1296 time to evaluate : 4.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 ARG cc_start: 0.8331 (mtt180) cc_final: 0.7830 (mmm-85) REVERT: A 359 ASN cc_start: 0.8592 (m-40) cc_final: 0.8360 (m110) REVERT: A 468 GLU cc_start: 0.7766 (mt-10) cc_final: 0.6998 (mt-10) REVERT: A 548 LEU cc_start: 0.7315 (mt) cc_final: 0.7111 (mp) REVERT: A 655 THR cc_start: 0.8661 (m) cc_final: 0.8450 (p) REVERT: A 663 ASP cc_start: 0.8074 (m-30) cc_final: 0.7857 (m-30) REVERT: A 681 GLU cc_start: 0.7130 (mp0) cc_final: 0.6822 (mp0) REVERT: A 692 GLU cc_start: 0.7126 (OUTLIER) cc_final: 0.6773 (pm20) REVERT: B 194 GLU cc_start: 0.8475 (mp0) cc_final: 0.7718 (mp0) REVERT: B 207 LYS cc_start: 0.8209 (mmtm) cc_final: 0.7864 (mmtm) REVERT: B 258 LYS cc_start: 0.8160 (tttt) cc_final: 0.7894 (tttm) REVERT: B 343 LYS cc_start: 0.9057 (ttpp) cc_final: 0.8769 (ttmt) REVERT: B 447 ASP cc_start: 0.7571 (m-30) cc_final: 0.7018 (m-30) REVERT: B 450 LYS cc_start: 0.8886 (ttpt) cc_final: 0.8644 (tttp) REVERT: B 451 ASN cc_start: 0.7789 (m-40) cc_final: 0.7312 (m-40) REVERT: B 565 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7863 (mm-30) REVERT: B 674 ASP cc_start: 0.8175 (OUTLIER) cc_final: 0.7926 (t0) REVERT: B 722 PHE cc_start: 0.9144 (OUTLIER) cc_final: 0.8651 (p90) REVERT: C 503 GLU cc_start: 0.8237 (tp30) cc_final: 0.7962 (tp30) REVERT: D 372 ARG cc_start: 0.7500 (ttp80) cc_final: 0.7198 (ttt90) REVERT: D 408 ARG cc_start: 0.8434 (ttp80) cc_final: 0.8136 (ttp80) REVERT: D 446 ARG cc_start: 0.6157 (ttp80) cc_final: 0.5826 (ttp80) REVERT: D 684 GLN cc_start: 0.8440 (tp40) cc_final: 0.8127 (tp-100) REVERT: D 719 GLU cc_start: 0.7629 (mm-30) cc_final: 0.7163 (mm-30) REVERT: E 651 ASP cc_start: 0.7610 (p0) cc_final: 0.7232 (p0) REVERT: E 672 GLN cc_start: 0.8799 (tt0) cc_final: 0.8510 (tt0) REVERT: F 229 TRP cc_start: 0.8087 (t60) cc_final: 0.7423 (t60) REVERT: F 259 TYR cc_start: 0.7476 (OUTLIER) cc_final: 0.7017 (t80) REVERT: F 340 ARG cc_start: 0.7436 (mmt180) cc_final: 0.6983 (mmm160) REVERT: F 365 TYR cc_start: 0.8150 (m-80) cc_final: 0.7937 (m-80) REVERT: F 465 LYS cc_start: 0.9121 (tppt) cc_final: 0.8843 (mmmm) REVERT: F 631 GLU cc_start: 0.8079 (mp0) cc_final: 0.7800 (mp0) REVERT: F 659 HIS cc_start: 0.8704 (m-70) cc_final: 0.8083 (m90) REVERT: F 719 GLU cc_start: 0.7949 (tp30) cc_final: 0.7344 (tp30) REVERT: H 36 GLU cc_start: 0.7099 (OUTLIER) cc_final: 0.6747 (mp0) REVERT: H 64 ASN cc_start: 0.9171 (t0) cc_final: 0.8928 (t0) REVERT: H 78 ASP cc_start: 0.8510 (m-30) cc_final: 0.7911 (m-30) REVERT: H 136 GLU cc_start: 0.8259 (tm-30) cc_final: 0.7729 (tm-30) REVERT: I 64 ASN cc_start: 0.9188 (t0) cc_final: 0.8978 (t0) REVERT: I 116 ASN cc_start: 0.8343 (m110) cc_final: 0.8009 (m110) REVERT: J 34 GLN cc_start: 0.7587 (mt0) cc_final: 0.7360 (mm-40) REVERT: J 125 LEU cc_start: 0.7203 (tp) cc_final: 0.6854 (tp) REVERT: J 150 ASN cc_start: 0.8507 (m110) cc_final: 0.8289 (m110) REVERT: K 18 ASP cc_start: 0.7995 (p0) cc_final: 0.7644 (p0) REVERT: K 78 ASP cc_start: 0.8821 (m-30) cc_final: 0.8545 (m-30) REVERT: K 141 GLU cc_start: 0.7887 (tp30) cc_final: 0.7274 (tp30) REVERT: K 145 VAL cc_start: 0.9311 (t) cc_final: 0.8733 (m) REVERT: K 151 GLU cc_start: 0.7872 (mt-10) cc_final: 0.7575 (mt-10) REVERT: K 155 LEU cc_start: 0.8705 (tp) cc_final: 0.8427 (tt) REVERT: L 155 LEU cc_start: 0.8756 (tt) cc_final: 0.8473 (mm) REVERT: L 161 LEU cc_start: 0.8370 (mt) cc_final: 0.8031 (tp) REVERT: M 172 ARG cc_start: 0.7343 (tpt-90) cc_final: 0.7114 (tpt-90) REVERT: M 178 GLU cc_start: 0.8082 (mp0) cc_final: 0.7612 (mp0) REVERT: N 22 ARG cc_start: 0.8430 (tpt-90) cc_final: 0.8189 (tpt170) REVERT: N 26 GLU cc_start: 0.8673 (mm-30) cc_final: 0.8463 (mm-30) REVERT: N 32 THR cc_start: 0.9117 (t) cc_final: 0.8804 (m) REVERT: N 136 GLU cc_start: 0.8665 (tm-30) cc_final: 0.8252 (tm-30) REVERT: N 166 ARG cc_start: 0.7681 (mmm-85) cc_final: 0.7392 (mmm-85) outliers start: 83 outliers final: 71 residues processed: 1323 average time/residue: 1.1467 time to fit residues: 2363.5334 Evaluate side-chains 1340 residues out of total 4071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 1264 time to evaluate : 4.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 634 LYS Chi-restraints excluded: chain A residue 692 GLU Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 613 GLU Chi-restraints excluded: chain B residue 639 GLU Chi-restraints excluded: chain B residue 642 ASN Chi-restraints excluded: chain B residue 674 ASP Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain D residue 321 SER Chi-restraints excluded: chain D residue 612 THR Chi-restraints excluded: chain D residue 637 THR Chi-restraints excluded: chain D residue 679 SER Chi-restraints excluded: chain D residue 690 LEU Chi-restraints excluded: chain D residue 722 PHE Chi-restraints excluded: chain D residue 743 THR Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 249 ASP Chi-restraints excluded: chain E residue 321 SER Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 332 GLU Chi-restraints excluded: chain E residue 347 THR Chi-restraints excluded: chain E residue 490 SER Chi-restraints excluded: chain E residue 564 ASP Chi-restraints excluded: chain E residue 654 SER Chi-restraints excluded: chain F residue 194 GLU Chi-restraints excluded: chain F residue 196 GLU Chi-restraints excluded: chain F residue 259 TYR Chi-restraints excluded: chain F residue 362 LYS Chi-restraints excluded: chain F residue 370 ASP Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 374 THR Chi-restraints excluded: chain F residue 426 ILE Chi-restraints excluded: chain F residue 447 ASP Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 583 ASN Chi-restraints excluded: chain F residue 621 HIS Chi-restraints excluded: chain F residue 623 ASP Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 15 ARG Chi-restraints excluded: chain I residue 58 ASP Chi-restraints excluded: chain I residue 123 GLN Chi-restraints excluded: chain I residue 157 THR Chi-restraints excluded: chain J residue 75 SER Chi-restraints excluded: chain J residue 117 SER Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain K residue 8 GLU Chi-restraints excluded: chain K residue 58 ASP Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain K residue 137 ILE Chi-restraints excluded: chain L residue 18 ASP Chi-restraints excluded: chain L residue 157 THR Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain M residue 94 GLN Chi-restraints excluded: chain M residue 117 SER Chi-restraints excluded: chain M residue 149 MET Chi-restraints excluded: chain M residue 174 LEU Chi-restraints excluded: chain N residue 7 ILE Chi-restraints excluded: chain N residue 18 ASP Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 119 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 448 optimal weight: 10.0000 chunk 52 optimal weight: 7.9990 chunk 265 optimal weight: 7.9990 chunk 339 optimal weight: 5.9990 chunk 263 optimal weight: 10.0000 chunk 391 optimal weight: 7.9990 chunk 259 optimal weight: 2.9990 chunk 463 optimal weight: 0.9990 chunk 290 optimal weight: 5.9990 chunk 282 optimal weight: 20.0000 chunk 214 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 730 GLN ** D 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 558 HIS ** H 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 81 GLN ** L 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 41 ASN N 81 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.4843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 38713 Z= 0.259 Angle : 0.518 9.887 52313 Z= 0.265 Chirality : 0.045 1.701 6001 Planarity : 0.004 0.076 6750 Dihedral : 9.317 166.646 5443 Min Nonbonded Distance : 1.761 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.28 % Allowed : 16.26 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.12), residues: 4809 helix: 0.75 (0.11), residues: 2446 sheet: -0.73 (0.20), residues: 641 loop : -0.40 (0.14), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 689 HIS 0.011 0.001 HIS F 570 PHE 0.040 0.001 PHE L 173 TYR 0.018 0.001 TYR I 128 ARG 0.011 0.000 ARG F 527 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 497 is missing expected H atoms. Skipping. Residue LYS 475 is missing expected H atoms. Skipping. Evaluate side-chains 1385 residues out of total 4071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 1292 time to evaluate : 4.693 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: A 266 ARG cc_start: 0.8376 (mtt180) cc_final: 0.7839 (mmm-85) REVERT: A 359 ASN cc_start: 0.8583 (m-40) cc_final: 0.8342 (m110) REVERT: A 468 GLU cc_start: 0.7688 (mt-10) cc_final: 0.7192 (mt-10) REVERT: A 655 THR cc_start: 0.8663 (m) cc_final: 0.8457 (p) REVERT: A 663 ASP cc_start: 0.8075 (m-30) cc_final: 0.7854 (m-30) REVERT: A 681 GLU cc_start: 0.7117 (mp0) cc_final: 0.6808 (mp0) REVERT: A 692 GLU cc_start: 0.7158 (OUTLIER) cc_final: 0.6814 (pm20) REVERT: B 194 GLU cc_start: 0.8466 (mp0) cc_final: 0.7729 (mp0) REVERT: B 207 LYS cc_start: 0.8219 (mmtm) cc_final: 0.7882 (mmtm) REVERT: B 258 LYS cc_start: 0.8167 (tttt) cc_final: 0.7885 (tttm) REVERT: B 343 LYS cc_start: 0.9046 (ttpp) cc_final: 0.8758 (ttmt) REVERT: B 447 ASP cc_start: 0.7573 (m-30) cc_final: 0.7104 (m-30) REVERT: B 450 LYS cc_start: 0.8892 (ttpt) cc_final: 0.8658 (tttp) REVERT: B 451 ASN cc_start: 0.7864 (m-40) cc_final: 0.7404 (m-40) REVERT: B 565 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7888 (mm-30) REVERT: B 674 ASP cc_start: 0.8182 (OUTLIER) cc_final: 0.7928 (t0) REVERT: B 722 PHE cc_start: 0.9220 (OUTLIER) cc_final: 0.8611 (p90) REVERT: C 503 GLU cc_start: 0.8257 (tp30) cc_final: 0.7976 (tp30) REVERT: D 186 ASP cc_start: 0.8196 (OUTLIER) cc_final: 0.7786 (m-30) REVERT: D 372 ARG cc_start: 0.7503 (ttp80) cc_final: 0.7201 (ttt90) REVERT: D 408 ARG cc_start: 0.8440 (ttp80) cc_final: 0.8121 (tmm-80) REVERT: D 446 ARG cc_start: 0.6096 (ttp80) cc_final: 0.5755 (ttp80) REVERT: D 684 GLN cc_start: 0.8471 (tp40) cc_final: 0.8157 (tp-100) REVERT: D 719 GLU cc_start: 0.7621 (mm-30) cc_final: 0.7116 (mm-30) REVERT: E 272 LYS cc_start: 0.8558 (tttt) cc_final: 0.8053 (ttmm) REVERT: E 651 ASP cc_start: 0.7702 (p0) cc_final: 0.7321 (p0) REVERT: F 229 TRP cc_start: 0.8050 (t60) cc_final: 0.7377 (t60) REVERT: F 259 TYR cc_start: 0.7522 (OUTLIER) cc_final: 0.7026 (t80) REVERT: F 340 ARG cc_start: 0.7432 (mmt180) cc_final: 0.6991 (mmm160) REVERT: F 365 TYR cc_start: 0.8169 (m-80) cc_final: 0.7963 (m-80) REVERT: F 465 LYS cc_start: 0.9125 (tppt) cc_final: 0.8922 (mmmm) REVERT: F 556 HIS cc_start: 0.8018 (m90) cc_final: 0.7718 (m170) REVERT: F 631 GLU cc_start: 0.8096 (mp0) cc_final: 0.7822 (mp0) REVERT: F 639 GLU cc_start: 0.8307 (pm20) cc_final: 0.8085 (pm20) REVERT: F 659 HIS cc_start: 0.8734 (m-70) cc_final: 0.8098 (m90) REVERT: F 719 GLU cc_start: 0.7962 (tp30) cc_final: 0.7391 (tp30) REVERT: H 36 GLU cc_start: 0.7115 (OUTLIER) cc_final: 0.6751 (mp0) REVERT: H 64 ASN cc_start: 0.9229 (t0) cc_final: 0.9015 (t0) REVERT: H 78 ASP cc_start: 0.8511 (m-30) cc_final: 0.7907 (m-30) REVERT: H 136 GLU cc_start: 0.8242 (tm-30) cc_final: 0.7764 (tm-30) REVERT: I 64 ASN cc_start: 0.9172 (t0) cc_final: 0.8954 (t0) REVERT: I 116 ASN cc_start: 0.8365 (m110) cc_final: 0.8000 (m110) REVERT: J 34 GLN cc_start: 0.7598 (mt0) cc_final: 0.7119 (mm-40) REVERT: J 125 LEU cc_start: 0.7207 (tp) cc_final: 0.6860 (tp) REVERT: J 172 ARG cc_start: 0.7880 (mmm-85) cc_final: 0.7668 (ttm-80) REVERT: K 18 ASP cc_start: 0.7982 (p0) cc_final: 0.7638 (p0) REVERT: K 78 ASP cc_start: 0.8800 (m-30) cc_final: 0.8521 (m-30) REVERT: K 141 GLU cc_start: 0.7877 (tp30) cc_final: 0.7421 (tp30) REVERT: K 145 VAL cc_start: 0.9288 (t) cc_final: 0.8690 (m) REVERT: K 155 LEU cc_start: 0.8729 (tp) cc_final: 0.8471 (tt) REVERT: L 161 LEU cc_start: 0.8363 (mt) cc_final: 0.8032 (tp) REVERT: M 22 ARG cc_start: 0.8289 (tpt-90) cc_final: 0.7279 (tpt-90) REVERT: M 26 GLU cc_start: 0.7832 (mp0) cc_final: 0.6581 (mp0) REVERT: M 172 ARG cc_start: 0.7332 (tpt-90) cc_final: 0.7094 (tpt-90) REVERT: M 178 GLU cc_start: 0.8149 (mp0) cc_final: 0.7613 (mp0) REVERT: N 22 ARG cc_start: 0.8451 (tpt-90) cc_final: 0.8173 (tpt170) REVERT: N 56 GLU cc_start: 0.7655 (mm-30) cc_final: 0.7404 (mm-30) REVERT: N 136 GLU cc_start: 0.8659 (tm-30) cc_final: 0.8279 (tm-30) REVERT: N 166 ARG cc_start: 0.7692 (mmm-85) cc_final: 0.7404 (mmm-85) REVERT: N 170 ARG cc_start: 0.8431 (tpp80) cc_final: 0.8200 (tpp80) outliers start: 93 outliers final: 81 residues processed: 1322 average time/residue: 1.1157 time to fit residues: 2292.3117 Evaluate side-chains 1353 residues out of total 4071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 1266 time to evaluate : 4.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 634 LYS Chi-restraints excluded: chain A residue 692 GLU Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 531 SER Chi-restraints excluded: chain B residue 613 GLU Chi-restraints excluded: chain B residue 622 GLN Chi-restraints excluded: chain B residue 639 GLU Chi-restraints excluded: chain B residue 642 ASN Chi-restraints excluded: chain B residue 674 ASP Chi-restraints excluded: chain B residue 710 ASP Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 321 SER Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain D residue 490 SER Chi-restraints excluded: chain D residue 637 THR Chi-restraints excluded: chain D residue 679 SER Chi-restraints excluded: chain D residue 690 LEU Chi-restraints excluded: chain D residue 722 PHE Chi-restraints excluded: chain D residue 743 THR Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 249 ASP Chi-restraints excluded: chain E residue 321 SER Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 347 THR Chi-restraints excluded: chain E residue 459 LEU Chi-restraints excluded: chain E residue 490 SER Chi-restraints excluded: chain E residue 564 ASP Chi-restraints excluded: chain E residue 654 SER Chi-restraints excluded: chain F residue 194 GLU Chi-restraints excluded: chain F residue 196 GLU Chi-restraints excluded: chain F residue 259 TYR Chi-restraints excluded: chain F residue 370 ASP Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 374 THR Chi-restraints excluded: chain F residue 426 ILE Chi-restraints excluded: chain F residue 447 ASP Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 583 ASN Chi-restraints excluded: chain F residue 604 THR Chi-restraints excluded: chain F residue 621 HIS Chi-restraints excluded: chain F residue 623 ASP Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 15 ARG Chi-restraints excluded: chain I residue 58 ASP Chi-restraints excluded: chain I residue 123 GLN Chi-restraints excluded: chain I residue 157 THR Chi-restraints excluded: chain J residue 75 SER Chi-restraints excluded: chain J residue 117 SER Chi-restraints excluded: chain J residue 134 ASP Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain K residue 8 GLU Chi-restraints excluded: chain K residue 58 ASP Chi-restraints excluded: chain K residue 120 MET Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain L residue 18 ASP Chi-restraints excluded: chain L residue 41 ASN Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain L residue 157 THR Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain M residue 79 THR Chi-restraints excluded: chain M residue 94 GLN Chi-restraints excluded: chain M residue 117 SER Chi-restraints excluded: chain M residue 149 MET Chi-restraints excluded: chain M residue 174 LEU Chi-restraints excluded: chain N residue 6 VAL Chi-restraints excluded: chain N residue 16 SER Chi-restraints excluded: chain N residue 18 ASP Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 119 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 286 optimal weight: 8.9990 chunk 185 optimal weight: 10.0000 chunk 276 optimal weight: 10.0000 chunk 139 optimal weight: 10.0000 chunk 91 optimal weight: 6.9990 chunk 89 optimal weight: 3.9990 chunk 294 optimal weight: 10.0000 chunk 315 optimal weight: 20.0000 chunk 229 optimal weight: 10.0000 chunk 43 optimal weight: 10.0000 chunk 364 optimal weight: 3.9990 overall best weight: 6.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 507 GLN ** D 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 670 GLN ** E 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 558 HIS ** H 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 81 GLN ** J 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 46 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.5083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 38713 Z= 0.350 Angle : 0.554 9.895 52313 Z= 0.286 Chirality : 0.046 1.700 6001 Planarity : 0.004 0.079 6750 Dihedral : 9.404 163.229 5443 Min Nonbonded Distance : 1.725 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.58 % Allowed : 16.26 % Favored : 81.16 % 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: 4809 helix: 0.71 (0.11), residues: 2414 sheet: -0.76 (0.20), residues: 627 loop : -0.50 (0.14), residues: 1768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 689 HIS 0.010 0.001 HIS L 122 PHE 0.031 0.002 PHE E 596 TYR 0.017 0.002 TYR B 524 ARG 0.008 0.000 ARG M 166 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 497 is missing expected H atoms. Skipping. Residue LYS 475 is missing expected H atoms. Skipping. Evaluate side-chains 1414 residues out of total 4071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 1309 time to evaluate : 5.674 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: A 266 ARG cc_start: 0.8380 (mtt180) cc_final: 0.7844 (mmm-85) REVERT: A 359 ASN cc_start: 0.8582 (m-40) cc_final: 0.8365 (m-40) REVERT: A 464 ASP cc_start: 0.8185 (m-30) cc_final: 0.7428 (p0) REVERT: A 468 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7141 (mt-10) REVERT: A 472 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7685 (mt-10) REVERT: A 655 THR cc_start: 0.8694 (m) cc_final: 0.8473 (p) REVERT: A 663 ASP cc_start: 0.8094 (m-30) cc_final: 0.7885 (m-30) REVERT: A 681 GLU cc_start: 0.7168 (mp0) cc_final: 0.6840 (mp0) REVERT: A 692 GLU cc_start: 0.7242 (OUTLIER) cc_final: 0.6900 (pm20) REVERT: B 194 GLU cc_start: 0.8500 (mp0) cc_final: 0.7713 (mp0) REVERT: B 207 LYS cc_start: 0.8323 (mmtm) cc_final: 0.7989 (mmtm) REVERT: B 258 LYS cc_start: 0.8177 (tttt) cc_final: 0.7866 (tttm) REVERT: B 262 ASP cc_start: 0.7999 (m-30) cc_final: 0.7748 (m-30) REVERT: B 343 LYS cc_start: 0.9056 (ttpp) cc_final: 0.8755 (ttmt) REVERT: B 447 ASP cc_start: 0.7626 (m-30) cc_final: 0.7190 (m-30) REVERT: B 450 LYS cc_start: 0.8915 (ttpt) cc_final: 0.8680 (tttp) REVERT: B 451 ASN cc_start: 0.7822 (m-40) cc_final: 0.7388 (m-40) REVERT: B 565 GLU cc_start: 0.8153 (mm-30) cc_final: 0.7945 (mm-30) REVERT: B 674 ASP cc_start: 0.8224 (OUTLIER) cc_final: 0.7957 (t0) REVERT: B 722 PHE cc_start: 0.9308 (OUTLIER) cc_final: 0.8659 (p90) REVERT: C 592 ARG cc_start: 0.8449 (mtm-85) cc_final: 0.8199 (mtm-85) REVERT: D 186 ASP cc_start: 0.8222 (OUTLIER) cc_final: 0.7811 (m-30) REVERT: D 372 ARG cc_start: 0.7500 (ttp80) cc_final: 0.7183 (ttt90) REVERT: D 408 ARG cc_start: 0.8488 (ttp80) cc_final: 0.8223 (ttp80) REVERT: D 446 ARG cc_start: 0.6093 (ttp80) cc_final: 0.5743 (ttp80) REVERT: D 684 GLN cc_start: 0.8530 (tp40) cc_final: 0.8207 (tp-100) REVERT: D 719 GLU cc_start: 0.7652 (mm-30) cc_final: 0.6992 (mm-30) REVERT: E 272 LYS cc_start: 0.8566 (tttt) cc_final: 0.8067 (ttmm) REVERT: E 651 ASP cc_start: 0.7821 (p0) cc_final: 0.7459 (p0) REVERT: F 259 TYR cc_start: 0.7556 (OUTLIER) cc_final: 0.7050 (t80) REVERT: F 268 LYS cc_start: 0.8616 (mmtp) cc_final: 0.8408 (mttp) REVERT: F 556 HIS cc_start: 0.8040 (m90) cc_final: 0.7726 (m170) REVERT: F 631 GLU cc_start: 0.8089 (mp0) cc_final: 0.7793 (mp0) REVERT: F 639 GLU cc_start: 0.8362 (pm20) cc_final: 0.8130 (pm20) REVERT: F 659 HIS cc_start: 0.8758 (m-70) cc_final: 0.8101 (m90) REVERT: F 711 ASN cc_start: 0.8158 (m110) cc_final: 0.7755 (m110) REVERT: F 719 GLU cc_start: 0.7970 (tp30) cc_final: 0.7390 (tp30) REVERT: H 36 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6796 (mp0) REVERT: H 78 ASP cc_start: 0.8517 (m-30) cc_final: 0.7977 (m-30) REVERT: H 136 GLU cc_start: 0.8275 (tm-30) cc_final: 0.7802 (tm-30) REVERT: I 64 ASN cc_start: 0.9193 (t0) cc_final: 0.8980 (t0) REVERT: I 116 ASN cc_start: 0.8403 (m110) cc_final: 0.8107 (m110) REVERT: J 34 GLN cc_start: 0.7266 (mt0) cc_final: 0.7034 (mm-40) REVERT: J 125 LEU cc_start: 0.7128 (tp) cc_final: 0.6792 (tp) REVERT: J 141 GLU cc_start: 0.6949 (tt0) cc_final: 0.6617 (mt-10) REVERT: J 172 ARG cc_start: 0.7893 (mmm-85) cc_final: 0.7668 (ttm-80) REVERT: K 18 ASP cc_start: 0.8075 (p0) cc_final: 0.7759 (p0) REVERT: K 78 ASP cc_start: 0.8835 (m-30) cc_final: 0.8635 (m-30) REVERT: K 141 GLU cc_start: 0.7843 (tp30) cc_final: 0.7341 (tp30) REVERT: K 145 VAL cc_start: 0.9275 (t) cc_final: 0.8638 (m) REVERT: K 155 LEU cc_start: 0.8754 (tp) cc_final: 0.8484 (tt) REVERT: L 161 LEU cc_start: 0.8346 (mt) cc_final: 0.8014 (tp) REVERT: M 22 ARG cc_start: 0.8376 (tpt-90) cc_final: 0.7316 (tpt-90) REVERT: M 26 GLU cc_start: 0.7890 (mp0) cc_final: 0.6556 (mp0) REVERT: M 56 GLU cc_start: 0.7466 (mp0) cc_final: 0.7171 (mp0) REVERT: M 172 ARG cc_start: 0.7356 (tpt-90) cc_final: 0.7057 (tpt-90) REVERT: M 178 GLU cc_start: 0.8165 (mp0) cc_final: 0.7583 (mp0) REVERT: N 26 GLU cc_start: 0.8652 (mm-30) cc_final: 0.8360 (mm-30) REVERT: N 32 THR cc_start: 0.9127 (t) cc_final: 0.8818 (m) REVERT: N 56 GLU cc_start: 0.7667 (mm-30) cc_final: 0.7340 (mm-30) REVERT: N 136 GLU cc_start: 0.8640 (tm-30) cc_final: 0.8284 (tm-30) REVERT: N 166 ARG cc_start: 0.7695 (mmm-85) cc_final: 0.7408 (mmm-85) outliers start: 105 outliers final: 91 residues processed: 1346 average time/residue: 1.1423 time to fit residues: 2382.3975 Evaluate side-chains 1397 residues out of total 4071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 1300 time to evaluate : 4.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 692 GLU Chi-restraints excluded: chain B residue 172 PHE Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 531 SER Chi-restraints excluded: chain B residue 613 GLU Chi-restraints excluded: chain B residue 622 GLN Chi-restraints excluded: chain B residue 639 GLU Chi-restraints excluded: chain B residue 642 ASN Chi-restraints excluded: chain B residue 674 ASP Chi-restraints excluded: chain B residue 710 ASP Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 321 SER Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 436 ILE Chi-restraints excluded: chain D residue 490 SER Chi-restraints excluded: chain D residue 637 THR Chi-restraints excluded: chain D residue 679 SER Chi-restraints excluded: chain D residue 690 LEU Chi-restraints excluded: chain D residue 722 PHE Chi-restraints excluded: chain D residue 743 THR Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 249 ASP Chi-restraints excluded: chain E residue 321 SER Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 332 GLU Chi-restraints excluded: chain E residue 347 THR Chi-restraints excluded: chain E residue 459 LEU Chi-restraints excluded: chain E residue 490 SER Chi-restraints excluded: chain E residue 654 SER Chi-restraints excluded: chain E residue 666 ILE Chi-restraints excluded: chain F residue 194 GLU Chi-restraints excluded: chain F residue 196 GLU Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 259 TYR Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain F residue 370 ASP Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 374 THR Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 447 ASP Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 583 ASN Chi-restraints excluded: chain F residue 604 THR Chi-restraints excluded: chain F residue 621 HIS Chi-restraints excluded: chain F residue 623 ASP Chi-restraints excluded: chain F residue 708 ILE Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 15 ARG Chi-restraints excluded: chain I residue 58 ASP Chi-restraints excluded: chain I residue 123 GLN Chi-restraints excluded: chain I residue 157 THR Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain J residue 75 SER Chi-restraints excluded: chain J residue 134 ASP Chi-restraints excluded: chain K residue 8 GLU Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain K residue 58 ASP Chi-restraints excluded: chain K residue 120 MET Chi-restraints excluded: chain L residue 18 ASP Chi-restraints excluded: chain L residue 41 ASN Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain L residue 157 THR Chi-restraints excluded: chain M residue 57 LYS Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain M residue 94 GLN Chi-restraints excluded: chain M residue 117 SER Chi-restraints excluded: chain M residue 149 MET Chi-restraints excluded: chain M residue 174 LEU Chi-restraints excluded: chain N residue 6 VAL Chi-restraints excluded: chain N residue 16 SER Chi-restraints excluded: chain N residue 18 ASP Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 79 THR Chi-restraints excluded: chain N residue 119 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 421 optimal weight: 9.9990 chunk 444 optimal weight: 8.9990 chunk 405 optimal weight: 0.9980 chunk 432 optimal weight: 5.9990 chunk 260 optimal weight: 9.9990 chunk 188 optimal weight: 5.9990 chunk 339 optimal weight: 0.2980 chunk 132 optimal weight: 4.9990 chunk 390 optimal weight: 4.9990 chunk 408 optimal weight: 5.9990 chunk 430 optimal weight: 6.9990 overall best weight: 3.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 579 GLN D 675 GLN ** D 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 558 HIS ** H 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 81 GLN ** J 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.5157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 38713 Z= 0.211 Angle : 0.515 9.875 52313 Z= 0.263 Chirality : 0.045 1.701 6001 Planarity : 0.004 0.087 6750 Dihedral : 9.183 162.967 5443 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.01 % Allowed : 17.15 % Favored : 80.84 % 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: 0.20 (0.12), residues: 4809 helix: 0.84 (0.11), residues: 2432 sheet: -0.68 (0.20), residues: 627 loop : -0.39 (0.15), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 689 HIS 0.009 0.001 HIS L 122 PHE 0.023 0.001 PHE E 596 TYR 0.017 0.001 TYR I 128 ARG 0.011 0.000 ARG E 455 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 497 is missing expected H atoms. Skipping. Residue LYS 475 is missing expected H atoms. Skipping. Evaluate side-chains 1388 residues out of total 4071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 1306 time to evaluate : 4.732 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: A 266 ARG cc_start: 0.8381 (mtt180) cc_final: 0.7838 (mmm-85) REVERT: A 359 ASN cc_start: 0.8558 (m-40) cc_final: 0.8323 (m-40) REVERT: A 384 LEU cc_start: 0.8985 (mt) cc_final: 0.8741 (mt) REVERT: A 464 ASP cc_start: 0.8139 (m-30) cc_final: 0.7343 (p0) REVERT: A 468 GLU cc_start: 0.7775 (mt-10) cc_final: 0.7122 (mt-10) REVERT: A 472 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7711 (mt-10) REVERT: A 592 ARG cc_start: 0.7708 (ttp80) cc_final: 0.7454 (ttp80) REVERT: A 655 THR cc_start: 0.8674 (m) cc_final: 0.8465 (p) REVERT: A 681 GLU cc_start: 0.7166 (mp0) cc_final: 0.6896 (mp0) REVERT: A 692 GLU cc_start: 0.7171 (OUTLIER) cc_final: 0.6838 (pm20) REVERT: A 741 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7546 (mm-30) REVERT: B 194 GLU cc_start: 0.8473 (mp0) cc_final: 0.7692 (mp0) REVERT: B 258 LYS cc_start: 0.8138 (tttt) cc_final: 0.7894 (tttm) REVERT: B 262 ASP cc_start: 0.7975 (m-30) cc_final: 0.7773 (m-30) REVERT: B 343 LYS cc_start: 0.9062 (ttpp) cc_final: 0.8752 (ttmt) REVERT: B 447 ASP cc_start: 0.7598 (m-30) cc_final: 0.7171 (m-30) REVERT: B 450 LYS cc_start: 0.8890 (ttpt) cc_final: 0.8660 (tttp) REVERT: B 451 ASN cc_start: 0.7828 (m-40) cc_final: 0.7375 (m-40) REVERT: B 565 GLU cc_start: 0.8063 (mm-30) cc_final: 0.7846 (mm-30) REVERT: B 722 PHE cc_start: 0.9252 (OUTLIER) cc_final: 0.8554 (p90) REVERT: C 527 ARG cc_start: 0.8323 (mtp-110) cc_final: 0.8076 (mtp-110) REVERT: D 186 ASP cc_start: 0.8192 (OUTLIER) cc_final: 0.7778 (m-30) REVERT: D 372 ARG cc_start: 0.7502 (ttp80) cc_final: 0.7193 (ttt90) REVERT: D 408 ARG cc_start: 0.8468 (ttp80) cc_final: 0.8178 (tmm-80) REVERT: D 446 ARG cc_start: 0.6061 (ttp80) cc_final: 0.5709 (ttp80) REVERT: D 684 GLN cc_start: 0.8486 (tp40) cc_final: 0.8160 (tp-100) REVERT: D 719 GLU cc_start: 0.7585 (mm-30) cc_final: 0.6978 (mm-30) REVERT: E 272 LYS cc_start: 0.8545 (tttt) cc_final: 0.8054 (ttmm) REVERT: E 525 MET cc_start: 0.8725 (mmm) cc_final: 0.8382 (mmm) REVERT: E 651 ASP cc_start: 0.7752 (p0) cc_final: 0.7394 (p0) REVERT: F 229 TRP cc_start: 0.8046 (t60) cc_final: 0.7369 (t60) REVERT: F 259 TYR cc_start: 0.7583 (OUTLIER) cc_final: 0.7065 (t80) REVERT: F 340 ARG cc_start: 0.7346 (mmt180) cc_final: 0.6895 (mmm160) REVERT: F 556 HIS cc_start: 0.8023 (m90) cc_final: 0.7714 (m170) REVERT: F 631 GLU cc_start: 0.8045 (mp0) cc_final: 0.7767 (mp0) REVERT: F 639 GLU cc_start: 0.8349 (pm20) cc_final: 0.8114 (pm20) REVERT: F 659 HIS cc_start: 0.8766 (m-70) cc_final: 0.8115 (m90) REVERT: F 687 ARG cc_start: 0.7826 (mtt90) cc_final: 0.7562 (mtt-85) REVERT: F 711 ASN cc_start: 0.8140 (m110) cc_final: 0.7634 (m110) REVERT: F 719 GLU cc_start: 0.7956 (tp30) cc_final: 0.7377 (tp30) REVERT: H 36 GLU cc_start: 0.7184 (OUTLIER) cc_final: 0.6797 (mp0) REVERT: H 78 ASP cc_start: 0.8497 (m-30) cc_final: 0.8000 (m-30) REVERT: H 136 GLU cc_start: 0.8239 (tm-30) cc_final: 0.7765 (tm-30) REVERT: I 116 ASN cc_start: 0.8363 (m110) cc_final: 0.8045 (m110) REVERT: J 34 GLN cc_start: 0.7262 (mt0) cc_final: 0.7042 (mm-40) REVERT: J 125 LEU cc_start: 0.7131 (tp) cc_final: 0.6791 (tp) REVERT: J 141 GLU cc_start: 0.6863 (tt0) cc_final: 0.6630 (mt-10) REVERT: J 172 ARG cc_start: 0.7825 (mmm-85) cc_final: 0.7613 (ttm-80) REVERT: K 18 ASP cc_start: 0.7968 (p0) cc_final: 0.7636 (p0) REVERT: K 78 ASP cc_start: 0.8789 (m-30) cc_final: 0.8548 (m-30) REVERT: K 141 GLU cc_start: 0.7838 (tp30) cc_final: 0.7340 (tp30) REVERT: K 155 LEU cc_start: 0.8727 (tp) cc_final: 0.8476 (tt) REVERT: L 121 ILE cc_start: 0.8514 (tp) cc_final: 0.8270 (pt) REVERT: L 161 LEU cc_start: 0.8310 (mt) cc_final: 0.7995 (tp) REVERT: M 56 GLU cc_start: 0.7457 (mp0) cc_final: 0.7161 (mp0) REVERT: M 172 ARG cc_start: 0.7352 (tpt-90) cc_final: 0.7038 (tpt-90) REVERT: M 178 GLU cc_start: 0.8157 (mp0) cc_final: 0.7549 (mp0) REVERT: N 32 THR cc_start: 0.9070 (t) cc_final: 0.8759 (m) REVERT: N 56 GLU cc_start: 0.7671 (mm-30) cc_final: 0.7372 (mm-30) REVERT: N 136 GLU cc_start: 0.8619 (tm-30) cc_final: 0.8254 (tm-30) REVERT: N 166 ARG cc_start: 0.7668 (mmm-85) cc_final: 0.7389 (mmm-85) outliers start: 82 outliers final: 70 residues processed: 1330 average time/residue: 1.1385 time to fit residues: 2341.4061 Evaluate side-chains 1362 residues out of total 4071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 1287 time to evaluate : 4.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 692 GLU Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 531 SER Chi-restraints excluded: chain B residue 613 GLU Chi-restraints excluded: chain B residue 622 GLN Chi-restraints excluded: chain B residue 639 GLU Chi-restraints excluded: chain B residue 642 ASN Chi-restraints excluded: chain B residue 710 ASP Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 564 ASP Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 321 SER Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 490 SER Chi-restraints excluded: chain D residue 679 SER Chi-restraints excluded: chain D residue 690 LEU Chi-restraints excluded: chain D residue 722 PHE Chi-restraints excluded: chain D residue 743 THR Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 249 ASP Chi-restraints excluded: chain E residue 321 SER Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 332 GLU Chi-restraints excluded: chain E residue 347 THR Chi-restraints excluded: chain E residue 459 LEU Chi-restraints excluded: chain E residue 490 SER Chi-restraints excluded: chain F residue 194 GLU Chi-restraints excluded: chain F residue 196 GLU Chi-restraints excluded: chain F residue 259 TYR Chi-restraints excluded: chain F residue 370 ASP Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 374 THR Chi-restraints excluded: chain F residue 447 ASP Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 583 ASN Chi-restraints excluded: chain F residue 621 HIS Chi-restraints excluded: chain F residue 623 ASP Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 15 ARG Chi-restraints excluded: chain I residue 58 ASP Chi-restraints excluded: chain I residue 123 GLN Chi-restraints excluded: chain I residue 157 THR Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain K residue 8 GLU Chi-restraints excluded: chain K residue 58 ASP Chi-restraints excluded: chain K residue 120 MET Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain L residue 18 ASP Chi-restraints excluded: chain L residue 41 ASN Chi-restraints excluded: chain L residue 157 THR Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain M residue 94 GLN Chi-restraints excluded: chain M residue 117 SER Chi-restraints excluded: chain M residue 174 LEU Chi-restraints excluded: chain N residue 6 VAL Chi-restraints excluded: chain N residue 16 SER Chi-restraints excluded: chain N residue 18 ASP Chi-restraints excluded: chain N residue 119 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 283 optimal weight: 9.9990 chunk 456 optimal weight: 2.9990 chunk 278 optimal weight: 2.9990 chunk 216 optimal weight: 1.9990 chunk 317 optimal weight: 4.9990 chunk 479 optimal weight: 5.9990 chunk 441 optimal weight: 9.9990 chunk 381 optimal weight: 5.9990 chunk 39 optimal weight: 9.9990 chunk 294 optimal weight: 10.0000 chunk 233 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 670 GLN ** D 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 670 GLN ** E 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 558 HIS H 116 ASN ** J 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 116 ASN ** L 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.5205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 38713 Z= 0.204 Angle : 0.516 9.937 52313 Z= 0.263 Chirality : 0.044 1.700 6001 Planarity : 0.004 0.080 6750 Dihedral : 9.088 164.424 5443 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.77 % Allowed : 17.59 % Favored : 80.64 % 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: 0.31 (0.12), residues: 4809 helix: 0.94 (0.11), residues: 2436 sheet: -0.66 (0.20), residues: 634 loop : -0.34 (0.15), residues: 1739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 689 HIS 0.015 0.001 HIS F 570 PHE 0.024 0.001 PHE L 173 TYR 0.017 0.001 TYR I 128 ARG 0.011 0.000 ARG I 140 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 497 is missing expected H atoms. Skipping. Residue LYS 475 is missing expected H atoms. Skipping. Evaluate side-chains 1376 residues out of total 4071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 1304 time to evaluate : 4.819 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: A 266 ARG cc_start: 0.8397 (mtt180) cc_final: 0.7862 (mmm-85) REVERT: A 384 LEU cc_start: 0.8951 (mt) cc_final: 0.8734 (mt) REVERT: A 464 ASP cc_start: 0.8104 (m-30) cc_final: 0.7308 (p0) REVERT: A 468 GLU cc_start: 0.7778 (mt-10) cc_final: 0.7138 (mt-10) REVERT: A 472 GLU cc_start: 0.7930 (mt-10) cc_final: 0.7710 (mt-10) REVERT: A 592 ARG cc_start: 0.7682 (ttp80) cc_final: 0.7461 (ttp80) REVERT: A 655 THR cc_start: 0.8662 (m) cc_final: 0.8451 (p) REVERT: A 681 GLU cc_start: 0.7172 (mp0) cc_final: 0.6907 (mp0) REVERT: A 692 GLU cc_start: 0.7180 (OUTLIER) cc_final: 0.6845 (pm20) REVERT: A 741 GLU cc_start: 0.7798 (mm-30) cc_final: 0.7557 (mm-30) REVERT: B 194 GLU cc_start: 0.8470 (mp0) cc_final: 0.7698 (mp0) REVERT: B 258 LYS cc_start: 0.8112 (tttt) cc_final: 0.7869 (tttm) REVERT: B 272 LYS cc_start: 0.7962 (tttt) cc_final: 0.7735 (ttmt) REVERT: B 275 GLU cc_start: 0.7310 (pt0) cc_final: 0.6779 (pm20) REVERT: B 447 ASP cc_start: 0.7593 (m-30) cc_final: 0.7196 (m-30) REVERT: B 450 LYS cc_start: 0.8889 (ttpt) cc_final: 0.8657 (tttp) REVERT: B 451 ASN cc_start: 0.7783 (m-40) cc_final: 0.7347 (m-40) REVERT: B 565 GLU cc_start: 0.8056 (mm-30) cc_final: 0.7850 (mm-30) REVERT: B 722 PHE cc_start: 0.9294 (OUTLIER) cc_final: 0.8717 (p90) REVERT: C 215 GLU cc_start: 0.8255 (mm-30) cc_final: 0.7995 (mm-30) REVERT: C 527 ARG cc_start: 0.8320 (mtp-110) cc_final: 0.8066 (mtp-110) REVERT: D 372 ARG cc_start: 0.7501 (ttp80) cc_final: 0.7207 (ttt90) REVERT: D 408 ARG cc_start: 0.8464 (ttp80) cc_final: 0.8220 (ttp80) REVERT: D 446 ARG cc_start: 0.6064 (ttp80) cc_final: 0.5720 (ttp80) REVERT: D 684 GLN cc_start: 0.8490 (tp40) cc_final: 0.8173 (tp-100) REVERT: D 719 GLU cc_start: 0.7538 (mm-30) cc_final: 0.6937 (mm-30) REVERT: E 272 LYS cc_start: 0.8536 (tttt) cc_final: 0.8054 (ttmm) REVERT: E 525 MET cc_start: 0.8742 (mmm) cc_final: 0.8413 (mmm) REVERT: E 651 ASP cc_start: 0.7758 (p0) cc_final: 0.7406 (p0) REVERT: F 229 TRP cc_start: 0.8029 (t60) cc_final: 0.7346 (t60) REVERT: F 259 TYR cc_start: 0.7597 (OUTLIER) cc_final: 0.7059 (t80) REVERT: F 340 ARG cc_start: 0.7336 (mmt180) cc_final: 0.6896 (mmm160) REVERT: F 631 GLU cc_start: 0.8061 (mp0) cc_final: 0.7774 (mp0) REVERT: F 639 GLU cc_start: 0.8346 (pm20) cc_final: 0.8104 (pm20) REVERT: F 659 HIS cc_start: 0.8778 (m-70) cc_final: 0.8116 (m90) REVERT: F 687 ARG cc_start: 0.7822 (mtt90) cc_final: 0.7555 (mtt-85) REVERT: F 711 ASN cc_start: 0.8109 (m110) cc_final: 0.7685 (m110) REVERT: F 719 GLU cc_start: 0.7945 (tp30) cc_final: 0.7494 (tp30) REVERT: H 36 GLU cc_start: 0.7115 (OUTLIER) cc_final: 0.6750 (mp0) REVERT: H 78 ASP cc_start: 0.8485 (m-30) cc_final: 0.7947 (m-30) REVERT: H 136 GLU cc_start: 0.8243 (tm-30) cc_final: 0.7783 (tm-30) REVERT: I 116 ASN cc_start: 0.8358 (m110) cc_final: 0.7943 (m110) REVERT: J 34 GLN cc_start: 0.7246 (mt0) cc_final: 0.7025 (mm-40) REVERT: J 125 LEU cc_start: 0.7132 (tp) cc_final: 0.6792 (tp) REVERT: J 141 GLU cc_start: 0.6811 (tt0) cc_final: 0.6439 (mt-10) REVERT: J 172 ARG cc_start: 0.7864 (mmm-85) cc_final: 0.7635 (ttm-80) REVERT: K 18 ASP cc_start: 0.7957 (p0) cc_final: 0.7645 (p0) REVERT: K 78 ASP cc_start: 0.8835 (m-30) cc_final: 0.8615 (m-30) REVERT: K 121 ILE cc_start: 0.7890 (tp) cc_final: 0.7592 (tp) REVERT: K 141 GLU cc_start: 0.7832 (tp30) cc_final: 0.7339 (tp30) REVERT: K 155 LEU cc_start: 0.8706 (tp) cc_final: 0.8466 (tt) REVERT: L 121 ILE cc_start: 0.8511 (tp) cc_final: 0.8022 (pt) REVERT: L 161 LEU cc_start: 0.8343 (mt) cc_final: 0.8023 (tp) REVERT: M 26 GLU cc_start: 0.7864 (mp0) cc_final: 0.6467 (mp0) REVERT: M 172 ARG cc_start: 0.7361 (tpt-90) cc_final: 0.7036 (tpt-90) REVERT: M 178 GLU cc_start: 0.8168 (mp0) cc_final: 0.7542 (mp0) REVERT: N 26 GLU cc_start: 0.8647 (mm-30) cc_final: 0.8413 (mm-30) REVERT: N 32 THR cc_start: 0.9060 (t) cc_final: 0.8730 (m) REVERT: N 56 GLU cc_start: 0.7676 (mm-30) cc_final: 0.7378 (mm-30) REVERT: N 136 GLU cc_start: 0.8591 (tm-30) cc_final: 0.8266 (tm-30) REVERT: N 155 LEU cc_start: 0.8734 (tp) cc_final: 0.8509 (tp) REVERT: N 166 ARG cc_start: 0.7669 (mmm-85) cc_final: 0.7392 (mmm-85) outliers start: 72 outliers final: 65 residues processed: 1327 average time/residue: 1.1161 time to fit residues: 2286.1274 Evaluate side-chains 1367 residues out of total 4071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 1298 time to evaluate : 4.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 692 GLU Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 531 SER Chi-restraints excluded: chain B residue 622 GLN Chi-restraints excluded: chain B residue 639 GLU Chi-restraints excluded: chain B residue 642 ASN Chi-restraints excluded: chain B residue 710 ASP Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 564 ASP Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 321 SER Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 490 SER Chi-restraints excluded: chain D residue 679 SER Chi-restraints excluded: chain D residue 690 LEU Chi-restraints excluded: chain D residue 722 PHE Chi-restraints excluded: chain D residue 743 THR Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 249 ASP Chi-restraints excluded: chain E residue 321 SER Chi-restraints excluded: chain E residue 332 GLU Chi-restraints excluded: chain E residue 347 THR Chi-restraints excluded: chain E residue 459 LEU Chi-restraints excluded: chain E residue 490 SER Chi-restraints excluded: chain F residue 194 GLU Chi-restraints excluded: chain F residue 196 GLU Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 259 TYR Chi-restraints excluded: chain F residue 370 ASP Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 374 THR Chi-restraints excluded: chain F residue 447 ASP Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 583 ASN Chi-restraints excluded: chain F residue 621 HIS Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 15 ARG Chi-restraints excluded: chain I residue 58 ASP Chi-restraints excluded: chain I residue 123 GLN Chi-restraints excluded: chain I residue 157 THR Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain K residue 58 ASP Chi-restraints excluded: chain K residue 120 MET Chi-restraints excluded: chain L residue 18 ASP Chi-restraints excluded: chain L residue 41 ASN Chi-restraints excluded: chain L residue 157 THR Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain M residue 94 GLN Chi-restraints excluded: chain M residue 117 SER Chi-restraints excluded: chain M residue 174 LEU Chi-restraints excluded: chain N residue 16 SER Chi-restraints excluded: chain N residue 18 ASP Chi-restraints excluded: chain N residue 119 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 303 optimal weight: 4.9990 chunk 406 optimal weight: 6.9990 chunk 116 optimal weight: 2.9990 chunk 351 optimal weight: 0.0000 chunk 56 optimal weight: 9.9990 chunk 106 optimal weight: 0.8980 chunk 382 optimal weight: 10.0000 chunk 159 optimal weight: 6.9990 chunk 392 optimal weight: 0.8980 chunk 48 optimal weight: 10.0000 chunk 70 optimal weight: 9.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 670 GLN ** E 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 556 HIS F 558 HIS ** F 570 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.155962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.117757 restraints weight = 145512.727| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 2.44 r_work: 0.2969 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.5233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 38713 Z= 0.166 Angle : 0.506 9.956 52313 Z= 0.256 Chirality : 0.044 1.700 6001 Planarity : 0.004 0.074 6750 Dihedral : 8.955 165.513 5443 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.72 % Allowed : 17.71 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.12), residues: 4809 helix: 1.04 (0.11), residues: 2433 sheet: -0.64 (0.20), residues: 629 loop : -0.29 (0.15), residues: 1747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 689 HIS 0.010 0.001 HIS F 556 PHE 0.018 0.001 PHE E 596 TYR 0.014 0.001 TYR I 128 ARG 0.012 0.000 ARG E 455 =============================================================================== Job complete usr+sys time: 31011.53 seconds wall clock time: 531 minutes 51.62 seconds (31911.62 seconds total)