Starting phenix.real_space_refine on Wed Dec 13 07:12:40 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sb3_10134/12_2023/6sb3_10134.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sb3_10134/12_2023/6sb3_10134.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sb3_10134/12_2023/6sb3_10134.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sb3_10134/12_2023/6sb3_10134.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sb3_10134/12_2023/6sb3_10134.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sb3_10134/12_2023/6sb3_10134.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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= 0.004 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: 4 Type Number sf(0) Gaussians S 496 5.16 5 C 48080 2.51 5 N 12608 2.21 5 O 14528 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 55": "NH1" <-> "NH2" Residue "A GLU 83": "OE1" <-> "OE2" Residue "A GLU 102": "OE1" <-> "OE2" Residue "A ARG 124": "NH1" <-> "NH2" Residue "A ARG 135": "NH1" <-> "NH2" Residue "A GLU 166": "OE1" <-> "OE2" Residue "A ASP 180": "OD1" <-> "OD2" Residue "A ASP 255": "OD1" <-> "OD2" Residue "A ASP 265": "OD1" <-> "OD2" Residue "A ARG 270": "NH1" <-> "NH2" Residue "A PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 339": "NH1" <-> "NH2" Residue "A TYR 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 354": "OD1" <-> "OD2" Residue "A PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 387": "OE1" <-> "OE2" Residue "A ASP 406": "OD1" <-> "OD2" Residue "A ARG 429": "NH1" <-> "NH2" Residue "A ASP 448": "OD1" <-> "OD2" Residue "A ARG 451": "NH1" <-> "NH2" Residue "A ARG 458": "NH1" <-> "NH2" Residue "A TYR 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 514": "OD1" <-> "OD2" Residue "A TYR 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 516": "OE1" <-> "OE2" Residue "A PHE 521": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 567": "OD1" <-> "OD2" Residue "A ARG 589": "NH1" <-> "NH2" Residue "A GLU 613": "OE1" <-> "OE2" Residue "A ASP 621": "OD1" <-> "OD2" Residue "A GLU 634": "OE1" <-> "OE2" Residue "B ARG 55": "NH1" <-> "NH2" Residue "B GLU 83": "OE1" <-> "OE2" Residue "B GLU 102": "OE1" <-> "OE2" Residue "B ARG 124": "NH1" <-> "NH2" Residue "B ARG 135": "NH1" <-> "NH2" Residue "B GLU 166": "OE1" <-> "OE2" Residue "B ASP 180": "OD1" <-> "OD2" Residue "B ASP 255": "OD1" <-> "OD2" Residue "B ASP 265": "OD1" <-> "OD2" Residue "B ARG 270": "NH1" <-> "NH2" Residue "B PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 339": "NH1" <-> "NH2" Residue "B TYR 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 354": "OD1" <-> "OD2" Residue "B PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 387": "OE1" <-> "OE2" Residue "B ASP 406": "OD1" <-> "OD2" Residue "B ARG 429": "NH1" <-> "NH2" Residue "B ASP 448": "OD1" <-> "OD2" Residue "B ARG 451": "NH1" <-> "NH2" Residue "B ARG 458": "NH1" <-> "NH2" Residue "B TYR 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 514": "OD1" <-> "OD2" Residue "B TYR 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 516": "OE1" <-> "OE2" Residue "B PHE 521": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 567": "OD1" <-> "OD2" Residue "B ARG 589": "NH1" <-> "NH2" Residue "B GLU 613": "OE1" <-> "OE2" Residue "B ASP 621": "OD1" <-> "OD2" Residue "B GLU 634": "OE1" <-> "OE2" Residue "C ARG 55": "NH1" <-> "NH2" Residue "C TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 83": "OE1" <-> "OE2" Residue "C GLU 102": "OE1" <-> "OE2" Residue "C ARG 124": "NH1" <-> "NH2" Residue "C ARG 135": "NH1" <-> "NH2" Residue "C GLU 166": "OE1" <-> "OE2" Residue "C ASP 180": "OD1" <-> "OD2" Residue "C ASP 255": "OD1" <-> "OD2" Residue "C ASP 265": "OD1" <-> "OD2" Residue "C ARG 270": "NH1" <-> "NH2" Residue "C PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 339": "NH1" <-> "NH2" Residue "C TYR 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 354": "OD1" <-> "OD2" Residue "C PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 387": "OE1" <-> "OE2" Residue "C ASP 406": "OD1" <-> "OD2" Residue "C ARG 429": "NH1" <-> "NH2" Residue "C ASP 448": "OD1" <-> "OD2" Residue "C ARG 451": "NH1" <-> "NH2" Residue "C ARG 458": "NH1" <-> "NH2" Residue "C TYR 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 514": "OD1" <-> "OD2" Residue "C TYR 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 516": "OE1" <-> "OE2" Residue "C PHE 521": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 567": "OD1" <-> "OD2" Residue "C ARG 589": "NH1" <-> "NH2" Residue "C GLU 613": "OE1" <-> "OE2" Residue "C ASP 621": "OD1" <-> "OD2" Residue "C GLU 634": "OE1" <-> "OE2" Residue "D ARG 55": "NH1" <-> "NH2" Residue "D TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 83": "OE1" <-> "OE2" Residue "D GLU 102": "OE1" <-> "OE2" Residue "D ARG 124": "NH1" <-> "NH2" Residue "D ARG 135": "NH1" <-> "NH2" Residue "D GLU 166": "OE1" <-> "OE2" Residue "D ASP 180": "OD1" <-> "OD2" Residue "D ASP 255": "OD1" <-> "OD2" Residue "D ASP 265": "OD1" <-> "OD2" Residue "D ARG 270": "NH1" <-> "NH2" Residue "D PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 339": "NH1" <-> "NH2" Residue "D TYR 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 354": "OD1" <-> "OD2" Residue "D PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 387": "OE1" <-> "OE2" Residue "D ASP 406": "OD1" <-> "OD2" Residue "D ARG 429": "NH1" <-> "NH2" Residue "D ASP 448": "OD1" <-> "OD2" Residue "D ARG 451": "NH1" <-> "NH2" Residue "D ARG 458": "NH1" <-> "NH2" Residue "D TYR 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 514": "OD1" <-> "OD2" Residue "D TYR 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 516": "OE1" <-> "OE2" Residue "D PHE 521": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 567": "OD1" <-> "OD2" Residue "D ARG 589": "NH1" <-> "NH2" Residue "D GLU 613": "OE1" <-> "OE2" Residue "D ASP 621": "OD1" <-> "OD2" Residue "D GLU 634": "OE1" <-> "OE2" Residue "E ARG 55": "NH1" <-> "NH2" Residue "E GLU 83": "OE1" <-> "OE2" Residue "E GLU 102": "OE1" <-> "OE2" Residue "E ARG 124": "NH1" <-> "NH2" Residue "E ARG 135": "NH1" <-> "NH2" Residue "E GLU 166": "OE1" <-> "OE2" Residue "E ASP 180": "OD1" <-> "OD2" Residue "E ASP 255": "OD1" <-> "OD2" Residue "E ASP 265": "OD1" <-> "OD2" Residue "E ARG 270": "NH1" <-> "NH2" Residue "E PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 339": "NH1" <-> "NH2" Residue "E TYR 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 354": "OD1" <-> "OD2" Residue "E PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 387": "OE1" <-> "OE2" Residue "E ASP 406": "OD1" <-> "OD2" Residue "E ARG 429": "NH1" <-> "NH2" Residue "E ASP 448": "OD1" <-> "OD2" Residue "E ARG 451": "NH1" <-> "NH2" Residue "E ARG 458": "NH1" <-> "NH2" Residue "E TYR 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 514": "OD1" <-> "OD2" Residue "E TYR 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 516": "OE1" <-> "OE2" Residue "E PHE 521": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 567": "OD1" <-> "OD2" Residue "E ARG 589": "NH1" <-> "NH2" Residue "E GLU 613": "OE1" <-> "OE2" Residue "E ASP 621": "OD1" <-> "OD2" Residue "E GLU 634": "OE1" <-> "OE2" Residue "F ARG 55": "NH1" <-> "NH2" Residue "F TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 83": "OE1" <-> "OE2" Residue "F GLU 102": "OE1" <-> "OE2" Residue "F ARG 124": "NH1" <-> "NH2" Residue "F ARG 135": "NH1" <-> "NH2" Residue "F GLU 166": "OE1" <-> "OE2" Residue "F ASP 180": "OD1" <-> "OD2" Residue "F ASP 255": "OD1" <-> "OD2" Residue "F ASP 265": "OD1" <-> "OD2" Residue "F ARG 270": "NH1" <-> "NH2" Residue "F PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 339": "NH1" <-> "NH2" Residue "F TYR 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 354": "OD1" <-> "OD2" Residue "F PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 387": "OE1" <-> "OE2" Residue "F ASP 406": "OD1" <-> "OD2" Residue "F ARG 429": "NH1" <-> "NH2" Residue "F ASP 448": "OD1" <-> "OD2" Residue "F ARG 451": "NH1" <-> "NH2" Residue "F ARG 458": "NH1" <-> "NH2" Residue "F TYR 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 514": "OD1" <-> "OD2" Residue "F TYR 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 516": "OE1" <-> "OE2" Residue "F PHE 521": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 567": "OD1" <-> "OD2" Residue "F ARG 589": "NH1" <-> "NH2" Residue "F GLU 613": "OE1" <-> "OE2" Residue "F ASP 621": "OD1" <-> "OD2" Residue "F GLU 634": "OE1" <-> "OE2" Residue "G ARG 55": "NH1" <-> "NH2" Residue "G GLU 83": "OE1" <-> "OE2" Residue "G GLU 102": "OE1" <-> "OE2" Residue "G ARG 124": "NH1" <-> "NH2" Residue "G ARG 135": "NH1" <-> "NH2" Residue "G GLU 166": "OE1" <-> "OE2" Residue "G ASP 180": "OD1" <-> "OD2" Residue "G ASP 255": "OD1" <-> "OD2" Residue "G ASP 265": "OD1" <-> "OD2" Residue "G ARG 270": "NH1" <-> "NH2" Residue "G PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 339": "NH1" <-> "NH2" Residue "G TYR 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 354": "OD1" <-> "OD2" Residue "G PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 387": "OE1" <-> "OE2" Residue "G ASP 406": "OD1" <-> "OD2" Residue "G ARG 429": "NH1" <-> "NH2" Residue "G ASP 448": "OD1" <-> "OD2" Residue "G ARG 451": "NH1" <-> "NH2" Residue "G ARG 458": "NH1" <-> "NH2" Residue "G TYR 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 514": "OD1" <-> "OD2" Residue "G TYR 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 516": "OE1" <-> "OE2" Residue "G PHE 521": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 567": "OD1" <-> "OD2" Residue "G ARG 589": "NH1" <-> "NH2" Residue "G GLU 613": "OE1" <-> "OE2" Residue "G ASP 621": "OD1" <-> "OD2" Residue "G GLU 634": "OE1" <-> "OE2" Residue "H ARG 55": "NH1" <-> "NH2" Residue "H TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 83": "OE1" <-> "OE2" Residue "H GLU 102": "OE1" <-> "OE2" Residue "H ARG 124": "NH1" <-> "NH2" Residue "H ARG 135": "NH1" <-> "NH2" Residue "H GLU 166": "OE1" <-> "OE2" Residue "H ASP 180": "OD1" <-> "OD2" Residue "H ASP 255": "OD1" <-> "OD2" Residue "H ASP 265": "OD1" <-> "OD2" Residue "H ARG 270": "NH1" <-> "NH2" Residue "H PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 339": "NH1" <-> "NH2" Residue "H TYR 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 354": "OD1" <-> "OD2" Residue "H PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 387": "OE1" <-> "OE2" Residue "H ASP 406": "OD1" <-> "OD2" Residue "H ARG 429": "NH1" <-> "NH2" Residue "H ASP 448": "OD1" <-> "OD2" Residue "H ARG 451": "NH1" <-> "NH2" Residue "H ARG 458": "NH1" <-> "NH2" Residue "H TYR 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 514": "OD1" <-> "OD2" Residue "H TYR 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 516": "OE1" <-> "OE2" Residue "H PHE 521": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 567": "OD1" <-> "OD2" Residue "H ARG 589": "NH1" <-> "NH2" Residue "H GLU 613": "OE1" <-> "OE2" Residue "H ASP 621": "OD1" <-> "OD2" Residue "H GLU 634": "OE1" <-> "OE2" Residue "I ARG 55": "NH1" <-> "NH2" Residue "I GLU 83": "OE1" <-> "OE2" Residue "I GLU 102": "OE1" <-> "OE2" Residue "I ARG 124": "NH1" <-> "NH2" Residue "I ARG 135": "NH1" <-> "NH2" Residue "I GLU 166": "OE1" <-> "OE2" Residue "I ASP 180": "OD1" <-> "OD2" Residue "I ASP 255": "OD1" <-> "OD2" Residue "I ASP 265": "OD1" <-> "OD2" Residue "I ARG 270": "NH1" <-> "NH2" Residue "I PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 339": "NH1" <-> "NH2" Residue "I TYR 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 354": "OD1" <-> "OD2" Residue "I PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 387": "OE1" <-> "OE2" Residue "I ASP 406": "OD1" <-> "OD2" Residue "I ARG 429": "NH1" <-> "NH2" Residue "I ASP 448": "OD1" <-> "OD2" Residue "I ARG 451": "NH1" <-> "NH2" Residue "I ARG 458": "NH1" <-> "NH2" Residue "I TYR 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 514": "OD1" <-> "OD2" Residue "I TYR 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 516": "OE1" <-> "OE2" Residue "I PHE 521": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 567": "OD1" <-> "OD2" Residue "I ARG 589": "NH1" <-> "NH2" Residue "I GLU 613": "OE1" <-> "OE2" Residue "I ASP 621": "OD1" <-> "OD2" Residue "I GLU 634": "OE1" <-> "OE2" Residue "J ARG 55": "NH1" <-> "NH2" Residue "J GLU 83": "OE1" <-> "OE2" Residue "J GLU 102": "OE1" <-> "OE2" Residue "J ARG 124": "NH1" <-> "NH2" Residue "J ARG 135": "NH1" <-> "NH2" Residue "J GLU 166": "OE1" <-> "OE2" Residue "J ASP 180": "OD1" <-> "OD2" Residue "J ASP 255": "OD1" <-> "OD2" Residue "J ASP 265": "OD1" <-> "OD2" Residue "J ARG 270": "NH1" <-> "NH2" Residue "J PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 339": "NH1" <-> "NH2" Residue "J TYR 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 354": "OD1" <-> "OD2" Residue "J PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 387": "OE1" <-> "OE2" Residue "J ASP 406": "OD1" <-> "OD2" Residue "J ARG 429": "NH1" <-> "NH2" Residue "J ASP 448": "OD1" <-> "OD2" Residue "J ARG 451": "NH1" <-> "NH2" Residue "J ARG 458": "NH1" <-> "NH2" Residue "J TYR 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 514": "OD1" <-> "OD2" Residue "J TYR 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 516": "OE1" <-> "OE2" Residue "J PHE 521": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 567": "OD1" <-> "OD2" Residue "J ARG 589": "NH1" <-> "NH2" Residue "J GLU 613": "OE1" <-> "OE2" Residue "J ASP 621": "OD1" <-> "OD2" Residue "J GLU 634": "OE1" <-> "OE2" Residue "K ARG 55": "NH1" <-> "NH2" Residue "K TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 83": "OE1" <-> "OE2" Residue "K GLU 102": "OE1" <-> "OE2" Residue "K ARG 124": "NH1" <-> "NH2" Residue "K ARG 135": "NH1" <-> "NH2" Residue "K GLU 166": "OE1" <-> "OE2" Residue "K ASP 180": "OD1" <-> "OD2" Residue "K ASP 255": "OD1" <-> "OD2" Residue "K ASP 265": "OD1" <-> "OD2" Residue "K ARG 270": "NH1" <-> "NH2" Residue "K PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 339": "NH1" <-> "NH2" Residue "K TYR 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 354": "OD1" <-> "OD2" Residue "K PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 387": "OE1" <-> "OE2" Residue "K ASP 406": "OD1" <-> "OD2" Residue "K ARG 429": "NH1" <-> "NH2" Residue "K ASP 448": "OD1" <-> "OD2" Residue "K ARG 451": "NH1" <-> "NH2" Residue "K ARG 458": "NH1" <-> "NH2" Residue "K TYR 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 514": "OD1" <-> "OD2" Residue "K TYR 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 516": "OE1" <-> "OE2" Residue "K PHE 521": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 567": "OD1" <-> "OD2" Residue "K ARG 589": "NH1" <-> "NH2" Residue "K GLU 613": "OE1" <-> "OE2" Residue "K ASP 621": "OD1" <-> "OD2" Residue "K GLU 634": "OE1" <-> "OE2" Residue "L ARG 55": "NH1" <-> "NH2" Residue "L GLU 83": "OE1" <-> "OE2" Residue "L GLU 102": "OE1" <-> "OE2" Residue "L ARG 124": "NH1" <-> "NH2" Residue "L ARG 135": "NH1" <-> "NH2" Residue "L GLU 166": "OE1" <-> "OE2" Residue "L ASP 180": "OD1" <-> "OD2" Residue "L ASP 255": "OD1" <-> "OD2" Residue "L ASP 265": "OD1" <-> "OD2" Residue "L ARG 270": "NH1" <-> "NH2" Residue "L PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 339": "NH1" <-> "NH2" Residue "L TYR 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 354": "OD1" <-> "OD2" Residue "L PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 387": "OE1" <-> "OE2" Residue "L ASP 406": "OD1" <-> "OD2" Residue "L ARG 429": "NH1" <-> "NH2" Residue "L ASP 448": "OD1" <-> "OD2" Residue "L ARG 451": "NH1" <-> "NH2" Residue "L ARG 458": "NH1" <-> "NH2" Residue "L TYR 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 514": "OD1" <-> "OD2" Residue "L TYR 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 516": "OE1" <-> "OE2" Residue "L PHE 521": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 567": "OD1" <-> "OD2" Residue "L ARG 589": "NH1" <-> "NH2" Residue "L GLU 613": "OE1" <-> "OE2" Residue "L ASP 621": "OD1" <-> "OD2" Residue "L GLU 634": "OE1" <-> "OE2" Residue "M ARG 55": "NH1" <-> "NH2" Residue "M TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 83": "OE1" <-> "OE2" Residue "M GLU 102": "OE1" <-> "OE2" Residue "M ARG 124": "NH1" <-> "NH2" Residue "M ARG 135": "NH1" <-> "NH2" Residue "M GLU 166": "OE1" <-> "OE2" Residue "M ASP 180": "OD1" <-> "OD2" Residue "M ASP 255": "OD1" <-> "OD2" Residue "M ASP 265": "OD1" <-> "OD2" Residue "M ARG 270": "NH1" <-> "NH2" Residue "M PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 339": "NH1" <-> "NH2" Residue "M TYR 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 354": "OD1" <-> "OD2" Residue "M PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 387": "OE1" <-> "OE2" Residue "M ASP 406": "OD1" <-> "OD2" Residue "M ARG 429": "NH1" <-> "NH2" Residue "M ASP 448": "OD1" <-> "OD2" Residue "M ARG 451": "NH1" <-> "NH2" Residue "M ARG 458": "NH1" <-> "NH2" Residue "M TYR 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 514": "OD1" <-> "OD2" Residue "M TYR 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 516": "OE1" <-> "OE2" Residue "M PHE 521": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 567": "OD1" <-> "OD2" Residue "M ARG 589": "NH1" <-> "NH2" Residue "M GLU 613": "OE1" <-> "OE2" Residue "M ASP 621": "OD1" <-> "OD2" Residue "M GLU 634": "OE1" <-> "OE2" Residue "N ARG 55": "NH1" <-> "NH2" Residue "N GLU 83": "OE1" <-> "OE2" Residue "N GLU 102": "OE1" <-> "OE2" Residue "N ARG 124": "NH1" <-> "NH2" Residue "N ARG 135": "NH1" <-> "NH2" Residue "N GLU 166": "OE1" <-> "OE2" Residue "N ASP 180": "OD1" <-> "OD2" Residue "N ASP 255": "OD1" <-> "OD2" Residue "N ASP 265": "OD1" <-> "OD2" Residue "N ARG 270": "NH1" <-> "NH2" Residue "N PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 339": "NH1" <-> "NH2" Residue "N TYR 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 354": "OD1" <-> "OD2" Residue "N PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 387": "OE1" <-> "OE2" Residue "N ASP 406": "OD1" <-> "OD2" Residue "N ARG 429": "NH1" <-> "NH2" Residue "N ASP 448": "OD1" <-> "OD2" Residue "N ARG 451": "NH1" <-> "NH2" Residue "N ARG 458": "NH1" <-> "NH2" Residue "N TYR 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 514": "OD1" <-> "OD2" Residue "N TYR 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 516": "OE1" <-> "OE2" Residue "N PHE 521": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 567": "OD1" <-> "OD2" Residue "N ARG 589": "NH1" <-> "NH2" Residue "N GLU 613": "OE1" <-> "OE2" Residue "N ASP 621": "OD1" <-> "OD2" Residue "N GLU 634": "OE1" <-> "OE2" Residue "O ARG 55": "NH1" <-> "NH2" Residue "O GLU 83": "OE1" <-> "OE2" Residue "O GLU 102": "OE1" <-> "OE2" Residue "O ARG 124": "NH1" <-> "NH2" Residue "O ARG 135": "NH1" <-> "NH2" Residue "O GLU 166": "OE1" <-> "OE2" Residue "O ASP 180": "OD1" <-> "OD2" Residue "O ASP 255": "OD1" <-> "OD2" Residue "O ASP 265": "OD1" <-> "OD2" Residue "O ARG 270": "NH1" <-> "NH2" Residue "O PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 339": "NH1" <-> "NH2" Residue "O TYR 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 354": "OD1" <-> "OD2" Residue "O PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 387": "OE1" <-> "OE2" Residue "O ASP 406": "OD1" <-> "OD2" Residue "O ARG 429": "NH1" <-> "NH2" Residue "O ASP 448": "OD1" <-> "OD2" Residue "O ARG 451": "NH1" <-> "NH2" Residue "O ARG 458": "NH1" <-> "NH2" Residue "O TYR 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 514": "OD1" <-> "OD2" Residue "O TYR 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 516": "OE1" <-> "OE2" Residue "O PHE 521": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 567": "OD1" <-> "OD2" Residue "O ARG 589": "NH1" <-> "NH2" Residue "O GLU 613": "OE1" <-> "OE2" Residue "O ASP 621": "OD1" <-> "OD2" Residue "O GLU 634": "OE1" <-> "OE2" Residue "P ARG 55": "NH1" <-> "NH2" Residue "P GLU 83": "OE1" <-> "OE2" Residue "P GLU 102": "OE1" <-> "OE2" Residue "P ARG 124": "NH1" <-> "NH2" Residue "P ARG 135": "NH1" <-> "NH2" Residue "P GLU 166": "OE1" <-> "OE2" Residue "P ASP 180": "OD1" <-> "OD2" Residue "P ASP 255": "OD1" <-> "OD2" Residue "P ASP 265": "OD1" <-> "OD2" Residue "P ARG 270": "NH1" <-> "NH2" Residue "P PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 339": "NH1" <-> "NH2" Residue "P TYR 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 354": "OD1" <-> "OD2" Residue "P PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 387": "OE1" <-> "OE2" Residue "P ASP 406": "OD1" <-> "OD2" Residue "P ARG 429": "NH1" <-> "NH2" Residue "P ASP 448": "OD1" <-> "OD2" Residue "P ARG 451": "NH1" <-> "NH2" Residue "P ARG 458": "NH1" <-> "NH2" Residue "P TYR 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 514": "OD1" <-> "OD2" Residue "P TYR 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 516": "OE1" <-> "OE2" Residue "P PHE 521": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 567": "OD1" <-> "OD2" Residue "P ARG 589": "NH1" <-> "NH2" Residue "P GLU 613": "OE1" <-> "OE2" Residue "P ASP 621": "OD1" <-> "OD2" Residue "P GLU 634": "OE1" <-> "OE2" Time to flip residues: 0.18s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 75712 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 4704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4704 Classifications: {'peptide': 604} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 571} Chain breaks: 1 Chain: "B" Number of atoms: 4704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4704 Classifications: {'peptide': 604} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 571} Chain breaks: 1 Chain: "C" Number of atoms: 4704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4704 Classifications: {'peptide': 604} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 571} Chain breaks: 1 Chain: "D" Number of atoms: 4704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4704 Classifications: {'peptide': 604} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 571} Chain breaks: 1 Chain: "E" Number of atoms: 4704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4704 Classifications: {'peptide': 604} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 571} Chain breaks: 1 Chain: "F" Number of atoms: 4704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4704 Classifications: {'peptide': 604} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 571} Chain breaks: 1 Chain: "G" Number of atoms: 4704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4704 Classifications: {'peptide': 604} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 571} Chain breaks: 1 Chain: "H" Number of atoms: 4704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4704 Classifications: {'peptide': 604} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 571} Chain breaks: 1 Chain: "I" Number of atoms: 4704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4704 Classifications: {'peptide': 604} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 571} Chain breaks: 1 Chain: "J" Number of atoms: 4704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4704 Classifications: {'peptide': 604} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 571} Chain breaks: 1 Chain: "K" Number of atoms: 4704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4704 Classifications: {'peptide': 604} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 571} Chain breaks: 1 Chain: "L" Number of atoms: 4704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4704 Classifications: {'peptide': 604} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 571} Chain breaks: 1 Chain: "M" Number of atoms: 4704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4704 Classifications: {'peptide': 604} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 571} Chain breaks: 1 Chain: "N" Number of atoms: 4704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4704 Classifications: {'peptide': 604} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 571} Chain breaks: 1 Chain: "O" Number of atoms: 4704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4704 Classifications: {'peptide': 604} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 571} Chain breaks: 1 Chain: "P" Number of atoms: 4704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4704 Classifications: {'peptide': 604} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 571} Chain breaks: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 28.31, per 1000 atoms: 0.37 Number of scatterers: 75712 At special positions: 0 Unit cell: (237.12, 237.12, 100.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 496 16.00 O 14528 8.00 N 12608 7.00 C 48080 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=112, symmetry=0 Simple disulfide: pdb=" SG CYS A 34 " - pdb=" SG CYS A 70 " distance=2.03 Simple disulfide: pdb=" SG CYS A 350 " - pdb=" SG CYS A 369 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 394 " distance=2.05 Simple disulfide: pdb=" SG CYS A 432 " - pdb=" SG CYS A 446 " distance=2.03 Simple disulfide: pdb=" SG CYS A 436 " - pdb=" SG CYS A 442 " distance=2.03 Simple disulfide: pdb=" SG CYS A 531 " - pdb=" SG CYS A 569 " distance=2.03 Simple disulfide: pdb=" SG CYS A 554 " - pdb=" SG CYS A 574 " distance=2.03 Simple disulfide: pdb=" SG CYS B 34 " - pdb=" SG CYS B 70 " distance=2.03 Simple disulfide: pdb=" SG CYS B 350 " - pdb=" SG CYS B 369 " distance=2.03 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 394 " distance=2.05 Simple disulfide: pdb=" SG CYS B 432 " - pdb=" SG CYS B 446 " distance=2.03 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 442 " distance=2.03 Simple disulfide: pdb=" SG CYS B 531 " - pdb=" SG CYS B 569 " distance=2.03 Simple disulfide: pdb=" SG CYS B 554 " - pdb=" SG CYS B 574 " distance=2.03 Simple disulfide: pdb=" SG CYS C 34 " - pdb=" SG CYS C 70 " distance=2.03 Simple disulfide: pdb=" SG CYS C 350 " - pdb=" SG CYS C 369 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 394 " distance=2.05 Simple disulfide: pdb=" SG CYS C 432 " - pdb=" SG CYS C 446 " distance=2.03 Simple disulfide: pdb=" SG CYS C 436 " - pdb=" SG CYS C 442 " distance=2.03 Simple disulfide: pdb=" SG CYS C 531 " - pdb=" SG CYS C 569 " distance=2.03 Simple disulfide: pdb=" SG CYS C 554 " - pdb=" SG CYS C 574 " distance=2.03 Simple disulfide: pdb=" SG CYS D 34 " - pdb=" SG CYS D 70 " distance=2.03 Simple disulfide: pdb=" SG CYS D 350 " - pdb=" SG CYS D 369 " distance=2.03 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 394 " distance=2.05 Simple disulfide: pdb=" SG CYS D 432 " - pdb=" SG CYS D 446 " distance=2.03 Simple disulfide: pdb=" SG CYS D 436 " - pdb=" SG CYS D 442 " distance=2.03 Simple disulfide: pdb=" SG CYS D 531 " - pdb=" SG CYS D 569 " distance=2.03 Simple disulfide: pdb=" SG CYS D 554 " - pdb=" SG CYS D 574 " distance=2.03 Simple disulfide: pdb=" SG CYS E 34 " - pdb=" SG CYS E 70 " distance=2.03 Simple disulfide: pdb=" SG CYS E 350 " - pdb=" SG CYS E 369 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 394 " distance=2.05 Simple disulfide: pdb=" SG CYS E 432 " - pdb=" SG CYS E 446 " distance=2.03 Simple disulfide: pdb=" SG CYS E 436 " - pdb=" SG CYS E 442 " distance=2.03 Simple disulfide: pdb=" SG CYS E 531 " - pdb=" SG CYS E 569 " distance=2.03 Simple disulfide: pdb=" SG CYS E 554 " - pdb=" SG CYS E 574 " distance=2.03 Simple disulfide: pdb=" SG CYS F 34 " - pdb=" SG CYS F 70 " distance=2.03 Simple disulfide: pdb=" SG CYS F 350 " - pdb=" SG CYS F 369 " distance=2.03 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 394 " distance=2.05 Simple disulfide: pdb=" SG CYS F 432 " - pdb=" SG CYS F 446 " distance=2.03 Simple disulfide: pdb=" SG CYS F 436 " - pdb=" SG CYS F 442 " distance=2.03 Simple disulfide: pdb=" SG CYS F 531 " - pdb=" SG CYS F 569 " distance=2.03 Simple disulfide: pdb=" SG CYS F 554 " - pdb=" SG CYS F 574 " distance=2.03 Simple disulfide: pdb=" SG CYS G 34 " - pdb=" SG CYS G 70 " distance=2.03 Simple disulfide: pdb=" SG CYS G 350 " - pdb=" SG CYS G 369 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 394 " distance=2.05 Simple disulfide: pdb=" SG CYS G 432 " - pdb=" SG CYS G 446 " distance=2.03 Simple disulfide: pdb=" SG CYS G 436 " - pdb=" SG CYS G 442 " distance=2.03 Simple disulfide: pdb=" SG CYS G 531 " - pdb=" SG CYS G 569 " distance=2.03 Simple disulfide: pdb=" SG CYS G 554 " - pdb=" SG CYS G 574 " distance=2.03 Simple disulfide: pdb=" SG CYS H 34 " - pdb=" SG CYS H 70 " distance=2.03 Simple disulfide: pdb=" SG CYS H 350 " - pdb=" SG CYS H 369 " distance=2.03 Simple disulfide: pdb=" SG CYS H 385 " - pdb=" SG CYS H 394 " distance=2.05 Simple disulfide: pdb=" SG CYS H 432 " - pdb=" SG CYS H 446 " distance=2.03 Simple disulfide: pdb=" SG CYS H 436 " - pdb=" SG CYS H 442 " distance=2.03 Simple disulfide: pdb=" SG CYS H 531 " - pdb=" SG CYS H 569 " distance=2.03 Simple disulfide: pdb=" SG CYS H 554 " - pdb=" SG CYS H 574 " distance=2.03 Simple disulfide: pdb=" SG CYS I 34 " - pdb=" SG CYS I 70 " distance=2.03 Simple disulfide: pdb=" SG CYS I 350 " - pdb=" SG CYS I 369 " distance=2.03 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 394 " distance=2.05 Simple disulfide: pdb=" SG CYS I 432 " - pdb=" SG CYS I 446 " distance=2.03 Simple disulfide: pdb=" SG CYS I 436 " - pdb=" SG CYS I 442 " distance=2.03 Simple disulfide: pdb=" SG CYS I 531 " - pdb=" SG CYS I 569 " distance=2.03 Simple disulfide: pdb=" SG CYS I 554 " - pdb=" SG CYS I 574 " distance=2.03 Simple disulfide: pdb=" SG CYS J 34 " - pdb=" SG CYS J 70 " distance=2.03 Simple disulfide: pdb=" SG CYS J 350 " - pdb=" SG CYS J 369 " distance=2.03 Simple disulfide: pdb=" SG CYS J 385 " - pdb=" SG CYS J 394 " distance=2.05 Simple disulfide: pdb=" SG CYS J 432 " - pdb=" SG CYS J 446 " distance=2.03 Simple disulfide: pdb=" SG CYS J 436 " - pdb=" SG CYS J 442 " distance=2.03 Simple disulfide: pdb=" SG CYS J 531 " - pdb=" SG CYS J 569 " distance=2.03 Simple disulfide: pdb=" SG CYS J 554 " - pdb=" SG CYS J 574 " distance=2.03 Simple disulfide: pdb=" SG CYS K 34 " - pdb=" SG CYS K 70 " distance=2.03 Simple disulfide: pdb=" SG CYS K 350 " - pdb=" SG CYS K 369 " distance=2.03 Simple disulfide: pdb=" SG CYS K 385 " - pdb=" SG CYS K 394 " distance=2.05 Simple disulfide: pdb=" SG CYS K 432 " - pdb=" SG CYS K 446 " distance=2.03 Simple disulfide: pdb=" SG CYS K 436 " - pdb=" SG CYS K 442 " distance=2.03 Simple disulfide: pdb=" SG CYS K 531 " - pdb=" SG CYS K 569 " distance=2.03 Simple disulfide: pdb=" SG CYS K 554 " - pdb=" SG CYS K 574 " distance=2.03 Simple disulfide: pdb=" SG CYS L 34 " - pdb=" SG CYS L 70 " distance=2.03 Simple disulfide: pdb=" SG CYS L 350 " - pdb=" SG CYS L 369 " distance=2.03 Simple disulfide: pdb=" SG CYS L 385 " - pdb=" SG CYS L 394 " distance=2.05 Simple disulfide: pdb=" SG CYS L 432 " - pdb=" SG CYS L 446 " distance=2.03 Simple disulfide: pdb=" SG CYS L 436 " - pdb=" SG CYS L 442 " distance=2.03 Simple disulfide: pdb=" SG CYS L 531 " - pdb=" SG CYS L 569 " distance=2.03 Simple disulfide: pdb=" SG CYS L 554 " - pdb=" SG CYS L 574 " distance=2.03 Simple disulfide: pdb=" SG CYS M 34 " - pdb=" SG CYS M 70 " distance=2.03 Simple disulfide: pdb=" SG CYS M 350 " - pdb=" SG CYS M 369 " distance=2.03 Simple disulfide: pdb=" SG CYS M 385 " - pdb=" SG CYS M 394 " distance=2.05 Simple disulfide: pdb=" SG CYS M 432 " - pdb=" SG CYS M 446 " distance=2.03 Simple disulfide: pdb=" SG CYS M 436 " - pdb=" SG CYS M 442 " distance=2.03 Simple disulfide: pdb=" SG CYS M 531 " - pdb=" SG CYS M 569 " distance=2.03 Simple disulfide: pdb=" SG CYS M 554 " - pdb=" SG CYS M 574 " distance=2.03 Simple disulfide: pdb=" SG CYS N 34 " - pdb=" SG CYS N 70 " distance=2.03 Simple disulfide: pdb=" SG CYS N 350 " - pdb=" SG CYS N 369 " distance=2.03 Simple disulfide: pdb=" SG CYS N 385 " - pdb=" SG CYS N 394 " distance=2.05 Simple disulfide: pdb=" SG CYS N 432 " - pdb=" SG CYS N 446 " distance=2.03 Simple disulfide: pdb=" SG CYS N 436 " - pdb=" SG CYS N 442 " distance=2.03 Simple disulfide: pdb=" SG CYS N 531 " - pdb=" SG CYS N 569 " distance=2.03 Simple disulfide: pdb=" SG CYS N 554 " - pdb=" SG CYS N 574 " distance=2.03 Simple disulfide: pdb=" SG CYS O 34 " - pdb=" SG CYS O 70 " distance=2.03 Simple disulfide: pdb=" SG CYS O 350 " - pdb=" SG CYS O 369 " distance=2.03 Simple disulfide: pdb=" SG CYS O 385 " - pdb=" SG CYS O 394 " distance=2.05 Simple disulfide: pdb=" SG CYS O 432 " - pdb=" SG CYS O 446 " distance=2.03 Simple disulfide: pdb=" SG CYS O 436 " - pdb=" SG CYS O 442 " distance=2.03 Simple disulfide: pdb=" SG CYS O 531 " - pdb=" SG CYS O 569 " distance=2.03 Simple disulfide: pdb=" SG CYS O 554 " - pdb=" SG CYS O 574 " distance=2.03 Simple disulfide: pdb=" SG CYS P 34 " - pdb=" SG CYS P 70 " distance=2.03 Simple disulfide: pdb=" SG CYS P 350 " - pdb=" SG CYS P 369 " distance=2.03 Simple disulfide: pdb=" SG CYS P 385 " - pdb=" SG CYS P 394 " distance=2.05 Simple disulfide: pdb=" SG CYS P 432 " - pdb=" SG CYS P 446 " distance=2.03 Simple disulfide: pdb=" SG CYS P 436 " - pdb=" SG CYS P 442 " distance=2.03 Simple disulfide: pdb=" SG CYS P 531 " - pdb=" SG CYS P 569 " distance=2.03 Simple disulfide: pdb=" SG CYS P 554 " - pdb=" SG CYS P 574 " distance=2.03 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 Links applied NAG-ASN " NAG A 701 " - " ASN A 185 " " NAG A 702 " - " ASN A 269 " " NAG B 701 " - " ASN B 185 " " NAG B 702 " - " ASN B 269 " " NAG C 701 " - " ASN C 185 " " NAG C 702 " - " ASN C 269 " " NAG D 701 " - " ASN D 185 " " NAG D 702 " - " ASN D 269 " " NAG E 701 " - " ASN E 185 " " NAG E 702 " - " ASN E 269 " " NAG F 701 " - " ASN F 185 " " NAG F 702 " - " ASN F 269 " " NAG G 701 " - " ASN G 185 " " NAG G 702 " - " ASN G 269 " " NAG H 701 " - " ASN H 185 " " NAG H 702 " - " ASN H 269 " " NAG I 701 " - " ASN I 185 " " NAG I 702 " - " ASN I 269 " " NAG J 701 " - " ASN J 185 " " NAG J 702 " - " ASN J 269 " " NAG K 701 " - " ASN K 185 " " NAG K 702 " - " ASN K 269 " " NAG L 701 " - " ASN L 185 " " NAG L 702 " - " ASN L 269 " " NAG M 701 " - " ASN M 185 " " NAG M 702 " - " ASN M 269 " " NAG N 701 " - " ASN N 185 " " NAG N 702 " - " ASN N 269 " " NAG O 701 " - " ASN O 185 " " NAG O 702 " - " ASN O 269 " " NAG P 701 " - " ASN P 185 " " NAG P 702 " - " ASN P 269 " Time building additional restraints: 23.94 Conformation dependent library (CDL) restraints added in 11.2 seconds 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 18048 Finding SS restraints... Secondary structure from input PDB file: 192 helices and 0 sheets defined 24.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.77 Creating SS restraints... Processing helix chain 'A' and resid 31 through 38 Processing helix chain 'A' and resid 130 through 141 removed outlier: 4.100A pdb=" N ARG A 135 " --> pdb=" O THR A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 184 Processing helix chain 'A' and resid 186 through 202 removed outlier: 3.593A pdb=" N THR A 191 " --> pdb=" O THR A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 229 Processing helix chain 'A' and resid 232 through 251 removed outlier: 4.181A pdb=" N LYS A 251 " --> pdb=" O ILE A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 269 Processing helix chain 'A' and resid 288 through 294 Processing helix chain 'A' and resid 310 through 314 Processing helix chain 'A' and resid 323 through 346 Processing helix chain 'A' and resid 393 through 398 removed outlier: 3.952A pdb=" N LEU A 397 " --> pdb=" O LEU A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 642 Processing helix chain 'B' and resid 32 through 38 Processing helix chain 'B' and resid 130 through 141 removed outlier: 4.100A pdb=" N ARG B 135 " --> pdb=" O THR B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 184 Processing helix chain 'B' and resid 186 through 202 removed outlier: 3.592A pdb=" N THR B 191 " --> pdb=" O THR B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 229 Processing helix chain 'B' and resid 232 through 251 removed outlier: 4.182A pdb=" N LYS B 251 " --> pdb=" O ILE B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 269 Processing helix chain 'B' and resid 288 through 294 Processing helix chain 'B' and resid 310 through 314 Processing helix chain 'B' and resid 323 through 346 Processing helix chain 'B' and resid 393 through 398 removed outlier: 3.951A pdb=" N LEU B 397 " --> pdb=" O LEU B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 642 Processing helix chain 'C' and resid 32 through 38 Processing helix chain 'C' and resid 130 through 141 removed outlier: 4.100A pdb=" N ARG C 135 " --> pdb=" O THR C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 184 Processing helix chain 'C' and resid 186 through 202 removed outlier: 3.593A pdb=" N THR C 191 " --> pdb=" O THR C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 229 Processing helix chain 'C' and resid 232 through 251 removed outlier: 4.181A pdb=" N LYS C 251 " --> pdb=" O ILE C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 269 Processing helix chain 'C' and resid 288 through 294 Processing helix chain 'C' and resid 310 through 314 Processing helix chain 'C' and resid 323 through 346 Processing helix chain 'C' and resid 393 through 398 removed outlier: 3.952A pdb=" N LEU C 397 " --> pdb=" O LEU C 393 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 642 Processing helix chain 'D' and resid 32 through 38 Processing helix chain 'D' and resid 130 through 141 removed outlier: 4.100A pdb=" N ARG D 135 " --> pdb=" O THR D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 184 Processing helix chain 'D' and resid 186 through 202 removed outlier: 3.593A pdb=" N THR D 191 " --> pdb=" O THR D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 229 Processing helix chain 'D' and resid 232 through 251 removed outlier: 4.181A pdb=" N LYS D 251 " --> pdb=" O ILE D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 269 Processing helix chain 'D' and resid 288 through 294 Processing helix chain 'D' and resid 310 through 314 Processing helix chain 'D' and resid 323 through 346 Processing helix chain 'D' and resid 393 through 398 removed outlier: 3.951A pdb=" N LEU D 397 " --> pdb=" O LEU D 393 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 642 Processing helix chain 'E' and resid 32 through 38 Processing helix chain 'E' and resid 130 through 141 removed outlier: 4.100A pdb=" N ARG E 135 " --> pdb=" O THR E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 184 Processing helix chain 'E' and resid 186 through 202 removed outlier: 3.593A pdb=" N THR E 191 " --> pdb=" O THR E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 229 Processing helix chain 'E' and resid 232 through 251 removed outlier: 4.181A pdb=" N LYS E 251 " --> pdb=" O ILE E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 269 Processing helix chain 'E' and resid 288 through 294 Processing helix chain 'E' and resid 310 through 314 Processing helix chain 'E' and resid 323 through 346 Processing helix chain 'E' and resid 393 through 398 removed outlier: 3.952A pdb=" N LEU E 397 " --> pdb=" O LEU E 393 " (cutoff:3.500A) Processing helix chain 'E' and resid 630 through 642 Processing helix chain 'F' and resid 32 through 38 Processing helix chain 'F' and resid 130 through 141 removed outlier: 4.101A pdb=" N ARG F 135 " --> pdb=" O THR F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 184 Processing helix chain 'F' and resid 186 through 202 removed outlier: 3.592A pdb=" N THR F 191 " --> pdb=" O THR F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 223 through 229 Processing helix chain 'F' and resid 232 through 251 removed outlier: 4.182A pdb=" N LYS F 251 " --> pdb=" O ILE F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 260 through 269 Processing helix chain 'F' and resid 288 through 294 Processing helix chain 'F' and resid 310 through 314 Processing helix chain 'F' and resid 323 through 346 Processing helix chain 'F' and resid 393 through 398 removed outlier: 3.952A pdb=" N LEU F 397 " --> pdb=" O LEU F 393 " (cutoff:3.500A) Processing helix chain 'F' and resid 630 through 642 Processing helix chain 'G' and resid 32 through 38 Processing helix chain 'G' and resid 130 through 141 removed outlier: 4.100A pdb=" N ARG G 135 " --> pdb=" O THR G 131 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 184 Processing helix chain 'G' and resid 186 through 202 removed outlier: 3.593A pdb=" N THR G 191 " --> pdb=" O THR G 187 " (cutoff:3.500A) Processing helix chain 'G' and resid 223 through 229 Processing helix chain 'G' and resid 232 through 251 removed outlier: 4.181A pdb=" N LYS G 251 " --> pdb=" O ILE G 247 " (cutoff:3.500A) Processing helix chain 'G' and resid 260 through 269 Processing helix chain 'G' and resid 288 through 294 Processing helix chain 'G' and resid 310 through 314 Processing helix chain 'G' and resid 323 through 346 Processing helix chain 'G' and resid 393 through 398 removed outlier: 3.952A pdb=" N LEU G 397 " --> pdb=" O LEU G 393 " (cutoff:3.500A) Processing helix chain 'G' and resid 630 through 642 Processing helix chain 'H' and resid 32 through 38 Processing helix chain 'H' and resid 130 through 141 removed outlier: 4.100A pdb=" N ARG H 135 " --> pdb=" O THR H 131 " (cutoff:3.500A) Processing helix chain 'H' and resid 168 through 184 Processing helix chain 'H' and resid 186 through 202 removed outlier: 3.593A pdb=" N THR H 191 " --> pdb=" O THR H 187 " (cutoff:3.500A) Processing helix chain 'H' and resid 223 through 229 Processing helix chain 'H' and resid 232 through 251 removed outlier: 4.181A pdb=" N LYS H 251 " --> pdb=" O ILE H 247 " (cutoff:3.500A) Processing helix chain 'H' and resid 260 through 269 Processing helix chain 'H' and resid 288 through 294 Processing helix chain 'H' and resid 310 through 314 Processing helix chain 'H' and resid 323 through 346 Processing helix chain 'H' and resid 393 through 398 removed outlier: 3.951A pdb=" N LEU H 397 " --> pdb=" O LEU H 393 " (cutoff:3.500A) Processing helix chain 'H' and resid 630 through 642 Processing helix chain 'I' and resid 32 through 38 Processing helix chain 'I' and resid 130 through 141 removed outlier: 4.100A pdb=" N ARG I 135 " --> pdb=" O THR I 131 " (cutoff:3.500A) Processing helix chain 'I' and resid 168 through 184 Processing helix chain 'I' and resid 186 through 202 removed outlier: 3.593A pdb=" N THR I 191 " --> pdb=" O THR I 187 " (cutoff:3.500A) Processing helix chain 'I' and resid 223 through 229 Processing helix chain 'I' and resid 232 through 251 removed outlier: 4.181A pdb=" N LYS I 251 " --> pdb=" O ILE I 247 " (cutoff:3.500A) Processing helix chain 'I' and resid 260 through 269 Processing helix chain 'I' and resid 288 through 294 Processing helix chain 'I' and resid 310 through 314 Processing helix chain 'I' and resid 323 through 346 Processing helix chain 'I' and resid 393 through 398 removed outlier: 3.952A pdb=" N LEU I 397 " --> pdb=" O LEU I 393 " (cutoff:3.500A) Processing helix chain 'I' and resid 630 through 642 Processing helix chain 'J' and resid 32 through 38 Processing helix chain 'J' and resid 130 through 141 removed outlier: 4.100A pdb=" N ARG J 135 " --> pdb=" O THR J 131 " (cutoff:3.500A) Processing helix chain 'J' and resid 168 through 184 Processing helix chain 'J' and resid 186 through 202 removed outlier: 3.593A pdb=" N THR J 191 " --> pdb=" O THR J 187 " (cutoff:3.500A) Processing helix chain 'J' and resid 223 through 229 Processing helix chain 'J' and resid 232 through 251 removed outlier: 4.181A pdb=" N LYS J 251 " --> pdb=" O ILE J 247 " (cutoff:3.500A) Processing helix chain 'J' and resid 260 through 269 Processing helix chain 'J' and resid 288 through 294 Processing helix chain 'J' and resid 310 through 314 Processing helix chain 'J' and resid 323 through 346 Processing helix chain 'J' and resid 393 through 398 removed outlier: 3.952A pdb=" N LEU J 397 " --> pdb=" O LEU J 393 " (cutoff:3.500A) Processing helix chain 'J' and resid 630 through 642 Processing helix chain 'K' and resid 32 through 38 Processing helix chain 'K' and resid 130 through 141 removed outlier: 4.101A pdb=" N ARG K 135 " --> pdb=" O THR K 131 " (cutoff:3.500A) Processing helix chain 'K' and resid 168 through 184 Processing helix chain 'K' and resid 186 through 202 removed outlier: 3.593A pdb=" N THR K 191 " --> pdb=" O THR K 187 " (cutoff:3.500A) Processing helix chain 'K' and resid 223 through 229 Processing helix chain 'K' and resid 232 through 251 removed outlier: 4.182A pdb=" N LYS K 251 " --> pdb=" O ILE K 247 " (cutoff:3.500A) Processing helix chain 'K' and resid 260 through 269 Processing helix chain 'K' and resid 288 through 294 Processing helix chain 'K' and resid 310 through 314 Processing helix chain 'K' and resid 323 through 346 Processing helix chain 'K' and resid 393 through 398 removed outlier: 3.952A pdb=" N LEU K 397 " --> pdb=" O LEU K 393 " (cutoff:3.500A) Processing helix chain 'K' and resid 630 through 642 Processing helix chain 'L' and resid 32 through 38 Processing helix chain 'L' and resid 130 through 141 removed outlier: 4.100A pdb=" N ARG L 135 " --> pdb=" O THR L 131 " (cutoff:3.500A) Processing helix chain 'L' and resid 168 through 184 Processing helix chain 'L' and resid 186 through 202 removed outlier: 3.592A pdb=" N THR L 191 " --> pdb=" O THR L 187 " (cutoff:3.500A) Processing helix chain 'L' and resid 223 through 229 Processing helix chain 'L' and resid 232 through 251 removed outlier: 4.182A pdb=" N LYS L 251 " --> pdb=" O ILE L 247 " (cutoff:3.500A) Processing helix chain 'L' and resid 260 through 269 Processing helix chain 'L' and resid 288 through 294 Processing helix chain 'L' and resid 310 through 314 Processing helix chain 'L' and resid 323 through 346 Processing helix chain 'L' and resid 393 through 398 removed outlier: 3.953A pdb=" N LEU L 397 " --> pdb=" O LEU L 393 " (cutoff:3.500A) Processing helix chain 'L' and resid 630 through 642 Processing helix chain 'M' and resid 32 through 38 Processing helix chain 'M' and resid 130 through 141 removed outlier: 4.101A pdb=" N ARG M 135 " --> pdb=" O THR M 131 " (cutoff:3.500A) Processing helix chain 'M' and resid 168 through 184 Processing helix chain 'M' and resid 186 through 202 removed outlier: 3.593A pdb=" N THR M 191 " --> pdb=" O THR M 187 " (cutoff:3.500A) Processing helix chain 'M' and resid 223 through 229 Processing helix chain 'M' and resid 232 through 251 removed outlier: 4.182A pdb=" N LYS M 251 " --> pdb=" O ILE M 247 " (cutoff:3.500A) Processing helix chain 'M' and resid 260 through 269 Processing helix chain 'M' and resid 288 through 294 Processing helix chain 'M' and resid 310 through 314 Processing helix chain 'M' and resid 323 through 346 Processing helix chain 'M' and resid 393 through 398 removed outlier: 3.953A pdb=" N LEU M 397 " --> pdb=" O LEU M 393 " (cutoff:3.500A) Processing helix chain 'M' and resid 630 through 642 Processing helix chain 'N' and resid 32 through 38 Processing helix chain 'N' and resid 130 through 141 removed outlier: 4.101A pdb=" N ARG N 135 " --> pdb=" O THR N 131 " (cutoff:3.500A) Processing helix chain 'N' and resid 168 through 184 Processing helix chain 'N' and resid 186 through 202 removed outlier: 3.592A pdb=" N THR N 191 " --> pdb=" O THR N 187 " (cutoff:3.500A) Processing helix chain 'N' and resid 223 through 229 Processing helix chain 'N' and resid 232 through 251 removed outlier: 4.181A pdb=" N LYS N 251 " --> pdb=" O ILE N 247 " (cutoff:3.500A) Processing helix chain 'N' and resid 260 through 269 Processing helix chain 'N' and resid 288 through 294 Processing helix chain 'N' and resid 310 through 314 Processing helix chain 'N' and resid 323 through 346 Processing helix chain 'N' and resid 393 through 398 removed outlier: 3.952A pdb=" N LEU N 397 " --> pdb=" O LEU N 393 " (cutoff:3.500A) Processing helix chain 'N' and resid 630 through 642 Processing helix chain 'O' and resid 32 through 38 Processing helix chain 'O' and resid 130 through 141 removed outlier: 4.101A pdb=" N ARG O 135 " --> pdb=" O THR O 131 " (cutoff:3.500A) Processing helix chain 'O' and resid 168 through 184 Processing helix chain 'O' and resid 186 through 202 removed outlier: 3.592A pdb=" N THR O 191 " --> pdb=" O THR O 187 " (cutoff:3.500A) Processing helix chain 'O' and resid 223 through 229 Processing helix chain 'O' and resid 232 through 251 removed outlier: 4.181A pdb=" N LYS O 251 " --> pdb=" O ILE O 247 " (cutoff:3.500A) Processing helix chain 'O' and resid 260 through 269 Processing helix chain 'O' and resid 288 through 294 Processing helix chain 'O' and resid 310 through 314 Processing helix chain 'O' and resid 323 through 346 Processing helix chain 'O' and resid 393 through 398 removed outlier: 3.952A pdb=" N LEU O 397 " --> pdb=" O LEU O 393 " (cutoff:3.500A) Processing helix chain 'O' and resid 630 through 642 Processing helix chain 'P' and resid 32 through 38 Processing helix chain 'P' and resid 130 through 141 removed outlier: 4.100A pdb=" N ARG P 135 " --> pdb=" O THR P 131 " (cutoff:3.500A) Processing helix chain 'P' and resid 168 through 184 Processing helix chain 'P' and resid 186 through 202 removed outlier: 3.593A pdb=" N THR P 191 " --> pdb=" O THR P 187 " (cutoff:3.500A) Processing helix chain 'P' and resid 223 through 229 Processing helix chain 'P' and resid 232 through 251 removed outlier: 4.181A pdb=" N LYS P 251 " --> pdb=" O ILE P 247 " (cutoff:3.500A) Processing helix chain 'P' and resid 260 through 269 Processing helix chain 'P' and resid 288 through 294 Processing helix chain 'P' and resid 310 through 314 Processing helix chain 'P' and resid 323 through 346 Processing helix chain 'P' and resid 393 through 398 removed outlier: 3.951A pdb=" N LEU P 397 " --> pdb=" O LEU P 393 " (cutoff:3.500A) Processing helix chain 'P' and resid 630 through 642 1489 hydrogen bonds defined for protein. 4467 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: 18.00 Time building geometry restraints manager: 26.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 24464 1.34 - 1.46: 17618 1.46 - 1.58: 34574 1.58 - 1.70: 0 1.70 - 1.82: 688 Bond restraints: 77344 Sorted by residual: bond pdb=" C1 NAG N 701 " pdb=" O5 NAG N 701 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.07e+00 bond pdb=" C1 NAG M 701 " pdb=" O5 NAG M 701 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.06e+00 bond pdb=" C1 NAG G 701 " pdb=" O5 NAG G 701 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.06e+00 bond pdb=" C1 NAG D 701 " pdb=" O5 NAG D 701 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.05e+00 bond pdb=" C1 NAG F 701 " pdb=" O5 NAG F 701 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 2.03e+00 ... (remaining 77339 not shown) Histogram of bond angle deviations from ideal: 100.48 - 107.20: 2808 107.20 - 113.91: 43894 113.91 - 120.63: 29719 120.63 - 127.34: 27996 127.34 - 134.06: 687 Bond angle restraints: 105104 Sorted by residual: angle pdb=" N VAL E 125 " pdb=" CA VAL E 125 " pdb=" C VAL E 125 " ideal model delta sigma weight residual 111.91 108.27 3.64 8.90e-01 1.26e+00 1.68e+01 angle pdb=" N VAL D 125 " pdb=" CA VAL D 125 " pdb=" C VAL D 125 " ideal model delta sigma weight residual 111.91 108.27 3.64 8.90e-01 1.26e+00 1.67e+01 angle pdb=" N VAL M 125 " pdb=" CA VAL M 125 " pdb=" C VAL M 125 " ideal model delta sigma weight residual 111.91 108.27 3.64 8.90e-01 1.26e+00 1.67e+01 angle pdb=" N VAL K 125 " pdb=" CA VAL K 125 " pdb=" C VAL K 125 " ideal model delta sigma weight residual 111.91 108.28 3.63 8.90e-01 1.26e+00 1.66e+01 angle pdb=" N VAL F 125 " pdb=" CA VAL F 125 " pdb=" C VAL F 125 " ideal model delta sigma weight residual 111.91 108.29 3.62 8.90e-01 1.26e+00 1.66e+01 ... (remaining 105099 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.83: 42497 16.83 - 33.67: 3775 33.67 - 50.50: 720 50.50 - 67.33: 144 67.33 - 84.17: 48 Dihedral angle restraints: 47184 sinusoidal: 19184 harmonic: 28000 Sorted by residual: dihedral pdb=" CB CYS D 554 " pdb=" SG CYS D 554 " pdb=" SG CYS D 574 " pdb=" CB CYS D 574 " ideal model delta sinusoidal sigma weight residual 93.00 50.95 42.05 1 1.00e+01 1.00e-02 2.47e+01 dihedral pdb=" CB CYS B 554 " pdb=" SG CYS B 554 " pdb=" SG CYS B 574 " pdb=" CB CYS B 574 " ideal model delta sinusoidal sigma weight residual 93.00 50.96 42.04 1 1.00e+01 1.00e-02 2.47e+01 dihedral pdb=" CB CYS E 554 " pdb=" SG CYS E 554 " pdb=" SG CYS E 574 " pdb=" CB CYS E 574 " ideal model delta sinusoidal sigma weight residual 93.00 50.96 42.04 1 1.00e+01 1.00e-02 2.47e+01 ... (remaining 47181 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 7505 0.031 - 0.061: 3136 0.061 - 0.092: 901 0.092 - 0.123: 556 0.123 - 0.153: 62 Chirality restraints: 12160 Sorted by residual: chirality pdb=" CB ILE O 608 " pdb=" CA ILE O 608 " pdb=" CG1 ILE O 608 " pdb=" CG2 ILE O 608 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.87e-01 chirality pdb=" CB ILE P 608 " pdb=" CA ILE P 608 " pdb=" CG1 ILE P 608 " pdb=" CG2 ILE P 608 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.80e-01 chirality pdb=" CB ILE I 608 " pdb=" CA ILE I 608 " pdb=" CG1 ILE I 608 " pdb=" CG2 ILE I 608 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.75e-01 ... (remaining 12157 not shown) Planarity restraints: 13520 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP J 621 " -0.036 5.00e-02 4.00e+02 5.40e-02 4.66e+00 pdb=" N PRO J 622 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO J 622 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO J 622 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP N 621 " 0.036 5.00e-02 4.00e+02 5.39e-02 4.65e+00 pdb=" N PRO N 622 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO N 622 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO N 622 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 621 " -0.036 5.00e-02 4.00e+02 5.39e-02 4.65e+00 pdb=" N PRO D 622 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO D 622 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 622 " -0.030 5.00e-02 4.00e+02 ... (remaining 13517 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 1347 2.66 - 3.22: 75332 3.22 - 3.78: 124117 3.78 - 4.34: 172734 4.34 - 4.90: 273643 Nonbonded interactions: 647173 Sorted by model distance: nonbonded pdb=" O MET B 59 " pdb=" OH TYR C 85 " model vdw 2.104 2.440 nonbonded pdb=" O MET E 59 " pdb=" OH TYR F 85 " model vdw 2.116 2.440 nonbonded pdb=" O MET G 59 " pdb=" OH TYR H 85 " model vdw 2.165 2.440 nonbonded pdb=" O MET M 59 " pdb=" OH TYR N 85 " model vdw 2.178 2.440 nonbonded pdb=" O MET A 59 " pdb=" OH TYR B 85 " model vdw 2.191 2.440 ... (remaining 647168 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 12.040 Check model and map are aligned: 0.840 Set scattering table: 0.520 Process input model: 142.750 Find NCS groups from input model: 4.290 Set up NCS constraints: 0.710 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 166.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6813 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 : 0.002 0.029 77344 Z= 0.163 Angle : 0.565 5.440 105104 Z= 0.317 Chirality : 0.041 0.153 12160 Planarity : 0.004 0.054 13488 Dihedral : 12.996 84.166 28800 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -2.84 (0.07), residues: 9600 helix: -1.50 (0.09), residues: 2288 sheet: -1.21 (0.12), residues: 1584 loop : -2.34 (0.07), residues: 5728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 51 HIS 0.002 0.000 HIS L 340 PHE 0.011 0.001 PHE N 133 TYR 0.011 0.001 TYR L 341 ARG 0.005 0.000 ARG J 153 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1985 residues out of total 8544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1985 time to evaluate : 6.142 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 outliers start: 0 outliers final: 0 residues processed: 1985 average time/residue: 0.7070 time to fit residues: 2395.6374 Evaluate side-chains 1143 residues out of total 8544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1143 time to evaluate : 6.176 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 9.3041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 960 random chunks: chunk 810 optimal weight: 5.9990 chunk 727 optimal weight: 1.9990 chunk 403 optimal weight: 10.0000 chunk 248 optimal weight: 1.9990 chunk 490 optimal weight: 3.9990 chunk 388 optimal weight: 0.9990 chunk 752 optimal weight: 9.9990 chunk 291 optimal weight: 2.9990 chunk 457 optimal weight: 6.9990 chunk 560 optimal weight: 0.9980 chunk 871 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 234 ASN ** A 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 GLN ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 421 GLN ** A 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 561 HIS B 32 GLN ** B 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 234 ASN B 345 ASN B 361 GLN B 363 ASN ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 421 GLN ** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 GLN ** C 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 HIS C 234 ASN ** C 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 421 GLN D 32 GLN ** D 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 234 ASN D 345 ASN ** D 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 421 GLN ** D 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 561 HIS D 625 ASN E 32 GLN ** E 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 233 GLN E 234 ASN ** E 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 421 GLN E 561 HIS E 625 ASN F 32 GLN ** F 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 234 ASN ** F 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 421 GLN F 625 ASN G 32 GLN ** G 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 220 HIS G 234 ASN ** G 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 421 GLN H 32 GLN ** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 234 ASN H 345 ASN ** H 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 421 GLN I 32 GLN I 234 ASN ** I 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 361 GLN I 363 ASN ** I 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 421 GLN ** I 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 625 ASN J 32 GLN ** J 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 234 ASN ** J 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 363 ASN ** J 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 421 GLN J 625 ASN K 32 GLN ** K 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 220 HIS K 234 ASN ** K 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 421 GLN L 32 GLN ** L 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 234 ASN L 345 ASN ** L 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 421 GLN M 32 GLN ** M 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 234 ASN ** M 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 361 GLN M 363 ASN ** M 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 421 GLN N 32 GLN N 186 GLN ** N 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 234 ASN ** N 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 421 GLN N 625 ASN O 32 GLN ** O 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 234 ASN O 299 HIS ** O 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 421 GLN P 32 GLN ** P 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 220 HIS P 234 ASN P 345 ASN ** P 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 421 GLN Total number of N/Q/H flips: 77 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.107 77344 Z= 0.333 Angle : 0.641 8.962 105104 Z= 0.321 Chirality : 0.046 0.248 12160 Planarity : 0.005 0.048 13488 Dihedral : 4.840 40.577 10928 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 17.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 3.86 % Allowed : 14.61 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -2.12 (0.08), residues: 9600 helix: -0.39 (0.10), residues: 2304 sheet: -1.54 (0.11), residues: 1936 loop : -1.83 (0.08), residues: 5360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 51 HIS 0.010 0.001 HIS A 204 PHE 0.032 0.002 PHE E 529 TYR 0.023 0.002 TYR B 341 ARG 0.012 0.001 ARG F 153 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1605 residues out of total 8544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 330 poor density : 1275 time to evaluate : 6.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 330 outliers final: 218 residues processed: 1511 average time/residue: 0.6875 time to fit residues: 1826.7664 Evaluate side-chains 1288 residues out of total 8544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 218 poor density : 1070 time to evaluate : 6.163 Switching outliers to nearest non-outliers outliers start: 218 outliers final: 0 residues processed: 218 average time/residue: 0.5770 time to fit residues: 251.6638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 960 random chunks: chunk 484 optimal weight: 1.9990 chunk 270 optimal weight: 0.9990 chunk 725 optimal weight: 0.8980 chunk 593 optimal weight: 7.9990 chunk 240 optimal weight: 1.9990 chunk 873 optimal weight: 4.9990 chunk 943 optimal weight: 10.0000 chunk 777 optimal weight: 5.9990 chunk 866 optimal weight: 0.6980 chunk 297 optimal weight: 7.9990 chunk 700 optimal weight: 0.0030 overall best weight: 0.9194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 234 ASN A 361 GLN ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 234 ASN ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 361 GLN ** C 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 492 GLN ** D 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 625 ASN ** E 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 140 GLN ** E 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 234 ASN ** E 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 625 ASN ** F 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 492 GLN F 625 ASN G 36 ASN ** G 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 361 GLN ** G 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 492 GLN ** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 234 ASN I 361 GLN ** I 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 625 ASN ** J 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 625 ASN K 361 GLN ** K 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 234 ASN ** L 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 234 ASN M 361 GLN ** M 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 186 GLN ** N 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 492 GLN N 625 ASN O 36 ASN ** O 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 361 GLN ** O 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 492 GLN P 56 ASN ** P 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 492 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 77344 Z= 0.215 Angle : 0.564 10.353 105104 Z= 0.279 Chirality : 0.042 0.229 12160 Planarity : 0.004 0.046 13488 Dihedral : 4.508 31.063 10928 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 1.73 % Allowed : 18.97 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.08), residues: 9600 helix: 0.05 (0.10), residues: 2288 sheet: -1.13 (0.12), residues: 1808 loop : -1.67 (0.08), residues: 5504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 51 HIS 0.007 0.001 HIS D 311 PHE 0.025 0.002 PHE E 529 TYR 0.018 0.001 TYR N 341 ARG 0.010 0.001 ARG F 153 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1362 residues out of total 8544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 1214 time to evaluate : 6.163 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 outliers start: 148 outliers final: 53 residues processed: 1306 average time/residue: 0.6757 time to fit residues: 1556.9526 Evaluate side-chains 1107 residues out of total 8544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 1054 time to evaluate : 6.163 Switching outliers to nearest non-outliers outliers start: 53 outliers final: 0 residues processed: 53 average time/residue: 0.5604 time to fit residues: 64.9577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 960 random chunks: chunk 862 optimal weight: 5.9990 chunk 656 optimal weight: 9.9990 chunk 453 optimal weight: 8.9990 chunk 96 optimal weight: 9.9990 chunk 416 optimal weight: 0.1980 chunk 586 optimal weight: 8.9990 chunk 876 optimal weight: 10.0000 chunk 927 optimal weight: 4.9990 chunk 457 optimal weight: 10.0000 chunk 830 optimal weight: 3.9990 chunk 250 optimal weight: 0.7980 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 234 ASN ** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 299 HIS ** C 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 234 ASN ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 36 ASN ** G 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 299 HIS ** G 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 299 HIS ** H 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 234 ASN ** I 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 361 GLN ** I 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 299 HIS K 361 GLN ** K 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 234 ASN ** L 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 234 ASN ** M 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 361 GLN ** M 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 230 GLN ** N 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 36 ASN ** O 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 361 GLN ** O 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.3779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.157 77344 Z= 0.523 Angle : 0.760 20.260 105104 Z= 0.387 Chirality : 0.050 0.236 12160 Planarity : 0.006 0.073 13488 Dihedral : 5.201 18.383 10928 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 21.86 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.70 % Favored : 91.17 % Rotamer: Outliers : 4.34 % Allowed : 20.51 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -2.23 (0.08), residues: 9600 helix: -0.61 (0.10), residues: 2352 sheet: -1.82 (0.11), residues: 1744 loop : -1.77 (0.08), residues: 5504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 51 HIS 0.010 0.002 HIS A 204 PHE 0.038 0.003 PHE P 313 TYR 0.026 0.003 TYR D 593 ARG 0.011 0.001 ARG D 135 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1564 residues out of total 8544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 371 poor density : 1193 time to evaluate : 6.330 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 outliers start: 371 outliers final: 236 residues processed: 1462 average time/residue: 0.7010 time to fit residues: 1793.9479 Evaluate side-chains 1255 residues out of total 8544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 236 poor density : 1019 time to evaluate : 6.248 Switching outliers to nearest non-outliers outliers start: 236 outliers final: 0 residues processed: 236 average time/residue: 0.5563 time to fit residues: 262.4787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 960 random chunks: chunk 772 optimal weight: 0.9990 chunk 526 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 690 optimal weight: 0.8980 chunk 382 optimal weight: 3.9990 chunk 791 optimal weight: 1.9990 chunk 641 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 473 optimal weight: 0.8980 chunk 832 optimal weight: 0.8980 chunk 234 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 140 GLN ** E 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 220 HIS E 234 ASN ** E 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 93 ASN ** G 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 234 ASN ** I 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 230 GLN ** J 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 361 GLN ** K 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 234 ASN ** L 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 234 ASN ** M 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 299 HIS ** O 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.3785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 77344 Z= 0.235 Angle : 0.606 11.795 105104 Z= 0.305 Chirality : 0.044 0.305 12160 Planarity : 0.005 0.073 13488 Dihedral : 4.741 19.099 10928 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 18.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 2.61 % Allowed : 21.75 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.08), residues: 9600 helix: -0.18 (0.10), residues: 2352 sheet: -1.48 (0.12), residues: 1648 loop : -1.67 (0.08), residues: 5600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP O 627 HIS 0.006 0.001 HIS H 311 PHE 0.031 0.002 PHE O 313 TYR 0.024 0.002 TYR L 78 ARG 0.009 0.001 ARG J 135 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1422 residues out of total 8544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 223 poor density : 1199 time to evaluate : 6.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 223 outliers final: 113 residues processed: 1347 average time/residue: 0.6653 time to fit residues: 1598.2639 Evaluate side-chains 1155 residues out of total 8544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 1042 time to evaluate : 6.164 Switching outliers to nearest non-outliers outliers start: 113 outliers final: 0 residues processed: 113 average time/residue: 0.5481 time to fit residues: 127.9035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 960 random chunks: chunk 312 optimal weight: 1.9990 chunk 835 optimal weight: 0.0970 chunk 183 optimal weight: 0.8980 chunk 544 optimal weight: 2.9990 chunk 229 optimal weight: 4.9990 chunk 928 optimal weight: 0.8980 chunk 771 optimal weight: 4.9990 chunk 430 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 chunk 307 optimal weight: 0.4980 chunk 487 optimal weight: 0.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 311 HIS ** D 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 36 ASN ** G 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 401 ASN ** H 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 401 ASN ** L 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 93 ASN ** N 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 56 ASN ** P 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 401 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.3845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 77344 Z= 0.204 Angle : 0.592 15.656 105104 Z= 0.295 Chirality : 0.043 0.241 12160 Planarity : 0.005 0.071 13488 Dihedral : 4.583 19.120 10928 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 16.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 1.91 % Allowed : 23.23 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.08), residues: 9600 helix: 0.05 (0.10), residues: 2352 sheet: -1.30 (0.13), residues: 1536 loop : -1.58 (0.08), residues: 5712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 627 HIS 0.010 0.001 HIS I 311 PHE 0.028 0.002 PHE O 313 TYR 0.021 0.002 TYR A 573 ARG 0.006 0.000 ARG P 135 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1278 residues out of total 8544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 1115 time to evaluate : 6.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 163 outliers final: 88 residues processed: 1207 average time/residue: 0.6653 time to fit residues: 1435.1150 Evaluate side-chains 1134 residues out of total 8544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 1046 time to evaluate : 7.647 Switching outliers to nearest non-outliers outliers start: 88 outliers final: 0 residues processed: 88 average time/residue: 0.5739 time to fit residues: 106.6541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 960 random chunks: chunk 895 optimal weight: 0.6980 chunk 104 optimal weight: 9.9990 chunk 529 optimal weight: 6.9990 chunk 678 optimal weight: 6.9990 chunk 525 optimal weight: 10.0000 chunk 781 optimal weight: 0.1980 chunk 518 optimal weight: 0.0870 chunk 925 optimal weight: 1.9990 chunk 579 optimal weight: 9.9990 chunk 564 optimal weight: 0.8980 chunk 427 optimal weight: 5.9990 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 234 ASN ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 ASN ** C 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 36 ASN G 116 ASN ** G 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 401 ASN ** I 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 116 ASN ** K 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 401 ASN ** M 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 56 ASN ** P 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.3934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 77344 Z= 0.205 Angle : 0.583 10.654 105104 Z= 0.291 Chirality : 0.043 0.252 12160 Planarity : 0.005 0.070 13488 Dihedral : 4.513 18.933 10928 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 16.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 1.59 % Allowed : 23.34 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.08), residues: 9600 helix: 0.17 (0.10), residues: 2336 sheet: -1.31 (0.13), residues: 1648 loop : -1.57 (0.08), residues: 5616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP N 627 HIS 0.012 0.001 HIS B 311 PHE 0.029 0.002 PHE E 313 TYR 0.018 0.002 TYR A 573 ARG 0.007 0.000 ARG J 339 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1216 residues out of total 8544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 1080 time to evaluate : 6.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 136 outliers final: 70 residues processed: 1152 average time/residue: 0.6766 time to fit residues: 1386.9742 Evaluate side-chains 1089 residues out of total 8544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 1019 time to evaluate : 6.184 Switching outliers to nearest non-outliers outliers start: 70 outliers final: 0 residues processed: 70 average time/residue: 0.5547 time to fit residues: 83.2531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 960 random chunks: chunk 572 optimal weight: 4.9990 chunk 369 optimal weight: 1.9990 chunk 552 optimal weight: 1.9990 chunk 278 optimal weight: 0.0050 chunk 181 optimal weight: 0.6980 chunk 179 optimal weight: 0.9980 chunk 588 optimal weight: 6.9990 chunk 630 optimal weight: 1.9990 chunk 457 optimal weight: 9.9990 chunk 86 optimal weight: 4.9990 chunk 727 optimal weight: 2.9990 overall best weight: 1.1398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 116 ASN ** A 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 36 ASN G 93 ASN ** G 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 311 HIS ** L 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 36 ASN O 116 ASN ** O 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.4097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 77344 Z= 0.240 Angle : 0.590 12.615 105104 Z= 0.295 Chirality : 0.044 0.266 12160 Planarity : 0.005 0.070 13488 Dihedral : 4.529 20.139 10928 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 16.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 1.36 % Allowed : 23.51 % Favored : 75.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.08), residues: 9600 helix: 0.15 (0.10), residues: 2336 sheet: -1.23 (0.13), residues: 1568 loop : -1.54 (0.08), residues: 5696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 627 HIS 0.009 0.001 HIS I 311 PHE 0.030 0.002 PHE H 376 TYR 0.022 0.002 TYR C 460 ARG 0.007 0.000 ARG P 274 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1177 residues out of total 8544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 1061 time to evaluate : 6.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 116 outliers final: 72 residues processed: 1140 average time/residue: 0.6744 time to fit residues: 1371.6098 Evaluate side-chains 1093 residues out of total 8544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 1021 time to evaluate : 6.217 Switching outliers to nearest non-outliers outliers start: 72 outliers final: 0 residues processed: 72 average time/residue: 0.5563 time to fit residues: 85.9439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 960 random chunks: chunk 841 optimal weight: 0.0030 chunk 886 optimal weight: 8.9990 chunk 808 optimal weight: 0.7980 chunk 862 optimal weight: 0.0970 chunk 518 optimal weight: 5.9990 chunk 375 optimal weight: 7.9990 chunk 677 optimal weight: 0.8980 chunk 264 optimal weight: 2.9990 chunk 779 optimal weight: 3.9990 chunk 815 optimal weight: 6.9990 chunk 859 optimal weight: 1.9990 overall best weight: 0.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 HIS ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 36 ASN ** G 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 36 ASN ** K 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 220 HIS ** L 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 36 ASN ** O 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.4147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 77344 Z= 0.201 Angle : 0.577 12.249 105104 Z= 0.289 Chirality : 0.043 0.284 12160 Planarity : 0.005 0.070 13488 Dihedral : 4.477 18.433 10928 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 0.59 % Allowed : 24.30 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.08), residues: 9600 helix: 0.27 (0.11), residues: 2320 sheet: -1.54 (0.12), residues: 1600 loop : -1.38 (0.08), residues: 5680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 627 HIS 0.011 0.001 HIS D 311 PHE 0.033 0.002 PHE H 376 TYR 0.021 0.002 TYR G 460 ARG 0.007 0.000 ARG J 339 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1123 residues out of total 8544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 1073 time to evaluate : 6.631 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 outliers start: 50 outliers final: 33 residues processed: 1094 average time/residue: 0.6893 time to fit residues: 1346.8008 Evaluate side-chains 1054 residues out of total 8544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 1021 time to evaluate : 6.246 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.5900 time to fit residues: 46.1521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 960 random chunks: chunk 566 optimal weight: 0.9980 chunk 911 optimal weight: 4.9990 chunk 556 optimal weight: 0.9990 chunk 432 optimal weight: 2.9990 chunk 633 optimal weight: 8.9990 chunk 956 optimal weight: 6.9990 chunk 880 optimal weight: 7.9990 chunk 761 optimal weight: 20.0000 chunk 79 optimal weight: 6.9990 chunk 588 optimal weight: 9.9990 chunk 466 optimal weight: 0.9980 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 116 ASN ** A 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 299 HIS ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 299 HIS B 345 ASN ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 ASN ** C 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 ASN ** C 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 299 HIS ** D 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 299 HIS ** E 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 299 HIS ** F 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 36 ASN ** G 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 116 ASN ** G 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 345 ASN ** H 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 299 HIS ** I 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 299 HIS ** J 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 36 ASN K 116 ASN ** K 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 345 ASN ** L 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 53 ASN ** M 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 204 HIS ** M 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 299 HIS ** N 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 36 ASN ** O 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 116 ASN ** O 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 220 HIS ** O 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 299 HIS ** P 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 345 ASN ** P 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.4573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.133 77344 Z= 0.381 Angle : 0.667 9.999 105104 Z= 0.339 Chirality : 0.048 0.297 12160 Planarity : 0.005 0.069 13488 Dihedral : 4.899 23.201 10928 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 19.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 0.63 % Allowed : 24.49 % Favored : 74.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.08), residues: 9600 helix: -0.18 (0.10), residues: 2336 sheet: -1.91 (0.12), residues: 1648 loop : -1.42 (0.08), residues: 5616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 461 HIS 0.011 0.001 HIS C 311 PHE 0.033 0.002 PHE A 313 TYR 0.024 0.002 TYR P 341 ARG 0.010 0.001 ARG B 305 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1126 residues out of total 8544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 1072 time to evaluate : 6.300 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 35 residues processed: 1102 average time/residue: 0.6912 time to fit residues: 1355.8789 Evaluate side-chains 1053 residues out of total 8544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 1018 time to evaluate : 6.168 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.5680 time to fit residues: 47.5046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 960 random chunks: chunk 604 optimal weight: 0.6980 chunk 811 optimal weight: 0.9980 chunk 233 optimal weight: 3.9990 chunk 702 optimal weight: 10.0000 chunk 112 optimal weight: 3.9990 chunk 211 optimal weight: 0.9980 chunk 762 optimal weight: 4.9990 chunk 319 optimal weight: 0.6980 chunk 783 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 140 optimal weight: 9.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 93 ASN C 116 ASN ** C 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 220 HIS ** F 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 36 ASN ** G 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 230 GLN ** G 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 230 GLN ** I 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 116 ASN ** K 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 93 ASN ** M 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 230 GLN ** M 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 230 GLN ** O 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.198686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.155489 restraints weight = 82501.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.156653 restraints weight = 69871.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.158242 restraints weight = 53326.997| |-----------------------------------------------------------------------------| r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3744 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3744 r_free = 0.3744 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3743 r_free = 0.3743 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3743 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.4607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 77344 Z= 0.269 Angle : 0.622 12.214 105104 Z= 0.314 Chirality : 0.045 0.315 12160 Planarity : 0.005 0.069 13488 Dihedral : 4.752 22.369 10928 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 18.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 0.75 % Allowed : 24.86 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.08), residues: 9600 helix: -0.02 (0.10), residues: 2336 sheet: -1.72 (0.12), residues: 1568 loop : -1.41 (0.08), residues: 5696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP L 627 HIS 0.008 0.001 HIS I 311 PHE 0.026 0.002 PHE H 376 TYR 0.026 0.002 TYR E 573 ARG 0.010 0.001 ARG G 339 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22236.99 seconds wall clock time: 392 minutes 48.47 seconds (23568.47 seconds total)