Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 28 22:13:52 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uix_26556/04_2023/7uix_26556_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uix_26556/04_2023/7uix_26556.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/7uix_26556/04_2023/7uix_26556.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uix_26556/04_2023/7uix_26556.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uix_26556/04_2023/7uix_26556_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uix_26556/04_2023/7uix_26556_neut_trim_updated.pdb" } resolution = 3.24 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 33 5.49 5 Mg 11 5.21 5 S 171 5.16 5 C 23846 2.51 5 N 6722 2.21 5 O 7238 1.98 5 H 38286 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 215": "OE1" <-> "OE2" Residue "A ASP 235": "OD1" <-> "OD2" Residue "A GLU 238": "OE1" <-> "OE2" Residue "A TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 264": "OE1" <-> "OE2" Residue "A ASP 277": "OD1" <-> "OD2" Residue "A GLU 286": "OE1" <-> "OE2" Residue "A ASP 302": "OD1" <-> "OD2" Residue "A GLU 332": "OE1" <-> "OE2" Residue "A ARG 335": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 352": "OE1" <-> "OE2" Residue "A GLU 353": "OE1" <-> "OE2" 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 ASP 400": "OD1" <-> "OD2" Residue "A ASP 445": "OD1" <-> "OD2" Residue "A ASP 454": "OD1" <-> "OD2" Residue "A PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 526": "OE1" <-> "OE2" Residue "A PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 544": "OD1" <-> "OD2" Residue "A ASP 588": "OD1" <-> "OD2" Residue "A PHE 596": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 GLU 639": "OE1" <-> "OE2" Residue "A PHE 650": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 651": "OD1" <-> "OD2" Residue "A PHE 665": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 681": "OE1" <-> "OE2" Residue "A GLU 692": "OE1" <-> "OE2" Residue "A PHE 746": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 196": "OE1" <-> "OE2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "B ASP 235": "OD1" <-> "OD2" Residue "B ASP 242": "OD1" <-> "OD2" Residue "B PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 264": "OE1" <-> "OE2" Residue "B ASP 277": "OD1" <-> "OD2" Residue "B ASP 285": "OD1" <-> "OD2" Residue "B TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 373": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 388": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 391": "OD1" <-> "OD2" Residue "B ASP 403": "OD1" <-> "OD2" Residue "B ASP 447": "OD1" <-> "OD2" Residue "B GLU 468": "OE1" <-> "OE2" Residue "B PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 503": "OE1" <-> "OE2" Residue "B GLU 515": "OE1" <-> "OE2" Residue "B PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 588": "OD1" <-> "OD2" Residue "B GLU 630": "OE1" <-> "OE2" Residue "B PHE 636": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 650": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 192": "OE1" <-> "OE2" Residue "C GLU 238": "OE1" <-> "OE2" Residue "C TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 302": "OD1" <-> "OD2" Residue "C TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 366": "OE1" <-> "OE2" Residue "C ASP 370": "OD1" <-> "OD2" Residue "C TYR 373": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 383": "OE1" <-> "OE2" Residue "C TYR 388": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 425": "OD1" <-> "OD2" Residue "C PHE 461": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 540": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 613": "OE1" <-> "OE2" Residue "C GLU 630": "OE1" <-> "OE2" Residue "C PHE 636": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 640": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 650": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 665": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 727": "OD1" <-> "OD2" Residue "D TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 332": "OE1" <-> "OE2" Residue "D ASP 345": "OD1" <-> "OD2" Residue "D TYR 373": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 447": "OD1" <-> "OD2" Residue "D PHE 461": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 540": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 567": "OE1" <-> "OE2" Residue "D ASP 627": "OD1" <-> "OD2" Residue "D GLU 631": "OE1" <-> "OE2" Residue "D PHE 636": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 640": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 665": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 736": "OD1" <-> "OD2" Residue "E PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 242": "OD1" <-> "OD2" Residue "E TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 262": "OD1" <-> "OD2" Residue "E TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 334": "OD1" <-> "OD2" Residue "E PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 373": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 383": "OE1" <-> "OE2" Residue "E ASP 400": "OD1" <-> "OD2" Residue "E ASP 445": "OD1" <-> "OD2" Residue "E PHE 461": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 472": "OE1" <-> "OE2" Residue "E PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 493": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 544": "OD1" <-> "OD2" Residue "E PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 611": "OE1" <-> "OE2" Residue "E ASP 627": "OD1" <-> "OD2" Residue "E PHE 636": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 674": "OD1" <-> "OD2" Residue "E GLU 692": "OE1" <-> "OE2" Residue "E ASP 736": "OD1" <-> "OD2" Residue "E GLU 738": "OE1" <-> "OE2" Residue "F PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 235": "OD1" <-> "OD2" Residue "F GLU 238": "OE1" <-> "OE2" Residue "F PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 264": "OE1" <-> "OE2" Residue "F PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 302": "OD1" <-> "OD2" Residue "F PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 ASP 370": "OD1" <-> "OD2" Residue "F ARG 410": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ASP 447": "OD1" <-> "OD2" Residue "F GLU 468": "OE1" <-> "OE2" Residue "F GLU 472": "OE1" <-> "OE2" Residue "F PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 564": "OD1" <-> "OD2" Residue "F GLU 565": "OE1" <-> "OE2" Residue "F ASP 595": "OD1" <-> "OD2" Residue "F GLU 630": "OE1" <-> "OE2" Residue "F PHE 636": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 639": "OE1" <-> "OE2" Residue "F PHE 640": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 651": "OD1" <-> "OD2" Residue "F PHE 665": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 668": "OE1" <-> "OE2" Residue "F GLU 681": "OE1" <-> "OE2" Residue "F ASP 696": "OD1" <-> "OD2" Residue "F ASP 710": "OD1" <-> "OD2" Residue "F GLU 719": "OE1" <-> "OE2" Residue "F GLU 738": "OE1" <-> "OE2" Residue "H GLU 8": "OE1" <-> "OE2" Residue "H ARG 12": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 53": "OE1" <-> "OE2" Residue "H GLU 56": "OE1" <-> "OE2" Residue "H ASP 58": "OD1" <-> "OD2" Residue "H PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 86": "OD1" <-> "OD2" Residue "H ARG 118": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 134": "OD1" <-> "OD2" Residue "H GLU 136": "OE1" <-> "OE2" Residue "H ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H GLU 151": "OE1" <-> "OE2" Residue "H GLU 162": "OE1" <-> "OE2" Residue "H GLU 165": "OE1" <-> "OE2" Residue "H ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 181": "OE1" <-> "OE2" Residue "H TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I ARG 12": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I GLU 14": "OE1" <-> "OE2" Residue "I ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ASP 58": "OD1" <-> "OD2" Residue "I TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I GLU 136": "OE1" <-> "OE2" 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 ASP 171": "OD1" <-> "OD2" Residue "I TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J GLU 8": "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 TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J ASP 78": "OD1" <-> "OD2" Residue "J PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J ASP 134": "OD1" <-> "OD2" Residue "J GLU 141": "OE1" <-> "OE2" Residue "J ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ARG 12": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ASP 78": "OD1" <-> "OD2" Residue "K TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K GLU 162": "OE1" <-> "OE2" Residue "K ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K GLU 169": "OE1" <-> "OE2" Residue "K ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L GLU 8": "OE1" <-> "OE2" 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 ARG 118": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ASP 134": "OD1" <-> "OD2" Residue "L ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L GLU 165": "OE1" <-> "OE2" Residue "L ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M ARG 12": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ASP 37": "OD1" <-> "OD2" Residue "M GLU 56": "OE1" <-> "OE2" Residue "M ASP 58": "OD1" <-> "OD2" Residue "M ASP 78": "OD1" <-> "OD2" 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 GLU 141": "OE1" <-> "OE2" Residue "M ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M GLU 162": "OE1" <-> "OE2" Residue "M GLU 165": "OE1" <-> "OE2" Residue "M ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M ARG 192": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 12": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N ASP 37": "OD1" <-> "OD2" Residue "N ASP 58": "OD1" <-> "OD2" Residue "N TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N ASP 78": "OD1" <-> "OD2" Residue "N PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N GLU 162": "OE1" <-> "OE2" Residue "N ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "S GLU 15": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 76307 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 9101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 9101 Classifications: {'peptide': 577} Link IDs: {'PTRANS': 18, 'TRANS': 558} Chain: "B" Number of atoms: 9042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 9042 Classifications: {'peptide': 571} Link IDs: {'PTRANS': 18, 'TRANS': 552} Chain breaks: 2 Chain: "C" Number of atoms: 9140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 580, 9140 Classifications: {'peptide': 580} Link IDs: {'PTRANS': 18, 'TRANS': 561} Chain breaks: 1 Chain: "D" 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: "E" Number of atoms: 9123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 580, 9123 Classifications: {'peptide': 580} Link IDs: {'PTRANS': 18, 'TRANS': 561} Chain: "F" Number of atoms: 9022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 9022 Classifications: {'peptide': 571} Link IDs: {'PTRANS': 18, 'TRANS': 552} Chain breaks: 2 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: 2977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 2977 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 7, 'TRANS': 182} Chain: "M" 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: "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: "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: "A" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 57 Unusual residues: {' MG': 3, 'ADP': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} 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: 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: "F" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 24.58, per 1000 atoms: 0.32 Number of scatterers: 76307 At special positions: 0 Unit cell: (150.51, 150.51, 159.21, 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 11 11.99 O 7238 8.00 N 6722 7.00 C 23846 6.00 H 38286 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: 52.83 Conformation dependent library (CDL) restraints added in 4.9 seconds 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8906 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 226 helices and 42 sheets defined 48.1% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.52 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: 3.836A pdb=" N ALA A 224 " --> pdb=" O LYS A 220 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA A 228 " --> pdb=" O ALA A 224 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TRP A 229 " --> pdb=" O GLU A 225 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE A 231 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 254 Processing helix chain 'A' and resid 262 through 277 Processing helix chain 'A' and resid 287 through 291 Processing helix chain 'A' and resid 304 through 313 removed outlier: 3.922A pdb=" N LYS A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Proline residue: A 309 - end of helix Processing helix chain 'A' and resid 324 through 330 Processing helix chain 'A' and resid 335 through 338 No H-bonds generated for 'chain 'A' and resid 335 through 338' Processing helix chain 'A' and resid 351 through 369 Proline residue: A 363 - end of helix Processing helix chain 'A' and resid 375 through 388 removed outlier: 3.537A pdb=" N VAL A 382 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU A 383 " --> pdb=" O ARG A 379 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL A 386 " --> pdb=" O VAL A 382 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N LYS A 387 " --> pdb=" O GLU A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 412 removed outlier: 3.599A pdb=" N ALA A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N ILE A 399 " --> pdb=" O PRO A 395 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP A 400 " --> pdb=" O ASP A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 434 removed outlier: 3.515A pdb=" N VAL A 429 " --> pdb=" O ASP A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 450 Processing helix chain 'A' and resid 452 through 457 Processing helix chain 'A' and resid 464 through 479 Processing helix chain 'A' and resid 501 through 511 Processing helix chain 'A' and resid 521 through 523 No H-bonds generated for 'chain 'A' and resid 521 through 523' Processing helix chain 'A' and resid 527 through 534 removed outlier: 3.884A pdb=" N SER A 531 " --> pdb=" O ARG A 527 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG A 532 " --> pdb=" O HIS A 528 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU A 533 " --> pdb=" O THR A 529 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE A 534 " --> pdb=" O VAL A 530 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 527 through 534' Processing helix chain 'A' and resid 541 through 545 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 573 through 583 Processing helix chain 'A' and resid 609 through 612 No H-bonds generated for 'chain 'A' and resid 609 through 612' Processing helix chain 'A' and resid 629 through 635 Processing helix chain 'A' and resid 638 through 643 removed outlier: 3.648A pdb=" N ARG A 643 " --> pdb=" O GLU A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 676 removed outlier: 4.035A pdb=" N LYS A 676 " --> pdb=" O GLN A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 684 through 694 Processing helix chain 'A' and resid 702 through 711 removed outlier: 3.541A pdb=" N ALA A 705 " --> pdb=" O ARG A 702 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL A 707 " --> pdb=" O MET A 704 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ILE A 708 " --> pdb=" O ALA A 705 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASN A 711 " --> pdb=" O ILE A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 721 removed outlier: 3.511A pdb=" N ASN A 718 " --> pdb=" O LYS A 714 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU A 719 " --> pdb=" O PRO A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 727 removed outlier: 4.332A pdb=" N ASP A 727 " --> pdb=" O SER A 724 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 724 through 727' Processing helix chain 'B' and resid 176 through 181 Processing helix chain 'B' and resid 192 through 203 Processing helix chain 'B' and resid 220 through 233 removed outlier: 3.672A pdb=" N ALA B 224 " --> pdb=" O LYS B 220 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA B 228 " --> pdb=" O ALA B 224 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TRP B 229 " --> pdb=" O GLU B 225 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL B 232 " --> pdb=" O ALA B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 254 Processing helix chain 'B' and resid 262 through 277 removed outlier: 4.048A pdb=" N ASP B 277 " --> pdb=" O GLN B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 291 Processing helix chain 'B' and resid 308 through 313 Processing helix chain 'B' and resid 324 through 330 Processing helix chain 'B' and resid 335 through 340 removed outlier: 3.960A pdb=" N ARG B 340 " --> pdb=" O ALA B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 369 removed outlier: 3.671A pdb=" N VAL B 355 " --> pdb=" O ILE B 351 " (cutoff:3.500A) removed outlier: 3.634A 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 Processing helix chain 'B' and resid 394 through 412 removed outlier: 3.500A pdb=" N ILE B 402 " --> pdb=" O ALA B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 434 Processing helix chain 'B' and resid 452 through 459 Processing helix chain 'B' and resid 464 through 479 Processing helix chain 'B' and resid 501 through 512 removed outlier: 3.994A pdb=" N THR B 505 " --> pdb=" O LYS B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 523 No H-bonds generated for 'chain 'B' and resid 521 through 523' Processing helix chain 'B' and resid 527 through 534 removed outlier: 3.665A pdb=" N ILE B 534 " --> pdb=" O SER B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 543 No H-bonds generated for 'chain 'B' and resid 541 through 543' Processing helix chain 'B' and resid 548 through 555 Processing helix chain 'B' and resid 566 through 568 No H-bonds generated for 'chain 'B' and resid 566 through 568' Processing helix chain 'B' and resid 571 through 583 Processing helix chain 'B' and resid 609 through 613 removed outlier: 3.511A pdb=" N GLU B 613 " --> pdb=" O VAL B 609 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 609 through 613' Processing helix chain 'B' and resid 625 through 635 Processing helix chain 'B' and resid 638 through 643 removed outlier: 3.511A pdb=" N ARG B 643 " --> pdb=" O GLU B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 676 removed outlier: 3.728A pdb=" N ASP B 663 " --> pdb=" O HIS B 659 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN B 675 " --> pdb=" O VAL B 671 " (cutoff:3.500A) removed outlier: 3.740A 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: 3.726A pdb=" N ARG B 706 " --> pdb=" O ARG B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 722 Processing helix chain 'B' and resid 724 through 726 No H-bonds generated for 'chain 'B' and resid 724 through 726' Processing helix chain 'C' and resid 176 through 181 Processing helix chain 'C' and resid 192 through 202 Processing helix chain 'C' and resid 220 through 233 removed outlier: 4.496A pdb=" N ALA C 228 " --> pdb=" O ALA C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 240 No H-bonds generated for 'chain 'C' and resid 238 through 240' Processing helix chain 'C' and resid 250 through 254 Processing helix chain 'C' and resid 262 through 277 Processing helix chain 'C' and resid 287 through 290 Processing helix chain 'C' and resid 303 through 312 Proline residue: C 309 - end of helix Processing helix chain 'C' and resid 335 through 340 removed outlier: 3.574A pdb=" N ARG C 340 " --> pdb=" O ALA C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 369 Proline residue: C 363 - end of helix Processing helix chain 'C' and resid 375 through 388 Processing helix chain 'C' and resid 394 through 412 removed outlier: 4.698A pdb=" N ILE C 399 " --> pdb=" O PRO C 395 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP C 400 " --> pdb=" O ASP C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 423 through 434 Processing helix chain 'C' and resid 443 through 450 removed outlier: 3.607A pdb=" N THR C 448 " --> pdb=" O SER C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 457 Processing helix chain 'C' and resid 464 through 478 Processing helix chain 'C' and resid 501 through 512 removed outlier: 3.947A pdb=" N THR C 505 " --> pdb=" O LYS C 501 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL C 506 " --> pdb=" O THR C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 523 No H-bonds generated for 'chain 'C' and resid 521 through 523' Processing helix chain 'C' and resid 529 through 534 removed outlier: 3.994A pdb=" N ILE C 534 " --> pdb=" O SER C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 555 Processing helix chain 'C' and resid 566 through 568 No H-bonds generated for 'chain 'C' and resid 566 through 568' Processing helix chain 'C' and resid 577 through 582 Processing helix chain 'C' and resid 610 through 613 No H-bonds generated for 'chain 'C' and resid 610 through 613' Processing helix chain 'C' and resid 625 through 635 Processing helix chain 'C' and resid 638 through 641 No H-bonds generated for 'chain 'C' and resid 638 through 641' Processing helix chain 'C' and resid 655 through 676 removed outlier: 3.949A pdb=" N LYS C 676 " --> pdb=" O GLN C 672 " (cutoff:3.500A) Processing helix chain 'C' and resid 684 through 694 Processing helix chain 'C' and resid 702 through 711 removed outlier: 3.744A pdb=" N ARG C 706 " --> pdb=" O ARG C 702 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 721 Processing helix chain 'D' and resid 176 through 181 Processing helix chain 'D' and resid 192 through 202 Processing helix chain 'D' and resid 220 through 233 removed outlier: 3.875A pdb=" N ALA D 228 " --> pdb=" O ALA D 224 " (cutoff:3.500A) removed outlier: 3.509A 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 263 through 277 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 Processing helix chain 'D' and resid 324 through 329 Processing helix chain 'D' and resid 335 through 340 removed outlier: 3.611A pdb=" N ARG D 340 " --> pdb=" O ALA D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 369 removed outlier: 3.574A pdb=" N GLN D 356 " --> pdb=" O GLU D 352 " (cutoff:3.500A) Proline residue: D 363 - end of helix Processing helix chain 'D' and resid 375 through 388 Processing helix chain 'D' and resid 394 through 411 Processing helix chain 'D' and resid 423 through 434 Processing helix chain 'D' and resid 443 through 450 removed outlier: 3.673A pdb=" N ASP D 447 " --> pdb=" O GLN D 443 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR D 448 " --> pdb=" O SER D 444 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 459 Processing helix chain 'D' and resid 464 through 479 Processing helix chain 'D' and resid 501 through 512 removed outlier: 3.674A pdb=" N THR D 505 " --> pdb=" O LYS D 501 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER D 509 " --> pdb=" O THR D 505 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS D 510 " --> pdb=" O VAL D 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 521 through 524 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: 3.842A pdb=" N GLN D 579 " --> pdb=" O ILE D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 609 through 613 Processing helix chain 'D' and resid 627 through 635 removed outlier: 3.570A pdb=" N ILE D 632 " --> pdb=" O ALA D 628 " (cutoff:3.500A) Processing helix chain 'D' and resid 638 through 643 removed outlier: 4.252A pdb=" N ARG D 643 " --> pdb=" O GLU D 639 " (cutoff:3.500A) Processing helix chain 'D' and resid 655 through 676 removed outlier: 3.587A pdb=" N GLN D 660 " --> pdb=" O ASP D 656 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP D 663 " --> pdb=" O HIS D 659 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN D 675 " --> pdb=" O VAL D 671 " (cutoff:3.500A) removed outlier: 3.945A 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: 3.514A pdb=" N ARG D 706 " --> pdb=" O ARG D 702 " (cutoff:3.500A) Processing helix chain 'D' and resid 713 through 722 Processing helix chain 'D' and resid 724 through 726 No H-bonds generated for 'chain 'D' and resid 724 through 726' Processing helix chain 'E' and resid 176 through 181 Processing helix chain 'E' and resid 192 through 203 Processing helix chain 'E' and resid 221 through 233 removed outlier: 4.192A pdb=" N ALA E 228 " --> pdb=" O ALA E 224 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N TRP E 229 " --> pdb=" O GLU E 225 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 254 Processing helix chain 'E' and resid 262 through 275 Processing helix chain 'E' and resid 287 through 290 removed outlier: 3.568A pdb=" N ILE E 290 " --> pdb=" O ILE E 287 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 287 through 290' Processing helix chain 'E' and resid 303 through 313 removed outlier: 3.845A pdb=" N LYS E 308 " --> pdb=" O ALA E 304 " (cutoff:3.500A) Proline residue: E 309 - end of helix Processing helix chain 'E' and resid 324 through 327 No H-bonds generated for 'chain 'E' and resid 324 through 327' Processing helix chain 'E' and resid 335 through 340 removed outlier: 3.552A pdb=" N ARG E 340 " --> pdb=" O ALA E 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 369 removed outlier: 3.588A 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 Processing helix chain 'E' and resid 394 through 412 removed outlier: 3.593A pdb=" N LEU E 411 " --> pdb=" O ALA E 407 " (cutoff:3.500A) Processing helix chain 'E' and resid 423 through 433 Processing helix chain 'E' and resid 444 through 450 Processing helix chain 'E' and resid 452 through 457 Processing helix chain 'E' and resid 464 through 479 Processing helix chain 'E' and resid 501 through 512 removed outlier: 3.692A pdb=" N THR E 505 " --> pdb=" O LYS E 501 " (cutoff:3.500A) Processing helix chain 'E' and resid 521 through 523 No H-bonds generated for 'chain 'E' and resid 521 through 523' Processing helix chain 'E' and resid 527 through 534 removed outlier: 3.953A pdb=" N VAL E 530 " --> pdb=" O ARG E 527 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER E 531 " --> pdb=" O HIS E 528 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ILE E 534 " --> pdb=" O SER E 531 " (cutoff:3.500A) Processing helix chain 'E' and resid 548 through 555 Processing helix chain 'E' and resid 574 through 583 removed outlier: 4.123A pdb=" N GLN E 579 " --> pdb=" O ASN E 575 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL E 580 " --> pdb=" O ILE E 576 " (cutoff:3.500A) Processing helix chain 'E' and resid 607 through 611 Processing helix chain 'E' and resid 631 through 635 Processing helix chain 'E' and resid 638 through 643 removed outlier: 3.543A pdb=" N ARG E 643 " --> pdb=" O GLU E 639 " (cutoff:3.500A) Processing helix chain 'E' and resid 655 through 676 removed outlier: 3.822A pdb=" N HIS E 659 " --> pdb=" O THR E 655 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN E 660 " --> pdb=" O ASP E 656 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LYS E 676 " --> pdb=" O GLN E 672 " (cutoff:3.500A) Processing helix chain 'E' and resid 684 through 694 Processing helix chain 'E' and resid 703 through 721 removed outlier: 4.213A pdb=" N LYS E 714 " --> pdb=" O ASP E 710 " (cutoff:3.500A) Proline residue: E 715 - end of helix removed outlier: 4.149A pdb=" N ASN E 718 " --> pdb=" O LYS E 714 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLU E 719 " --> pdb=" O PRO E 715 " (cutoff:3.500A) Processing helix chain 'E' and resid 724 through 727 removed outlier: 3.977A pdb=" N ASP E 727 " --> pdb=" O SER E 724 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 724 through 727' Processing helix chain 'F' and resid 176 through 182 Processing helix chain 'F' and resid 192 through 202 Processing helix chain 'F' and resid 220 through 233 removed outlier: 3.668A pdb=" N ALA F 224 " --> pdb=" O LYS F 220 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA F 228 " --> pdb=" O ALA F 224 " (cutoff:3.500A) Processing helix chain 'F' and resid 238 through 240 No H-bonds generated for 'chain 'F' and resid 238 through 240' Processing helix chain 'F' and resid 250 through 253 No H-bonds generated for 'chain 'F' and resid 250 through 253' Processing helix chain 'F' and resid 262 through 275 Processing helix chain 'F' and resid 287 through 292 Processing helix chain 'F' and resid 305 through 312 Proline residue: F 309 - end of helix Processing helix chain 'F' and resid 324 through 329 Processing helix chain 'F' and resid 335 through 340 removed outlier: 3.838A pdb=" N ARG F 340 " --> pdb=" O ALA F 336 " (cutoff:3.500A) Processing helix chain 'F' and resid 351 through 369 Proline residue: F 363 - end of helix Processing helix chain 'F' and resid 375 through 388 Processing helix chain 'F' and resid 394 through 412 removed outlier: 3.709A pdb=" N ILE F 399 " --> pdb=" O PRO F 395 " (cutoff:3.500A) Processing helix chain 'F' and resid 423 through 434 Processing helix chain 'F' and resid 445 through 450 Processing helix chain 'F' and resid 452 through 457 Processing helix chain 'F' and resid 464 through 478 Processing helix chain 'F' and resid 501 through 512 removed outlier: 3.877A pdb=" N LYS F 510 " --> pdb=" O VAL F 506 " (cutoff:3.500A) Processing helix chain 'F' and resid 521 through 523 No H-bonds generated for 'chain 'F' and resid 521 through 523' Processing helix chain 'F' and resid 530 through 534 removed outlier: 3.617A pdb=" N ILE F 534 " --> pdb=" O SER F 531 " (cutoff:3.500A) Processing helix chain 'F' and resid 548 through 555 Processing helix chain 'F' and resid 566 through 568 No H-bonds generated for 'chain 'F' and resid 566 through 568' Processing helix chain 'F' and resid 571 through 583 Processing helix chain 'F' and resid 630 through 635 Processing helix chain 'F' and resid 638 through 643 removed outlier: 3.668A pdb=" N ARG F 643 " --> pdb=" O GLU F 639 " (cutoff:3.500A) Processing helix chain 'F' and resid 655 through 675 removed outlier: 3.678A pdb=" N HIS F 659 " --> pdb=" O THR F 655 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLN F 660 " --> pdb=" O ASP F 656 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP F 663 " --> pdb=" O HIS F 659 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS F 664 " --> pdb=" O GLN F 660 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N PHE F 665 " --> pdb=" O VAL F 661 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN F 675 " --> pdb=" O VAL F 671 " (cutoff:3.500A) Processing helix chain 'F' and resid 684 through 694 removed outlier: 4.285A pdb=" N TRP F 689 " --> pdb=" O GLU F 685 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU F 692 " --> pdb=" O ASN F 688 " (cutoff:3.500A) Processing helix chain 'F' and resid 702 through 710 removed outlier: 4.367A pdb=" N ARG F 706 " --> pdb=" O ARG F 702 " (cutoff:3.500A) Processing helix chain 'F' and resid 714 through 721 removed outlier: 3.617A pdb=" N ASN F 718 " --> pdb=" O LYS F 714 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU F 719 " --> pdb=" O PRO F 715 " (cutoff:3.500A) Processing helix chain 'H' and resid 19 through 26 removed outlier: 4.032A pdb=" N GLU H 26 " --> pdb=" O ARG H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 53 removed outlier: 3.776A pdb=" N ASN H 41 " --> pdb=" O ASP H 37 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU H 42 " --> pdb=" O HIS H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 70 through 82 removed outlier: 3.822A pdb=" N SER H 75 " --> pdb=" O THR H 71 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE H 76 " --> pdb=" O ALA H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 105 Processing helix chain 'H' and resid 132 through 157 Processing helix chain 'H' and resid 161 through 169 Processing helix chain 'H' and resid 176 through 182 removed outlier: 3.856A pdb=" N VAL H 180 " --> pdb=" O ALA H 176 " (cutoff:3.500A) Processing helix chain 'I' and resid 19 through 26 removed outlier: 3.569A pdb=" N LEU I 23 " --> pdb=" O ILE I 19 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU I 26 " --> pdb=" O ARG I 22 " (cutoff:3.500A) Processing helix chain 'I' and resid 37 through 53 Processing helix chain 'I' and resid 70 through 82 removed outlier: 3.617A pdb=" N SER I 75 " --> pdb=" O THR I 71 " (cutoff:3.500A) removed outlier: 3.869A 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: 3.534A pdb=" N GLU I 141 " --> pdb=" O ILE I 137 " (cutoff:3.500A) Processing helix chain 'I' and resid 161 through 169 Processing helix chain 'I' and resid 176 through 182 Processing helix chain 'J' and resid 19 through 26 removed outlier: 3.532A pdb=" N GLU J 26 " --> pdb=" O ARG J 22 " (cutoff:3.500A) Processing helix chain 'J' and resid 37 through 53 removed outlier: 3.519A pdb=" N LEU J 42 " --> pdb=" O HIS J 38 " (cutoff:3.500A) Processing helix chain 'J' and resid 70 through 82 removed outlier: 3.804A pdb=" N SER J 75 " --> pdb=" O THR J 71 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ILE J 76 " --> pdb=" O ALA J 72 " (cutoff:3.500A) Processing helix chain 'J' and resid 100 through 104 Processing helix chain 'J' and resid 132 through 157 Processing helix chain 'J' and resid 161 through 167 Processing helix chain 'J' and resid 176 through 182 Processing helix chain 'K' and resid 19 through 26 removed outlier: 3.572A pdb=" N GLU K 26 " --> pdb=" O ARG K 22 " (cutoff:3.500A) Processing helix chain 'K' and resid 37 through 53 removed outlier: 3.551A pdb=" N ALA K 52 " --> pdb=" O LEU K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 70 through 82 removed outlier: 3.734A pdb=" N SER K 75 " --> pdb=" O THR K 71 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE K 76 " --> pdb=" O ALA K 72 " (cutoff:3.500A) Processing helix chain 'K' and resid 100 through 105 Processing helix chain 'K' and resid 132 through 157 removed outlier: 3.543A pdb=" N GLU K 141 " --> pdb=" O ILE K 137 " (cutoff:3.500A) Processing helix chain 'K' and resid 161 through 169 Processing helix chain 'K' and resid 176 through 182 removed outlier: 3.748A pdb=" N VAL K 180 " --> pdb=" O ALA K 176 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU K 181 " --> pdb=" O PRO K 177 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 26 removed outlier: 3.800A pdb=" N GLU L 26 " --> pdb=" O ARG L 22 " (cutoff:3.500A) Processing helix chain 'L' and resid 37 through 53 Processing helix chain 'L' and resid 70 through 82 removed outlier: 3.788A pdb=" N SER L 75 " --> pdb=" O THR L 71 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE L 76 " --> pdb=" O ALA L 72 " (cutoff:3.500A) Processing helix chain 'L' and resid 100 through 105 Processing helix chain 'L' and resid 132 through 157 Processing helix chain 'L' and resid 161 through 168 Processing helix chain 'L' and resid 176 through 182 Processing helix chain 'M' and resid 19 through 25 Processing helix chain 'M' and resid 37 through 53 removed outlier: 3.580A pdb=" N ASN M 41 " --> pdb=" O ASP M 37 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU M 42 " --> pdb=" O HIS M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 70 through 82 removed outlier: 3.597A pdb=" N SER M 75 " --> pdb=" O THR M 71 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE M 76 " --> pdb=" O ALA M 72 " (cutoff:3.500A) Processing helix chain 'M' and resid 97 through 103 Processing helix chain 'M' and resid 132 through 157 removed outlier: 3.500A 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 removed outlier: 3.689A pdb=" N GLU M 181 " --> pdb=" O PRO M 177 " (cutoff:3.500A) Processing helix chain 'N' and resid 19 through 26 Processing helix chain 'N' and resid 37 through 53 Processing helix chain 'N' and resid 70 through 82 removed outlier: 3.791A pdb=" N SER N 75 " --> pdb=" O THR N 71 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE N 76 " --> pdb=" O ALA N 72 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE N 82 " --> pdb=" O ASP N 78 " (cutoff:3.500A) Processing helix chain 'N' and resid 97 through 105 Processing helix chain 'N' and resid 132 through 157 removed outlier: 4.085A pdb=" N ILE N 137 " --> pdb=" O THR N 133 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU N 143 " --> pdb=" O ALA N 139 " (cutoff:3.500A) Processing helix chain 'N' and resid 161 through 168 Processing helix chain 'N' and resid 176 through 182 removed outlier: 3.572A pdb=" N VAL N 180 " --> pdb=" O ALA N 176 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU N 181 " --> pdb=" O PRO N 177 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 341 through 345 removed outlier: 7.089A pdb=" N ASN A 209 " --> pdb=" O GLN A 342 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ILE A 344 " --> pdb=" O ASN A 209 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N LEU A 211 " --> pdb=" O ILE A 344 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N GLY A 320 " --> pdb=" O LEU A 212 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 246 through 248 removed outlier: 6.933A pdb=" N ARG A 317 " --> pdb=" O LEU A 282 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N ILE A 284 " --> pdb=" O ARG A 317 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ILE A 319 " --> pdb=" O ILE A 284 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 646 through 649 removed outlier: 4.215A pdb=" N ASN A 646 " --> pdb=" O SER A 490 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU A 492 " --> pdb=" O ASN A 646 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU A 601 " --> pdb=" O PHE A 491 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N PHE A 493 " --> pdb=" O LEU A 601 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N MET A 603 " --> pdb=" O PHE A 493 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 730 through 736 removed outlier: 3.690A pdb=" N GLN A 747 " --> pdb=" O GLN A 730 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 342 through 346 removed outlier: 6.985A pdb=" N VAL B 318 " --> pdb=" O PRO B 210 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N LEU B 212 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N GLY B 320 " --> pdb=" O LEU B 212 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N GLY B 214 " --> pdb=" O GLY B 320 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N THR B 322 " --> pdb=" O GLY B 214 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 646 through 650 removed outlier: 3.540A pdb=" N ASN B 646 " --> pdb=" O SER B 490 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LEU B 601 " --> pdb=" O PHE B 491 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N PHE B 493 " --> pdb=" O LEU B 601 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N MET B 603 " --> pdb=" O PHE B 493 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N GLY B 495 " --> pdb=" O MET B 603 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N LEU B 561 " --> pdb=" O VAL B 602 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N THR B 604 " --> pdb=" O LEU B 561 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LEU B 563 " --> pdb=" O THR B 604 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 585 through 587 Processing sheet with id= H, first strand: chain 'B' and resid 678 through 682 removed outlier: 7.087A pdb=" N GLY B 729 " --> pdb=" O SER B 679 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N GLU B 681 " --> pdb=" O GLY B 729 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL B 731 " --> pdb=" O GLU B 681 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR B 732 " --> pdb=" O GLY B 745 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU B 741 " --> pdb=" O ASP B 736 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 173 through 175 removed outlier: 4.494A pdb=" N ASP C 285 " --> pdb=" O LEU C 248 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER C 321 " --> pdb=" O ILE C 284 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 646 through 650 removed outlier: 3.749A pdb=" N ASN C 646 " --> pdb=" O SER C 490 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N GLU C 515 " --> pdb=" O VAL C 560 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N LEU C 562 " --> pdb=" O GLU C 515 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LEU C 517 " --> pdb=" O LEU C 562 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N ASP C 564 " --> pdb=" O LEU C 517 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N PHE C 519 " --> pdb=" O ASP C 564 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 585 through 587 Processing sheet with id= L, first strand: chain 'C' and resid 678 through 682 removed outlier: 6.557A pdb=" N GLY C 729 " --> pdb=" O SER C 679 " (cutoff:3.500A) removed outlier: 8.699A pdb=" N GLU C 681 " --> pdb=" O GLY C 729 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL C 731 " --> pdb=" O GLU C 681 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR C 732 " --> pdb=" O GLY C 745 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 173 through 175 removed outlier: 4.691A pdb=" N ASP D 285 " --> pdb=" O LEU D 248 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SER D 321 " --> pdb=" O ILE D 284 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N GLN D 342 " --> pdb=" O LEU D 211 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL D 213 " --> pdb=" O GLN D 342 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ILE D 344 " --> pdb=" O VAL D 213 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 490 through 494 removed outlier: 6.620A pdb=" N LEU D 601 " --> pdb=" O PHE D 491 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N PHE D 493 " --> pdb=" O LEU D 601 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N MET D 603 " --> pdb=" O PHE D 493 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N GLU D 515 " --> pdb=" O VAL D 560 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N LEU D 562 " --> pdb=" O GLU D 515 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LEU D 517 " --> pdb=" O LEU D 562 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ASP D 564 " --> pdb=" O LEU D 517 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N PHE D 519 " --> pdb=" O ASP D 564 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 680 through 682 removed outlier: 7.004A pdb=" N VAL D 731 " --> pdb=" O GLU D 681 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 173 through 175 Processing sheet with id= Q, first strand: chain 'E' and resid 342 through 345 removed outlier: 6.573A pdb=" N GLY E 320 " --> pdb=" O LEU E 212 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N GLY E 214 " --> pdb=" O GLY E 320 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N THR E 322 " --> pdb=" O GLY E 214 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 646 through 650 removed outlier: 3.634A pdb=" N ASN E 646 " --> pdb=" O SER E 490 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU E 601 " --> pdb=" O PHE E 491 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N PHE E 493 " --> pdb=" O LEU E 601 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N MET E 603 " --> pdb=" O PHE E 493 " (cutoff:3.500A) removed outlier: 8.358A pdb=" N GLY E 495 " --> pdb=" O MET E 603 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N GLU E 515 " --> pdb=" O VAL E 560 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N LEU E 562 " --> pdb=" O GLU E 515 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU E 517 " --> pdb=" O LEU E 562 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N ASP E 564 " --> pdb=" O LEU E 517 " (cutoff:3.500A) removed outlier: 7.387A 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 Processing sheet with id= T, first strand: chain 'E' and resid 732 through 736 removed outlier: 4.082A pdb=" N THR E 732 " --> pdb=" O GLY E 745 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY E 745 " --> pdb=" O THR E 732 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU E 741 " --> pdb=" O ASP E 736 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'F' and resid 342 through 345 removed outlier: 6.105A pdb=" N VAL F 318 " --> pdb=" O PRO F 210 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N LEU F 212 " --> pdb=" O VAL F 318 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLY F 320 " --> pdb=" O LEU F 212 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N GLY F 214 " --> pdb=" O GLY F 320 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N THR F 322 " --> pdb=" O GLY F 214 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER F 321 " --> pdb=" O ILE F 284 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'F' and resid 489 through 494 Processing sheet with id= W, first strand: chain 'F' and resid 585 through 587 Processing sheet with id= X, first strand: chain 'F' and resid 730 through 735 Processing sheet with id= Y, first strand: chain 'H' and resid 28 through 32 removed outlier: 6.308A pdb=" N TYR H 60 " --> pdb=" O ILE H 29 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N LEU H 31 " --> pdb=" O TYR H 60 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N TYR H 62 " --> pdb=" O LEU H 31 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'H' and resid 119 through 121 removed outlier: 3.576A pdb=" N ILE H 121 " --> pdb=" O ARG H 172 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ARG H 172 " --> pdb=" O ILE H 121 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'I' and resid 28 through 32 removed outlier: 6.418A pdb=" N TYR I 60 " --> pdb=" O ILE I 29 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N LEU I 31 " --> pdb=" O TYR I 60 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N TYR I 62 " --> pdb=" O LEU I 31 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'I' and resid 118 through 121 Processing sheet with id= AC, first strand: chain 'J' and resid 5 through 9 Processing sheet with id= AD, first strand: chain 'J' and resid 28 through 32 removed outlier: 6.440A pdb=" N TYR J 60 " --> pdb=" O ILE J 29 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N LEU J 31 " --> pdb=" O TYR J 60 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N TYR J 62 " --> pdb=" O LEU J 31 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'K' and resid 5 through 8 Processing sheet with id= AF, first strand: chain 'K' and resid 28 through 32 removed outlier: 6.560A pdb=" N TYR K 60 " --> pdb=" O ILE K 29 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N LEU K 31 " --> pdb=" O TYR K 60 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N TYR K 62 " --> pdb=" O LEU K 31 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'K' and resid 118 through 121 Processing sheet with id= AH, first strand: chain 'L' and resid 5 through 8 removed outlier: 3.533A pdb=" N ARG L 15 " --> pdb=" O GLU L 8 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'L' and resid 28 through 32 removed outlier: 6.720A pdb=" N TYR L 60 " --> pdb=" O ILE L 29 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N LEU L 31 " --> pdb=" O TYR L 60 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N TYR L 62 " --> pdb=" O LEU L 31 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'L' and resid 118 through 121 Processing sheet with id= AK, first strand: chain 'M' and resid 5 through 8 Processing sheet with id= AL, first strand: chain 'M' and resid 28 through 32 removed outlier: 6.446A pdb=" N TYR M 60 " --> pdb=" O ILE M 29 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N LEU M 31 " --> pdb=" O TYR M 60 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N TYR M 62 " --> pdb=" O LEU M 31 " (cutoff:3.500A) No H-bonds generated for sheet with id= AL Processing sheet with id= AM, first strand: chain 'M' and resid 118 through 121 Processing sheet with id= AN, first strand: chain 'N' and resid 5 through 8 Processing sheet with id= AO, first strand: chain 'N' and resid 28 through 31 removed outlier: 6.067A pdb=" N TYR N 60 " --> pdb=" O ILE N 29 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N LEU N 31 " --> pdb=" O TYR N 60 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N TYR N 62 " --> pdb=" O LEU N 31 " (cutoff:3.500A) No H-bonds generated for sheet with id= AO Processing sheet with id= AP, first strand: chain 'N' and resid 118 through 121 1472 hydrogen bonds defined for protein. 4275 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 29.47 Time building geometry restraints manager: 55.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.06: 38260 1.06 - 1.28: 6537 1.28 - 1.50: 15509 1.50 - 1.73: 16270 1.73 - 1.95: 307 Bond restraints: 76883 Sorted by residual: bond pdb=" C4 ADP A 802 " pdb=" C5 ADP A 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 F 801 " pdb=" C5 ADP F 801 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.96e+01 bond pdb=" C4 ADP A 801 " pdb=" C5 ADP A 801 " ideal model delta sigma weight residual 1.490 1.382 0.108 2.00e-02 2.50e+03 2.94e+01 bond pdb=" CA SER E 440 " pdb=" CB SER E 440 " ideal model delta sigma weight residual 1.528 1.457 0.071 1.35e-02 5.49e+03 2.80e+01 bond pdb=" C5 ADP A 802 " pdb=" C6 ADP A 802 " ideal model delta sigma weight residual 1.490 1.407 0.083 2.00e-02 2.50e+03 1.74e+01 ... (remaining 76878 not shown) Histogram of bond angle deviations from ideal: 99.00 - 106.12: 1057 106.12 - 113.24: 92638 113.24 - 120.37: 24106 120.37 - 127.49: 21163 127.49 - 134.61: 369 Bond angle restraints: 139333 Sorted by residual: angle pdb=" N GLN E 443 " pdb=" CA GLN E 443 " pdb=" C GLN E 443 " ideal model delta sigma weight residual 113.72 106.34 7.38 1.30e+00 5.92e-01 3.22e+01 angle pdb=" PA AGS E 802 " pdb=" O3A AGS E 802 " pdb=" PB AGS E 802 " ideal model delta sigma weight residual 119.76 133.11 -13.35 3.00e+00 1.11e-01 1.98e+01 angle pdb=" CA LYS E 439 " pdb=" C LYS E 439 " pdb=" O LYS E 439 " ideal model delta sigma weight residual 121.00 116.44 4.56 1.05e+00 9.07e-01 1.89e+01 angle pdb=" PB AGS D 801 " pdb=" O3B AGS D 801 " pdb=" PG AGS D 801 " ideal model delta sigma weight residual 120.12 132.66 -12.54 3.00e+00 1.11e-01 1.75e+01 angle pdb=" PA ADP A 802 " pdb=" O3A ADP A 802 " pdb=" PB ADP A 802 " ideal model delta sigma weight residual 120.50 132.48 -11.98 3.00e+00 1.11e-01 1.59e+01 ... (remaining 139328 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.55: 29469 28.55 - 57.10: 739 57.10 - 85.64: 107 85.64 - 114.19: 8 114.19 - 142.74: 14 Dihedral angle restraints: 30337 sinusoidal: 14817 harmonic: 15520 Sorted by residual: dihedral pdb=" C5' ADP F 801 " pdb=" O5' ADP F 801 " pdb=" PA ADP F 801 " pdb=" O2A ADP F 801 " ideal model delta sinusoidal sigma weight residual -60.00 82.74 -142.74 1 2.00e+01 2.50e-03 4.31e+01 dihedral pdb=" O2A ADP F 801 " pdb=" O3A ADP F 801 " pdb=" PA ADP F 801 " pdb=" PB ADP F 801 " ideal model delta sinusoidal sigma weight residual 300.00 178.68 121.32 1 2.00e+01 2.50e-03 3.65e+01 dihedral pdb=" O2A ADP A 801 " pdb=" O3A ADP A 801 " pdb=" PA ADP A 801 " pdb=" PB ADP A 801 " ideal model delta sinusoidal sigma weight residual -60.00 60.89 -120.89 1 2.00e+01 2.50e-03 3.63e+01 ... (remaining 30334 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 4492 0.043 - 0.087: 1119 0.087 - 0.130: 313 0.130 - 0.174: 53 0.174 - 0.217: 8 Chirality restraints: 5985 Sorted by residual: chirality pdb=" C3' ADP A 802 " pdb=" C2' ADP A 802 " pdb=" C4' ADP A 802 " pdb=" O3' ADP A 802 " both_signs ideal model delta sigma weight residual False -2.51 -2.73 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" C3' ADP A 801 " pdb=" C2' ADP A 801 " pdb=" C4' ADP A 801 " pdb=" O3' ADP A 801 " both_signs ideal model delta sigma weight residual False -2.51 -2.72 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CB VAL E 441 " pdb=" CA VAL E 441 " pdb=" CG1 VAL E 441 " pdb=" CG2 VAL E 441 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.19 2.00e-01 2.50e+01 9.43e-01 ... (remaining 5982 not shown) Planarity restraints: 11358 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG B 702 " 0.060 5.00e-02 4.00e+02 9.09e-02 1.32e+01 pdb=" N PRO B 703 " -0.157 5.00e-02 4.00e+02 pdb=" CA PRO B 703 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO B 703 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER E 442 " 0.017 2.00e-02 2.50e+03 3.07e-02 9.43e+00 pdb=" N GLN E 443 " -0.053 2.00e-02 2.50e+03 pdb=" CA GLN E 443 " 0.014 2.00e-02 2.50e+03 pdb=" H GLN E 443 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET C 412 " 0.050 5.00e-02 4.00e+02 7.62e-02 9.28e+00 pdb=" N PRO C 413 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO C 413 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 413 " 0.042 5.00e-02 4.00e+02 ... (remaining 11355 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.24: 7301 2.24 - 2.83: 173975 2.83 - 3.42: 200582 3.42 - 4.01: 278034 4.01 - 4.60: 427981 Nonbonded interactions: 1087873 Sorted by model distance: nonbonded pdb=" H PHE A 493 " pdb=" O MET A 603 " model vdw 1.649 1.850 nonbonded pdb=" O LYS F 387 " pdb=" HE2 HIS F 558 " model vdw 1.677 1.850 nonbonded pdb=" O ALA H 96 " pdb=" H ALA H 100 " model vdw 1.679 1.850 nonbonded pdb=" O ALA M 96 " pdb=" H ALA M 100 " model vdw 1.680 1.850 nonbonded pdb=" HG1 THR C 221 " pdb="MG MG C 803 " model vdw 1.685 1.700 ... (remaining 1087868 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 294 or (resid 295 and (name N or name CA or na \ me C or name O or name CB or name HA or name HB1 or name HB2 or name HB3)) or re \ sid 305 through 439 or (resid 440 and (name N or name CA or name C or name O or \ name CB or name OG or name H or name HA )) or (resid 441 and (name N or name CA \ or name C or name O or name CB or name CG1 or name CG2 or name H or name HA )) o \ r (resid 442 and (name N or name CA or name C or name O or name CB or name OG or \ name H or name HA )) or (resid 443 and (name N or name CA or name C or name O o \ r name CB or name CG or name CD or name OE1 or name NE2 or name H or name HA )) \ or resid 444 through 501 or (resid 502 and (name N or name CA or name C or name \ O or name CB or name OG1 or name CG2 or name H or name HA or name HB or name HG2 \ 1 or name HG22 or name HG23)) or resid 503 through 606 or resid 612 through 626 \ or resid 629 through 748)) selection = (chain 'B' and (resid 172 through 220 or (resid 221 and (name N or name CA or na \ me C or name O or name CB or name OG1 or name CG2 or name H or name HA or name H \ B or name HG21 or name HG22 or name HG23)) or resid 222 through 439 or (resid 44 \ 0 and (name N or name CA or name C or name O or name CB or name OG or name H or \ name HA )) or (resid 441 and (name N or name CA or name C or name O or name CB o \ r name CG1 or name CG2 or name H or name HA )) or (resid 442 and (name N or name \ CA or name C or name O or name CB or name OG or name H or name HA )) or (resid \ 443 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 resid 444 through 606 or resi \ d 612 through 626 or resid 629 through 748)) selection = (chain 'C' and (resid 172 through 220 or (resid 221 and (name N or name CA or na \ me C or name O or name CB or name OG1 or name CG2 or name H or name HA or name H \ B or name HG21 or name HG22 or name HG23)) or resid 222 through 294 or (resid 29 \ 5 and (name N or name CA or name C or name O or name CB or name HA or name HB1 o \ r name HB2 or name HB3)) or resid 305 through 439 or (resid 440 and (name N or n \ ame CA or name C or name O or name CB or name OG or name H or name HA )) or (res \ id 441 and (name N or name CA or name C or name O or name CB or name CG1 or name \ CG2 or name H or name HA )) or (resid 442 and (name N or name CA or name C or n \ ame O or name CB or name OG or name H or name HA )) or (resid 443 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 nam \ e NE2 or name H or name HA )) or resid 444 through 606 or resid 612 through 626 \ or resid 629 through 748)) selection = (chain 'D' and (resid 172 through 294 or (resid 295 and (name N or name CA or na \ me C or name O or name CB or name HA or name HB1 or name HB2 or name HB3)) or re \ sid 305 through 439 or (resid 440 and (name N or name CA or name C or name O or \ name CB or name OG or name H or name HA )) or (resid 441 and (name N or name CA \ or name C or name O or name CB or name CG1 or name CG2 or name H or name HA )) o \ r (resid 442 and (name N or name CA or name C or name O or name CB or name OG or \ name H or name HA )) or (resid 443 and (name N or name CA or name C or name O o \ r name CB or name CG or name CD or name OE1 or name NE2 or name H or name HA )) \ or resid 444 through 606 or resid 612 through 626 or resid 629 through 748)) selection = (chain 'E' and (resid 172 through 294 or (resid 295 and (name N or name CA or na \ me C or name O or name CB or name HA or name HB1 or name HB2 or name HB3)) or re \ sid 305 through 606 or resid 612 through 626 or resid 629 through 748)) selection = (chain 'F' and (resid 172 through 220 or (resid 221 and (name N or name CA or na \ me C or name O or name CB or name OG1 or name CG2 or name H or name HA or name H \ B or name HG21 or name HG22 or name HG23)) or resid 222 through 294 or (resid 29 \ 5 and (name N or name CA or name C or name O or name CB or name HA or name HB1 o \ r name HB2 or name HB3)) or resid 305 through 439 or (resid 440 and (name N or n \ ame CA or name C or name O or name CB or name OG or name H or name HA )) or (res \ id 441 and (name N or name CA or name C or name O or name CB or name CG1 or name \ CG2 or name H or name HA )) or (resid 442 and (name N or name CA or name C or n \ ame O or name CB or name OG or name H or name HA )) or (resid 443 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 nam \ e NE2 or name H or name HA )) or resid 444 through 501 or (resid 502 and (name N \ or name CA or name C or name O or name CB or name OG1 or name CG2 or name H or \ name HA or name HB or name HG21 or name HG22 or name HG23)) or resid 503 through \ 748)) } 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' selection = (chain 'M' and resid 2 through 191) 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: 0.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.890 Extract box with map and model: 7.300 Check model and map are aligned: 0.900 Set scattering table: 0.560 Process input model: 193.240 Find NCS groups from input model: 3.470 Set up NCS constraints: 0.240 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:2.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 209.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 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 38597 Z= 0.284 Angle : 0.786 13.345 52148 Z= 0.402 Chirality : 0.043 0.217 5985 Planarity : 0.004 0.091 6722 Dihedral : 14.125 142.739 14619 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.02 % Allowed : 0.06 % Favored : 99.92 % Rotamer Outliers : 0.02 % 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: -0.81 (0.11), residues: 4782 helix: 0.03 (0.10), residues: 2332 sheet: -1.41 (0.19), residues: 668 loop : -0.72 (0.13), residues: 1782 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue SER 440 is missing expected H atoms. Skipping. Residue VAL 441 is missing expected H atoms. Skipping. Residue SER 442 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Evaluate side-chains 1418 residues out of total 4062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1417 time to evaluate : 4.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 1418 average time/residue: 1.1601 time to fit residues: 2567.9502 Evaluate side-chains 1141 residues out of total 4062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1140 time to evaluate : 4.796 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.6949 time to fit residues: 7.5027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 405 optimal weight: 10.0000 chunk 363 optimal weight: 5.9990 chunk 201 optimal weight: 8.9990 chunk 124 optimal weight: 2.9990 chunk 245 optimal weight: 6.9990 chunk 194 optimal weight: 4.9990 chunk 376 optimal weight: 3.9990 chunk 145 optimal weight: 9.9990 chunk 228 optimal weight: 2.9990 chunk 280 optimal weight: 10.0000 chunk 435 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 624 ASN A 642 ASN ** A 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN A 688 ASN B 583 ASN B 709 GLN C 359 ASN C 624 ASN ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 305 ASN E 329 ASN E 670 GLN E 711 ASN F 200 GLN F 356 GLN F 675 GLN ** F 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 740 ASN H 41 ASN H 191 HIS I 156 HIS I 163 GLN J 41 ASN ** L 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 64 ASN M 116 ASN ** M 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 159 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 38597 Z= 0.268 Angle : 0.561 6.758 52148 Z= 0.299 Chirality : 0.041 0.158 5985 Planarity : 0.004 0.092 6722 Dihedral : 8.391 155.128 5321 Min Nonbonded Distance : 1.765 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer Outliers : 1.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.11), residues: 4782 helix: 0.84 (0.10), residues: 2382 sheet: -1.23 (0.18), residues: 667 loop : -0.50 (0.14), residues: 1733 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue SER 440 is missing expected H atoms. Skipping. Residue VAL 441 is missing expected H atoms. Skipping. Residue SER 442 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Evaluate side-chains 1273 residues out of total 4062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 1222 time to evaluate : 4.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 51 outliers final: 32 residues processed: 1242 average time/residue: 1.1471 time to fit residues: 2237.5951 Evaluate side-chains 1188 residues out of total 4062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 1156 time to evaluate : 4.856 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.7521 time to fit residues: 51.3345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 242 optimal weight: 10.0000 chunk 135 optimal weight: 6.9990 chunk 362 optimal weight: 30.0000 chunk 296 optimal weight: 6.9990 chunk 120 optimal weight: 9.9990 chunk 436 optimal weight: 9.9990 chunk 471 optimal weight: 20.0000 chunk 388 optimal weight: 5.9990 chunk 433 optimal weight: 8.9990 chunk 148 optimal weight: 5.9990 chunk 350 optimal weight: 20.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 HIS A 672 GLN A 740 ASN ** C 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 276 GLN D 342 GLN E 463 GLN ** E 558 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 670 GLN ** F 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 583 ASN F 675 GLN H 81 GLN I 41 ASN K 46 GLN K 122 HIS ** K 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 122 HIS ** M 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 122 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.059 38597 Z= 0.368 Angle : 0.581 7.038 52148 Z= 0.306 Chirality : 0.042 0.167 5985 Planarity : 0.005 0.111 6722 Dihedral : 8.528 166.310 5321 Min Nonbonded Distance : 1.722 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer Outliers : 1.01 % 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: 4782 helix: 0.77 (0.10), residues: 2385 sheet: -1.21 (0.19), residues: 641 loop : -0.53 (0.14), residues: 1756 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue SER 440 is missing expected H atoms. Skipping. Residue VAL 441 is missing expected H atoms. Skipping. Residue SER 442 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Evaluate side-chains 1262 residues out of total 4062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 1221 time to evaluate : 4.853 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 outliers start: 41 outliers final: 25 residues processed: 1237 average time/residue: 1.1356 time to fit residues: 2172.5452 Evaluate side-chains 1183 residues out of total 4062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 1158 time to evaluate : 4.927 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.7192 time to fit residues: 39.9382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 431 optimal weight: 10.0000 chunk 328 optimal weight: 10.0000 chunk 226 optimal weight: 5.9990 chunk 48 optimal weight: 9.9990 chunk 208 optimal weight: 1.9990 chunk 293 optimal weight: 2.9990 chunk 438 optimal weight: 4.9990 chunk 463 optimal weight: 9.9990 chunk 228 optimal weight: 10.0000 chunk 415 optimal weight: 7.9990 chunk 125 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 660 GLN A 730 GLN ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 583 ASN B 709 GLN C 356 GLN ** C 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 718 ASN D 273 GLN E 325 GLN E 329 ASN E 624 ASN E 670 GLN ** F 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 583 ASN H 191 HIS I 41 ASN I 150 ASN ** K 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 129 GLN ** N 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.3750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 38597 Z= 0.250 Angle : 0.514 6.690 52148 Z= 0.267 Chirality : 0.040 0.223 5985 Planarity : 0.004 0.065 6722 Dihedral : 8.480 168.006 5321 Min Nonbonded Distance : 1.736 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer Outliers : 0.98 % 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: 0.16 (0.12), residues: 4782 helix: 0.93 (0.10), residues: 2411 sheet: -1.15 (0.19), residues: 636 loop : -0.40 (0.14), residues: 1735 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue SER 440 is missing expected H atoms. Skipping. Residue VAL 441 is missing expected H atoms. Skipping. Residue SER 442 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Evaluate side-chains 1221 residues out of total 4062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 1181 time to evaluate : 4.935 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 outliers start: 40 outliers final: 28 residues processed: 1196 average time/residue: 1.1618 time to fit residues: 2167.9712 Evaluate side-chains 1175 residues out of total 4062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 1147 time to evaluate : 4.891 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.7806 time to fit residues: 45.6048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 386 optimal weight: 10.0000 chunk 263 optimal weight: 9.9990 chunk 6 optimal weight: 30.0000 chunk 345 optimal weight: 30.0000 chunk 191 optimal weight: 4.9990 chunk 395 optimal weight: 5.9990 chunk 320 optimal weight: 9.9990 chunk 0 optimal weight: 40.0000 chunk 236 optimal weight: 8.9990 chunk 416 optimal weight: 9.9990 chunk 117 optimal weight: 10.0000 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 HIS A 528 HIS A 622 GLN ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 356 GLN ** C 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 558 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 670 GLN E 718 ASN F 171 ASN F 305 ASN ** F 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 579 GLN F 583 ASN I 41 ASN ** K 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 150 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.4295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.056 38597 Z= 0.435 Angle : 0.593 8.103 52148 Z= 0.312 Chirality : 0.043 0.207 5985 Planarity : 0.004 0.056 6722 Dihedral : 8.642 163.501 5321 Min Nonbonded Distance : 1.685 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.22 % Favored : 96.76 % Rotamer Outliers : 1.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.12), residues: 4782 helix: 0.62 (0.10), residues: 2435 sheet: -1.13 (0.19), residues: 649 loop : -0.55 (0.14), residues: 1698 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue SER 440 is missing expected H atoms. Skipping. Residue VAL 441 is missing expected H atoms. Skipping. Residue SER 442 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Evaluate side-chains 1266 residues out of total 4062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 1209 time to evaluate : 4.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 57 outliers final: 35 residues processed: 1232 average time/residue: 1.1479 time to fit residues: 2205.2189 Evaluate side-chains 1199 residues out of total 4062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 1164 time to evaluate : 4.885 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.7422 time to fit residues: 54.0185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 156 optimal weight: 5.9990 chunk 417 optimal weight: 9.9990 chunk 91 optimal weight: 6.9990 chunk 272 optimal weight: 8.9990 chunk 114 optimal weight: 10.0000 chunk 464 optimal weight: 20.0000 chunk 385 optimal weight: 2.9990 chunk 215 optimal weight: 5.9990 chunk 38 optimal weight: 20.0000 chunk 153 optimal weight: 3.9990 chunk 243 optimal weight: 7.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 688 ASN ** C 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 356 GLN ** C 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 718 ASN ** D 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 670 GLN E 718 ASN F 583 ASN F 711 ASN I 41 ASN I 150 ASN ** K 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.4475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 38597 Z= 0.280 Angle : 0.528 6.629 52148 Z= 0.275 Chirality : 0.040 0.155 5985 Planarity : 0.004 0.062 6722 Dihedral : 8.603 166.654 5321 Min Nonbonded Distance : 1.722 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer Outliers : 0.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.12), residues: 4782 helix: 0.79 (0.10), residues: 2426 sheet: -1.22 (0.20), residues: 612 loop : -0.49 (0.14), residues: 1744 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue SER 440 is missing expected H atoms. Skipping. Residue VAL 441 is missing expected H atoms. Skipping. Residue SER 442 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Evaluate side-chains 1227 residues out of total 4062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 1190 time to evaluate : 4.895 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 outliers start: 37 outliers final: 30 residues processed: 1208 average time/residue: 1.1401 time to fit residues: 2138.0206 Evaluate side-chains 1195 residues out of total 4062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 1165 time to evaluate : 4.862 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.7343 time to fit residues: 46.6691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 447 optimal weight: 20.0000 chunk 52 optimal weight: 9.9990 chunk 264 optimal weight: 6.9990 chunk 339 optimal weight: 30.0000 chunk 262 optimal weight: 7.9990 chunk 390 optimal weight: 6.9990 chunk 259 optimal weight: 10.0000 chunk 462 optimal weight: 10.0000 chunk 289 optimal weight: 0.1980 chunk 282 optimal weight: 10.0000 chunk 213 optimal weight: 6.9990 overall best weight: 5.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 675 GLN ** C 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 356 GLN ** C 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 670 GLN E 718 ASN F 583 ASN I 41 ASN ** K 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 123 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.4656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.041 38597 Z= 0.328 Angle : 0.540 6.695 52148 Z= 0.281 Chirality : 0.041 0.149 5985 Planarity : 0.004 0.065 6722 Dihedral : 8.578 165.320 5321 Min Nonbonded Distance : 1.716 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer Outliers : 0.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.12), residues: 4782 helix: 0.81 (0.10), residues: 2425 sheet: -1.19 (0.20), residues: 605 loop : -0.48 (0.14), residues: 1752 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue SER 440 is missing expected H atoms. Skipping. Residue VAL 441 is missing expected H atoms. Skipping. Residue SER 442 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Evaluate side-chains 1236 residues out of total 4062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 1199 time to evaluate : 5.149 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 outliers start: 37 outliers final: 30 residues processed: 1211 average time/residue: 1.1500 time to fit residues: 2170.8360 Evaluate side-chains 1203 residues out of total 4062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 1173 time to evaluate : 4.900 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.8325 time to fit residues: 49.3797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 286 optimal weight: 20.0000 chunk 184 optimal weight: 0.9990 chunk 276 optimal weight: 8.9990 chunk 139 optimal weight: 4.9990 chunk 90 optimal weight: 6.9990 chunk 89 optimal weight: 0.9980 chunk 294 optimal weight: 7.9990 chunk 315 optimal weight: 30.0000 chunk 228 optimal weight: 9.9990 chunk 43 optimal weight: 10.0000 chunk 363 optimal weight: 30.0000 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 GLN ** C 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 528 HIS E 670 GLN E 718 ASN F 356 GLN F 583 ASN F 711 ASN I 34 GLN I 150 ASN K 9 GLN K 116 ASN N 123 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.4738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.063 38597 Z= 0.254 Angle : 0.519 6.628 52148 Z= 0.268 Chirality : 0.040 0.168 5985 Planarity : 0.004 0.066 6722 Dihedral : 8.521 167.696 5321 Min Nonbonded Distance : 1.747 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer Outliers : 0.59 % 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: 0.16 (0.12), residues: 4782 helix: 0.94 (0.11), residues: 2421 sheet: -1.18 (0.20), residues: 594 loop : -0.45 (0.14), residues: 1767 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue SER 440 is missing expected H atoms. Skipping. Residue VAL 441 is missing expected H atoms. Skipping. Residue SER 442 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Evaluate side-chains 1221 residues out of total 4062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 1197 time to evaluate : 4.976 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 outliers start: 24 outliers final: 18 residues processed: 1207 average time/residue: 1.1204 time to fit residues: 2097.4603 Evaluate side-chains 1188 residues out of total 4062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 1170 time to evaluate : 4.886 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 3 residues processed: 18 average time/residue: 0.7569 time to fit residues: 31.1804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 420 optimal weight: 7.9990 chunk 443 optimal weight: 0.9990 chunk 404 optimal weight: 4.9990 chunk 431 optimal weight: 8.9990 chunk 259 optimal weight: 10.0000 chunk 187 optimal weight: 8.9990 chunk 338 optimal weight: 20.0000 chunk 132 optimal weight: 4.9990 chunk 389 optimal weight: 9.9990 chunk 407 optimal weight: 1.9990 chunk 429 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 675 GLN ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 583 ASN ** C 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 624 ASN ** D 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 670 GLN F 583 ASN I 41 ASN K 9 GLN ** K 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 191 HIS ** N 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.4786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 38597 Z= 0.219 Angle : 0.512 6.684 52148 Z= 0.263 Chirality : 0.039 0.151 5985 Planarity : 0.004 0.065 6722 Dihedral : 8.446 169.026 5321 Min Nonbonded Distance : 1.770 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer Outliers : 0.42 % 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: 0.30 (0.12), residues: 4782 helix: 1.06 (0.11), residues: 2420 sheet: -1.13 (0.20), residues: 593 loop : -0.38 (0.14), residues: 1769 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue SER 440 is missing expected H atoms. Skipping. Residue VAL 441 is missing expected H atoms. Skipping. Residue SER 442 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Evaluate side-chains 1202 residues out of total 4062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 1185 time to evaluate : 4.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 12 residues processed: 1192 average time/residue: 1.1262 time to fit residues: 2087.1285 Evaluate side-chains 1186 residues out of total 4062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 1174 time to evaluate : 4.875 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 3 residues processed: 12 average time/residue: 0.7907 time to fit residues: 23.1125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 283 optimal weight: 0.2980 chunk 455 optimal weight: 10.0000 chunk 278 optimal weight: 10.0000 chunk 216 optimal weight: 4.9990 chunk 316 optimal weight: 0.5980 chunk 478 optimal weight: 0.8980 chunk 440 optimal weight: 0.9990 chunk 380 optimal weight: 20.0000 chunk 39 optimal weight: 10.0000 chunk 294 optimal weight: 5.9990 chunk 233 optimal weight: 7.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 670 GLN F 583 ASN I 41 ASN ** K 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.4808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 38597 Z= 0.154 Angle : 0.497 7.933 52148 Z= 0.253 Chirality : 0.039 0.271 5985 Planarity : 0.004 0.070 6722 Dihedral : 8.330 175.517 5321 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer Outliers : 0.25 % 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: 0.56 (0.12), residues: 4782 helix: 1.28 (0.11), residues: 2422 sheet: -1.08 (0.20), residues: 607 loop : -0.23 (0.15), residues: 1753 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue SER 440 is missing expected H atoms. Skipping. Residue VAL 441 is missing expected H atoms. Skipping. Residue SER 442 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Evaluate side-chains 1197 residues out of total 4062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 1187 time to evaluate : 5.056 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 outliers start: 10 outliers final: 7 residues processed: 1191 average time/residue: 1.1091 time to fit residues: 2050.3594 Evaluate side-chains 1180 residues out of total 4062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 1173 time to evaluate : 4.923 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 7 average time/residue: 0.9930 time to fit residues: 17.8228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 302 optimal weight: 9.9990 chunk 405 optimal weight: 10.0000 chunk 116 optimal weight: 8.9990 chunk 351 optimal weight: 9.9990 chunk 56 optimal weight: 7.9990 chunk 105 optimal weight: 4.9990 chunk 381 optimal weight: 7.9990 chunk 159 optimal weight: 9.9990 chunk 391 optimal weight: 1.9990 chunk 48 optimal weight: 10.0000 chunk 70 optimal weight: 30.0000 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 209 ASN A 688 ASN ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 583 ASN ** C 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 624 ASN C 718 ASN D 273 GLN ** E 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 670 GLN F 583 ASN F 711 ASN I 41 ASN K 9 GLN ** K 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.151896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.109727 restraints weight = 141370.327| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 1.97 r_work: 0.2976 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.4945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.044 38597 Z= 0.347 Angle : 0.550 6.666 52148 Z= 0.285 Chirality : 0.041 0.209 5985 Planarity : 0.004 0.065 6722 Dihedral : 8.398 165.625 5321 Min Nonbonded Distance : 1.703 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer Outliers : 0.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.12), residues: 4782 helix: 1.09 (0.11), residues: 2419 sheet: -1.10 (0.20), residues: 607 loop : -0.37 (0.14), residues: 1756 =============================================================================== Job complete usr+sys time: 28673.79 seconds wall clock time: 493 minutes 8.11 seconds (29588.11 seconds total)