Starting phenix.real_space_refine on Sat Mar 16 22:37:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sb3_10134/03_2024/6sb3_10134.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sb3_10134/03_2024/6sb3_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_10134/03_2024/6sb3_10134.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sb3_10134/03_2024/6sb3_10134.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sb3_10134/03_2024/6sb3_10134.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sb3_10134/03_2024/6sb3_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-dev-5265/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: 29.00, per 1000 atoms: 0.38 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: 23.65 Conformation dependent library (CDL) restraints added in 10.5 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: 4.04 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: 16.04 Time building geometry restraints manager: 26.13 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: 2.850 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: 0.080 Extract box with map and model: 11.950 Check model and map are aligned: 0.820 Set scattering table: 0.520 Process input model: 140.020 Find NCS groups from input model: 4.260 Set up NCS constraints: 0.690 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:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 163.770 ------------------------------------------------------------------------------- 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 : 6.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 LEU cc_start: 0.8065 (tp) cc_final: 0.7666 (tp) REVERT: A 492 GLN cc_start: 0.6073 (tt0) cc_final: 0.5748 (mm-40) REVERT: A 516 GLU cc_start: 0.6150 (tp30) cc_final: 0.5893 (tp30) REVERT: A 639 MET cc_start: 0.5102 (ttm) cc_final: 0.4777 (tpp) REVERT: B 43 LEU cc_start: 0.8152 (tp) cc_final: 0.7821 (tp) REVERT: B 154 ASN cc_start: 0.8668 (p0) cc_final: 0.8431 (p0) REVERT: B 303 ILE cc_start: 0.6868 (mm) cc_final: 0.6634 (mm) REVERT: B 335 GLU cc_start: 0.6752 (tp30) cc_final: 0.6546 (tp30) REVERT: B 516 GLU cc_start: 0.6417 (tp30) cc_final: 0.6164 (tp30) REVERT: B 586 LEU cc_start: 0.6999 (mt) cc_final: 0.6777 (mt) REVERT: C 151 GLN cc_start: 0.7207 (pt0) cc_final: 0.6864 (pt0) REVERT: C 154 ASN cc_start: 0.8549 (p0) cc_final: 0.8315 (p0) REVERT: C 492 GLN cc_start: 0.6387 (tt0) cc_final: 0.5715 (mm-40) REVERT: D 151 GLN cc_start: 0.7282 (pt0) cc_final: 0.7033 (pt0) REVERT: D 492 GLN cc_start: 0.6066 (tt0) cc_final: 0.5591 (mm-40) REVERT: E 492 GLN cc_start: 0.6012 (tt0) cc_final: 0.5643 (mm-40) REVERT: E 516 GLU cc_start: 0.5925 (tp30) cc_final: 0.5526 (tp30) REVERT: F 113 LEU cc_start: 0.7116 (tp) cc_final: 0.6458 (mp) REVERT: F 151 GLN cc_start: 0.7086 (pt0) cc_final: 0.6847 (pt0) REVERT: F 236 VAL cc_start: 0.7830 (t) cc_final: 0.7339 (t) REVERT: F 492 GLN cc_start: 0.6610 (tt0) cc_final: 0.5866 (mm-40) REVERT: F 586 LEU cc_start: 0.7150 (mt) cc_final: 0.6724 (mt) REVERT: G 151 GLN cc_start: 0.7170 (pt0) cc_final: 0.6666 (pt0) REVERT: G 154 ASN cc_start: 0.8592 (p0) cc_final: 0.8305 (p0) REVERT: G 236 VAL cc_start: 0.7616 (t) cc_final: 0.7058 (t) REVERT: G 322 LEU cc_start: 0.6987 (mp) cc_final: 0.6760 (mp) REVERT: G 492 GLN cc_start: 0.6460 (tt0) cc_final: 0.5942 (mm-40) REVERT: H 43 LEU cc_start: 0.8305 (tp) cc_final: 0.8104 (tp) REVERT: H 151 GLN cc_start: 0.7265 (pt0) cc_final: 0.6814 (pt0) REVERT: H 154 ASN cc_start: 0.8795 (p0) cc_final: 0.8358 (p0) REVERT: H 236 VAL cc_start: 0.7770 (t) cc_final: 0.7173 (t) REVERT: H 322 LEU cc_start: 0.7205 (mp) cc_final: 0.6912 (mp) REVERT: H 492 GLN cc_start: 0.6342 (tt0) cc_final: 0.5551 (mm-40) REVERT: I 154 ASN cc_start: 0.8689 (p0) cc_final: 0.8407 (p0) REVERT: I 492 GLN cc_start: 0.6677 (tt0) cc_final: 0.5937 (mm-40) REVERT: J 113 LEU cc_start: 0.6998 (tp) cc_final: 0.6367 (mp) REVERT: J 151 GLN cc_start: 0.7027 (pt0) cc_final: 0.6735 (pt0) REVERT: J 154 ASN cc_start: 0.8794 (p0) cc_final: 0.8454 (p0) REVERT: J 236 VAL cc_start: 0.7700 (t) cc_final: 0.7169 (t) REVERT: J 492 GLN cc_start: 0.6087 (tt0) cc_final: 0.5529 (mm-40) REVERT: K 151 GLN cc_start: 0.7159 (pt0) cc_final: 0.6685 (pt0) REVERT: K 154 ASN cc_start: 0.8578 (p0) cc_final: 0.8310 (p0) REVERT: K 492 GLN cc_start: 0.6406 (tt0) cc_final: 0.5733 (mm-40) REVERT: L 151 GLN cc_start: 0.7192 (pt0) cc_final: 0.6803 (pt0) REVERT: L 322 LEU cc_start: 0.7178 (mp) cc_final: 0.6880 (mp) REVERT: L 492 GLN cc_start: 0.6251 (tt0) cc_final: 0.5541 (mm-40) REVERT: M 151 GLN cc_start: 0.6967 (pt0) cc_final: 0.6719 (pt0) REVERT: M 322 LEU cc_start: 0.7410 (mp) cc_final: 0.7082 (mp) REVERT: M 492 GLN cc_start: 0.6489 (tt0) cc_final: 0.5849 (mm-40) REVERT: N 113 LEU cc_start: 0.7068 (tp) cc_final: 0.6436 (mp) REVERT: N 151 GLN cc_start: 0.7040 (pt0) cc_final: 0.6736 (pt0) REVERT: N 236 VAL cc_start: 0.7777 (t) cc_final: 0.7278 (t) REVERT: N 492 GLN cc_start: 0.6391 (tt0) cc_final: 0.5901 (mm-40) REVERT: N 586 LEU cc_start: 0.7221 (mt) cc_final: 0.6852 (mt) REVERT: O 151 GLN cc_start: 0.7163 (pt0) cc_final: 0.6739 (pt0) REVERT: O 154 ASN cc_start: 0.8659 (p0) cc_final: 0.8457 (p0) REVERT: O 236 VAL cc_start: 0.7709 (t) cc_final: 0.7262 (t) REVERT: O 492 GLN cc_start: 0.6289 (tt0) cc_final: 0.5811 (mm-40) REVERT: P 56 ASN cc_start: 0.4679 (t0) cc_final: 0.3691 (t0) REVERT: P 151 GLN cc_start: 0.7153 (pt0) cc_final: 0.6759 (pt0) REVERT: P 154 ASN cc_start: 0.8739 (p0) cc_final: 0.8334 (p0) REVERT: P 236 VAL cc_start: 0.7660 (t) cc_final: 0.7073 (t) REVERT: P 322 LEU cc_start: 0.7165 (mp) cc_final: 0.6851 (mp) REVERT: P 492 GLN cc_start: 0.6451 (tt0) cc_final: 0.5588 (mm-40) outliers start: 0 outliers final: 0 residues processed: 1985 average time/residue: 0.6955 time to fit residues: 2356.3931 Evaluate side-chains 1182 residues out of total 8544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1182 time to evaluate : 6.150 ------------------------------------------------------------------------------- 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: 0.8980 chunk 403 optimal weight: 9.9990 chunk 248 optimal weight: 2.9990 chunk 490 optimal weight: 2.9990 chunk 388 optimal weight: 0.5980 chunk 752 optimal weight: 4.9990 chunk 291 optimal weight: 2.9990 chunk 457 optimal weight: 0.0870 chunk 560 optimal weight: 0.9980 chunk 871 optimal weight: 2.9990 overall best weight: 1.1160 ------------------------------------------------------------------------------- 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 345 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 561 HIS B 32 GLN ** B 53 ASN ** 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 53 ASN ** 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 561 HIS ** D 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 GLN ** E 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 GLN ** E 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 233 GLN E 234 ASN E 345 ASN ** E 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 421 GLN E 561 HIS E 625 ASN F 32 GLN ** F 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 220 HIS ** 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 53 ASN ** 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 53 ASN ** 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 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 625 ASN J 32 GLN ** J 53 ASN ** 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 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 220 HIS 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 53 ASN ** 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 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 186 GLN 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 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 234 ASN ** 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 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: 79 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 77344 Z= 0.245 Angle : 0.590 8.737 105104 Z= 0.295 Chirality : 0.044 0.231 12160 Planarity : 0.005 0.052 13488 Dihedral : 4.747 43.223 10928 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 3.02 % Allowed : 14.58 % Favored : 82.40 % 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: -1.97 (0.08), residues: 9600 helix: -0.27 (0.10), residues: 2288 sheet: -1.21 (0.12), residues: 1808 loop : -1.84 (0.08), residues: 5504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 461 HIS 0.009 0.001 HIS A 204 PHE 0.035 0.002 PHE G 225 TYR 0.023 0.002 TYR B 341 ARG 0.004 0.001 ARG D 589 *********************** 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 1561 residues out of total 8544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 258 poor density : 1303 time to evaluate : 6.187 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: A 169 LEU cc_start: 0.7187 (mt) cc_final: 0.6542 (mt) REVERT: A 335 GLU cc_start: 0.6998 (tp30) cc_final: 0.6714 (tp30) REVERT: A 492 GLN cc_start: 0.6188 (tt0) cc_final: 0.5697 (mm-40) REVERT: B 154 ASN cc_start: 0.8762 (p0) cc_final: 0.8461 (p0) REVERT: B 516 GLU cc_start: 0.6451 (tp30) cc_final: 0.6163 (tp30) REVERT: C 176 MET cc_start: 0.7498 (OUTLIER) cc_final: 0.7029 (mmp) REVERT: C 492 GLN cc_start: 0.6241 (tt0) cc_final: 0.5724 (mm-40) REVERT: D 154 ASN cc_start: 0.8485 (p0) cc_final: 0.8249 (p0) REVERT: D 169 LEU cc_start: 0.7192 (mt) cc_final: 0.6595 (mt) REVERT: D 308 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8711 (pp) REVERT: D 492 GLN cc_start: 0.6291 (tt0) cc_final: 0.5634 (mm-40) REVERT: E 96 MET cc_start: 0.8029 (mpp) cc_final: 0.7644 (mmt) REVERT: E 169 LEU cc_start: 0.7115 (mt) cc_final: 0.6527 (mt) REVERT: E 264 LYS cc_start: 0.7005 (mmtm) cc_final: 0.6714 (mmtt) REVERT: E 335 GLU cc_start: 0.7231 (tp30) cc_final: 0.7028 (tp30) REVERT: E 492 GLN cc_start: 0.6211 (tt0) cc_final: 0.5618 (mm-40) REVERT: F 364 MET cc_start: 0.7522 (mtp) cc_final: 0.7296 (mtp) REVERT: F 492 GLN cc_start: 0.6539 (tt0) cc_final: 0.6044 (mm-40) REVERT: G 169 LEU cc_start: 0.7254 (mt) cc_final: 0.6780 (mt) REVERT: G 458 ARG cc_start: 0.7089 (mtt90) cc_final: 0.6877 (ptp90) REVERT: G 492 GLN cc_start: 0.6353 (tt0) cc_final: 0.5805 (mm-40) REVERT: H 105 MET cc_start: 0.8001 (mmm) cc_final: 0.7801 (mmm) REVERT: H 169 LEU cc_start: 0.7197 (mt) cc_final: 0.6654 (mt) REVERT: H 366 ASP cc_start: 0.7846 (OUTLIER) cc_final: 0.7580 (p0) REVERT: H 492 GLN cc_start: 0.6461 (tt0) cc_final: 0.5832 (mm-40) REVERT: I 44 GLU cc_start: 0.8299 (tt0) cc_final: 0.7985 (tt0) REVERT: I 57 VAL cc_start: 0.8512 (m) cc_final: 0.8287 (m) REVERT: I 59 MET cc_start: 0.6921 (mmm) cc_final: 0.6432 (mmt) REVERT: I 96 MET cc_start: 0.8097 (mpp) cc_final: 0.7708 (mmt) REVERT: I 169 LEU cc_start: 0.7254 (mt) cc_final: 0.6649 (mt) REVERT: I 492 GLN cc_start: 0.6630 (tt0) cc_final: 0.5766 (mm-40) REVERT: J 248 VAL cc_start: 0.7649 (t) cc_final: 0.6495 (m) REVERT: J 492 GLN cc_start: 0.6414 (tt0) cc_final: 0.5974 (mm-40) REVERT: K 169 LEU cc_start: 0.7283 (mt) cc_final: 0.6621 (mt) REVERT: K 492 GLN cc_start: 0.6142 (tt0) cc_final: 0.5665 (mm-40) REVERT: L 169 LEU cc_start: 0.7154 (mt) cc_final: 0.6594 (mt) REVERT: L 492 GLN cc_start: 0.6453 (tt0) cc_final: 0.5812 (mm-40) REVERT: M 44 GLU cc_start: 0.8201 (tt0) cc_final: 0.7898 (tt0) REVERT: M 57 VAL cc_start: 0.8512 (m) cc_final: 0.8226 (m) REVERT: M 59 MET cc_start: 0.6900 (mmm) cc_final: 0.6364 (mmt) REVERT: M 96 MET cc_start: 0.8116 (mpp) cc_final: 0.7731 (mmt) REVERT: M 169 LEU cc_start: 0.7207 (mt) cc_final: 0.6617 (mt) REVERT: M 492 GLN cc_start: 0.6498 (tt0) cc_final: 0.5643 (mm-40) REVERT: N 364 MET cc_start: 0.7527 (mtp) cc_final: 0.7311 (mtp) REVERT: N 492 GLN cc_start: 0.6444 (tt0) cc_final: 0.6044 (mm-40) REVERT: O 169 LEU cc_start: 0.7279 (mt) cc_final: 0.6771 (mt) REVERT: O 492 GLN cc_start: 0.6339 (tt0) cc_final: 0.5801 (mm-40) REVERT: P 56 ASN cc_start: 0.5821 (t0) cc_final: 0.5151 (t0) REVERT: P 154 ASN cc_start: 0.8759 (p0) cc_final: 0.8506 (p0) REVERT: P 322 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7906 (tp) REVERT: P 492 GLN cc_start: 0.6536 (tt0) cc_final: 0.5833 (mm-40) outliers start: 258 outliers final: 158 residues processed: 1468 average time/residue: 0.6934 time to fit residues: 1790.6249 Evaluate side-chains 1249 residues out of total 8544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 1087 time to evaluate : 6.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 366 ASP Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain C residue 594 THR Chi-restraints excluded: chain C residue 610 THR Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 195 GLU Chi-restraints excluded: chain D residue 234 ASN Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 366 ASP Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 610 THR Chi-restraints excluded: chain D residue 628 LYS Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 327 VAL Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 538 VAL Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 234 ASN Chi-restraints excluded: chain F residue 277 SER Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 322 LEU Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 366 ASP Chi-restraints excluded: chain F residue 499 ILE Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain F residue 594 THR Chi-restraints excluded: chain F residue 610 THR Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain G residue 176 MET Chi-restraints excluded: chain G residue 234 ASN Chi-restraints excluded: chain G residue 277 SER Chi-restraints excluded: chain G residue 308 LEU Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 366 ASP Chi-restraints excluded: chain G residue 503 LEU Chi-restraints excluded: chain G residue 538 VAL Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 113 LEU Chi-restraints excluded: chain H residue 234 ASN Chi-restraints excluded: chain H residue 277 SER Chi-restraints excluded: chain H residue 327 VAL Chi-restraints excluded: chain H residue 333 THR Chi-restraints excluded: chain H residue 366 ASP Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain H residue 610 THR Chi-restraints excluded: chain H residue 628 LYS Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 277 SER Chi-restraints excluded: chain I residue 308 LEU Chi-restraints excluded: chain I residue 327 VAL Chi-restraints excluded: chain I residue 333 THR Chi-restraints excluded: chain I residue 366 ASP Chi-restraints excluded: chain I residue 538 VAL Chi-restraints excluded: chain J residue 234 ASN Chi-restraints excluded: chain J residue 267 LEU Chi-restraints excluded: chain J residue 277 SER Chi-restraints excluded: chain J residue 308 LEU Chi-restraints excluded: chain J residue 322 LEU Chi-restraints excluded: chain J residue 333 THR Chi-restraints excluded: chain J residue 366 ASP Chi-restraints excluded: chain J residue 499 ILE Chi-restraints excluded: chain J residue 538 VAL Chi-restraints excluded: chain J residue 594 THR Chi-restraints excluded: chain J residue 610 THR Chi-restraints excluded: chain K residue 38 LEU Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain K residue 113 LEU Chi-restraints excluded: chain K residue 234 ASN Chi-restraints excluded: chain K residue 277 SER Chi-restraints excluded: chain K residue 308 LEU Chi-restraints excluded: chain K residue 333 THR Chi-restraints excluded: chain K residue 366 ASP Chi-restraints excluded: chain K residue 499 ILE Chi-restraints excluded: chain K residue 503 LEU Chi-restraints excluded: chain K residue 538 VAL Chi-restraints excluded: chain K residue 610 THR Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain L residue 113 LEU Chi-restraints excluded: chain L residue 277 SER Chi-restraints excluded: chain L residue 327 VAL Chi-restraints excluded: chain L residue 333 THR Chi-restraints excluded: chain L residue 366 ASP Chi-restraints excluded: chain L residue 538 VAL Chi-restraints excluded: chain L residue 610 THR Chi-restraints excluded: chain L residue 628 LYS Chi-restraints excluded: chain M residue 277 SER Chi-restraints excluded: chain M residue 308 LEU Chi-restraints excluded: chain M residue 327 VAL Chi-restraints excluded: chain M residue 333 THR Chi-restraints excluded: chain M residue 366 ASP Chi-restraints excluded: chain M residue 538 VAL Chi-restraints excluded: chain N residue 38 LEU Chi-restraints excluded: chain N residue 131 THR Chi-restraints excluded: chain N residue 234 ASN Chi-restraints excluded: chain N residue 277 SER Chi-restraints excluded: chain N residue 308 LEU Chi-restraints excluded: chain N residue 333 THR Chi-restraints excluded: chain N residue 538 VAL Chi-restraints excluded: chain N residue 594 THR Chi-restraints excluded: chain N residue 610 THR Chi-restraints excluded: chain O residue 84 VAL Chi-restraints excluded: chain O residue 113 LEU Chi-restraints excluded: chain O residue 234 ASN Chi-restraints excluded: chain O residue 277 SER Chi-restraints excluded: chain O residue 308 LEU Chi-restraints excluded: chain O residue 333 THR Chi-restraints excluded: chain O residue 366 ASP Chi-restraints excluded: chain O residue 538 VAL Chi-restraints excluded: chain O residue 594 THR Chi-restraints excluded: chain O residue 610 THR Chi-restraints excluded: chain P residue 84 VAL Chi-restraints excluded: chain P residue 195 GLU Chi-restraints excluded: chain P residue 234 ASN Chi-restraints excluded: chain P residue 277 SER Chi-restraints excluded: chain P residue 322 LEU Chi-restraints excluded: chain P residue 327 VAL Chi-restraints excluded: chain P residue 333 THR Chi-restraints excluded: chain P residue 366 ASP Chi-restraints excluded: chain P residue 538 VAL Chi-restraints excluded: chain P residue 610 THR Chi-restraints excluded: chain P residue 628 LYS 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: 5.9990 chunk 725 optimal weight: 4.9990 chunk 593 optimal weight: 9.9990 chunk 240 optimal weight: 1.9990 chunk 873 optimal weight: 9.9990 chunk 943 optimal weight: 9.9990 chunk 777 optimal weight: 0.0070 chunk 866 optimal weight: 2.9990 chunk 297 optimal weight: 8.9990 chunk 700 optimal weight: 0.5980 overall best weight: 1.5204 ------------------------------------------------------------------------------- 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 561 HIS ** B 200 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 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 361 GLN ** C 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 561 HIS ** E 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 GLN ** E 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 234 ASN ** E 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 561 HIS E 625 ASN ** F 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 357 ASN ** 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 625 ASN ** G 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 234 ASN G 361 GLN ** G 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 625 ASN ** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 234 ASN I 361 GLN ** I 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 625 ASN ** J 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 234 ASN ** J 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 625 ASN ** 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 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 234 ASN M 361 GLN ** M 395 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 234 ASN ** N 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 220 HIS O 234 ASN O 361 GLN ** O 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 77344 Z= 0.281 Angle : 0.577 9.119 105104 Z= 0.288 Chirality : 0.043 0.220 12160 Planarity : 0.005 0.049 13488 Dihedral : 4.571 32.113 10928 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 16.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 3.68 % Allowed : 17.51 % Favored : 78.82 % 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: -1.76 (0.08), residues: 9600 helix: 0.05 (0.10), residues: 2288 sheet: -1.38 (0.12), residues: 1824 loop : -1.66 (0.08), residues: 5488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 51 HIS 0.008 0.001 HIS A 204 PHE 0.029 0.002 PHE P 225 TYR 0.020 0.002 TYR N 341 ARG 0.007 0.001 ARG C 222 *********************** 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 1499 residues out of total 8544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 314 poor density : 1185 time to evaluate : 6.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 LEU cc_start: 0.7238 (mt) cc_final: 0.6672 (mt) REVERT: A 492 GLN cc_start: 0.6473 (tt0) cc_final: 0.5986 (mm-40) REVERT: A 516 GLU cc_start: 0.6562 (tp30) cc_final: 0.6163 (tp30) REVERT: B 135 ARG cc_start: 0.8007 (ttp-110) cc_final: 0.7652 (mtm110) REVERT: B 169 LEU cc_start: 0.7509 (mt) cc_final: 0.6890 (mt) REVERT: B 189 MET cc_start: 0.8575 (tpt) cc_final: 0.8334 (tpp) REVERT: B 314 ILE cc_start: 0.8419 (OUTLIER) cc_final: 0.7830 (mt) REVERT: C 314 ILE cc_start: 0.8496 (OUTLIER) cc_final: 0.8016 (mt) REVERT: C 492 GLN cc_start: 0.6281 (tt0) cc_final: 0.5805 (mm-40) REVERT: D 169 LEU cc_start: 0.7275 (mt) cc_final: 0.6763 (mt) REVERT: D 308 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8846 (pp) REVERT: D 335 GLU cc_start: 0.7566 (tp30) cc_final: 0.7299 (tp30) REVERT: D 399 GLN cc_start: 0.6741 (pp30) cc_final: 0.5576 (pp30) REVERT: D 492 GLN cc_start: 0.6615 (tt0) cc_final: 0.5918 (mm-40) REVERT: E 169 LEU cc_start: 0.7291 (mt) cc_final: 0.6694 (mt) REVERT: E 218 GLU cc_start: 0.7471 (mt-10) cc_final: 0.7166 (mt-10) REVERT: E 492 GLN cc_start: 0.6378 (tt0) cc_final: 0.5695 (mm-40) REVERT: F 59 MET cc_start: 0.6592 (mmm) cc_final: 0.6316 (mmt) REVERT: F 154 ASN cc_start: 0.8472 (p0) cc_final: 0.8249 (p0) REVERT: F 364 MET cc_start: 0.7629 (mtp) cc_final: 0.7411 (mtp) REVERT: F 492 GLN cc_start: 0.6577 (tt0) cc_final: 0.6133 (mm-40) REVERT: F 510 CYS cc_start: 0.6220 (m) cc_final: 0.5774 (m) REVERT: G 105 MET cc_start: 0.7760 (mmm) cc_final: 0.7498 (mmm) REVERT: G 169 LEU cc_start: 0.7245 (mt) cc_final: 0.6646 (mt) REVERT: G 492 GLN cc_start: 0.6431 (tt0) cc_final: 0.5926 (mm-40) REVERT: H 169 LEU cc_start: 0.7313 (mt) cc_final: 0.6764 (mt) REVERT: H 335 GLU cc_start: 0.7304 (tp30) cc_final: 0.6992 (tp30) REVERT: H 492 GLN cc_start: 0.6736 (tt0) cc_final: 0.6058 (mm-40) REVERT: I 44 GLU cc_start: 0.8484 (tt0) cc_final: 0.8232 (tt0) REVERT: I 57 VAL cc_start: 0.8658 (m) cc_final: 0.8440 (m) REVERT: I 59 MET cc_start: 0.6872 (mmm) cc_final: 0.6312 (mmt) REVERT: I 96 MET cc_start: 0.8157 (mpp) cc_final: 0.7621 (mmt) REVERT: I 169 LEU cc_start: 0.7448 (mt) cc_final: 0.6789 (mt) REVERT: I 335 GLU cc_start: 0.7118 (tp30) cc_final: 0.6748 (tp30) REVERT: I 492 GLN cc_start: 0.6716 (tt0) cc_final: 0.5960 (mm-40) REVERT: J 154 ASN cc_start: 0.8574 (p0) cc_final: 0.8247 (p0) REVERT: J 492 GLN cc_start: 0.6550 (tt0) cc_final: 0.6124 (mm-40) REVERT: J 510 CYS cc_start: 0.6101 (m) cc_final: 0.5716 (m) REVERT: K 169 LEU cc_start: 0.7485 (mt) cc_final: 0.6899 (mt) REVERT: K 322 LEU cc_start: 0.8263 (tp) cc_final: 0.8039 (tp) REVERT: K 460 TYR cc_start: 0.7061 (m-80) cc_final: 0.6796 (m-80) REVERT: K 492 GLN cc_start: 0.6300 (tt0) cc_final: 0.5798 (mm-40) REVERT: L 59 MET cc_start: 0.6673 (mmm) cc_final: 0.6087 (mmt) REVERT: L 154 ASN cc_start: 0.8763 (p0) cc_final: 0.8552 (p0) REVERT: L 169 LEU cc_start: 0.7324 (mt) cc_final: 0.6797 (mt) REVERT: L 335 GLU cc_start: 0.7274 (tp30) cc_final: 0.6979 (tp30) REVERT: L 492 GLN cc_start: 0.6728 (tt0) cc_final: 0.5999 (mm-40) REVERT: M 44 GLU cc_start: 0.8421 (tt0) cc_final: 0.8181 (tt0) REVERT: M 57 VAL cc_start: 0.8555 (m) cc_final: 0.8325 (m) REVERT: M 59 MET cc_start: 0.6820 (mmm) cc_final: 0.6234 (mmt) REVERT: M 169 LEU cc_start: 0.7330 (mt) cc_final: 0.6741 (mt) REVERT: M 492 GLN cc_start: 0.6551 (tt0) cc_final: 0.5690 (mm-40) REVERT: N 59 MET cc_start: 0.6782 (mmm) cc_final: 0.6337 (mmt) REVERT: N 154 ASN cc_start: 0.8492 (p0) cc_final: 0.8242 (p0) REVERT: N 364 MET cc_start: 0.7541 (mtp) cc_final: 0.7320 (mtp) REVERT: N 399 GLN cc_start: 0.7090 (pp30) cc_final: 0.5971 (pp30) REVERT: N 492 GLN cc_start: 0.6566 (tt0) cc_final: 0.6089 (mm-40) REVERT: O 189 MET cc_start: 0.8607 (tpp) cc_final: 0.8211 (tpp) REVERT: O 458 ARG cc_start: 0.7337 (ptp90) cc_final: 0.7031 (mtt90) REVERT: O 492 GLN cc_start: 0.6299 (tt0) cc_final: 0.5801 (mm-40) REVERT: P 169 LEU cc_start: 0.7332 (mt) cc_final: 0.6771 (mt) REVERT: P 335 GLU cc_start: 0.7224 (tp30) cc_final: 0.6951 (tp30) REVERT: P 492 GLN cc_start: 0.6730 (tt0) cc_final: 0.5990 (mm-40) outliers start: 314 outliers final: 194 residues processed: 1416 average time/residue: 0.6561 time to fit residues: 1644.2733 Evaluate side-chains 1267 residues out of total 8544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 1070 time to evaluate : 6.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 499 ILE Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 594 THR Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 366 ASP Chi-restraints excluded: chain C residue 422 THR Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain C residue 610 THR Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 195 GLU Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 366 ASP Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 628 LYS Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 327 VAL Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 499 ILE Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 277 SER Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 366 ASP Chi-restraints excluded: chain F residue 499 ILE Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain G residue 147 THR Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 236 VAL Chi-restraints excluded: chain G residue 277 SER Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 366 ASP Chi-restraints excluded: chain G residue 416 VAL Chi-restraints excluded: chain G residue 503 LEU Chi-restraints excluded: chain G residue 538 VAL Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 113 LEU Chi-restraints excluded: chain H residue 147 THR Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 195 GLU Chi-restraints excluded: chain H residue 239 SER Chi-restraints excluded: chain H residue 277 SER Chi-restraints excluded: chain H residue 333 THR Chi-restraints excluded: chain H residue 366 ASP Chi-restraints excluded: chain H residue 416 VAL Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain H residue 628 LYS Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 147 THR Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 277 SER Chi-restraints excluded: chain I residue 308 LEU Chi-restraints excluded: chain I residue 322 LEU Chi-restraints excluded: chain I residue 327 VAL Chi-restraints excluded: chain I residue 333 THR Chi-restraints excluded: chain I residue 366 ASP Chi-restraints excluded: chain I residue 416 VAL Chi-restraints excluded: chain I residue 538 VAL Chi-restraints excluded: chain J residue 45 VAL Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 277 SER Chi-restraints excluded: chain J residue 333 THR Chi-restraints excluded: chain J residue 366 ASP Chi-restraints excluded: chain J residue 499 ILE Chi-restraints excluded: chain K residue 38 LEU Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain K residue 93 ASN Chi-restraints excluded: chain K residue 113 LEU Chi-restraints excluded: chain K residue 147 THR Chi-restraints excluded: chain K residue 159 VAL Chi-restraints excluded: chain K residue 277 SER Chi-restraints excluded: chain K residue 333 THR Chi-restraints excluded: chain K residue 366 ASP Chi-restraints excluded: chain K residue 416 VAL Chi-restraints excluded: chain K residue 499 ILE Chi-restraints excluded: chain K residue 503 LEU Chi-restraints excluded: chain K residue 538 VAL Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 113 LEU Chi-restraints excluded: chain L residue 147 THR Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 195 GLU Chi-restraints excluded: chain L residue 277 SER Chi-restraints excluded: chain L residue 333 THR Chi-restraints excluded: chain L residue 366 ASP Chi-restraints excluded: chain L residue 416 VAL Chi-restraints excluded: chain L residue 538 VAL Chi-restraints excluded: chain L residue 628 LYS Chi-restraints excluded: chain M residue 86 THR Chi-restraints excluded: chain M residue 147 THR Chi-restraints excluded: chain M residue 159 VAL Chi-restraints excluded: chain M residue 277 SER Chi-restraints excluded: chain M residue 308 LEU Chi-restraints excluded: chain M residue 322 LEU Chi-restraints excluded: chain M residue 333 THR Chi-restraints excluded: chain M residue 366 ASP Chi-restraints excluded: chain M residue 416 VAL Chi-restraints excluded: chain M residue 538 VAL Chi-restraints excluded: chain N residue 38 LEU Chi-restraints excluded: chain N residue 86 THR Chi-restraints excluded: chain N residue 131 THR Chi-restraints excluded: chain N residue 147 THR Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain N residue 277 SER Chi-restraints excluded: chain N residue 322 LEU Chi-restraints excluded: chain N residue 333 THR Chi-restraints excluded: chain N residue 366 ASP Chi-restraints excluded: chain N residue 538 VAL Chi-restraints excluded: chain O residue 84 VAL Chi-restraints excluded: chain O residue 86 THR Chi-restraints excluded: chain O residue 93 ASN Chi-restraints excluded: chain O residue 113 LEU Chi-restraints excluded: chain O residue 119 LEU Chi-restraints excluded: chain O residue 147 THR Chi-restraints excluded: chain O residue 159 VAL Chi-restraints excluded: chain O residue 277 SER Chi-restraints excluded: chain O residue 333 THR Chi-restraints excluded: chain O residue 366 ASP Chi-restraints excluded: chain O residue 416 VAL Chi-restraints excluded: chain O residue 538 VAL Chi-restraints excluded: chain O residue 571 VAL Chi-restraints excluded: chain P residue 84 VAL Chi-restraints excluded: chain P residue 86 THR Chi-restraints excluded: chain P residue 119 LEU Chi-restraints excluded: chain P residue 147 THR Chi-restraints excluded: chain P residue 159 VAL Chi-restraints excluded: chain P residue 195 GLU Chi-restraints excluded: chain P residue 239 SER Chi-restraints excluded: chain P residue 277 SER Chi-restraints excluded: chain P residue 327 VAL Chi-restraints excluded: chain P residue 333 THR Chi-restraints excluded: chain P residue 366 ASP Chi-restraints excluded: chain P residue 416 VAL Chi-restraints excluded: chain P residue 503 LEU Chi-restraints excluded: chain P residue 538 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 960 random chunks: chunk 862 optimal weight: 0.0770 chunk 656 optimal weight: 10.0000 chunk 453 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 416 optimal weight: 1.9990 chunk 586 optimal weight: 0.2980 chunk 876 optimal weight: 5.9990 chunk 927 optimal weight: 4.9990 chunk 457 optimal weight: 9.9990 chunk 830 optimal weight: 7.9990 chunk 250 optimal weight: 0.4980 overall best weight: 1.3742 ------------------------------------------------------------------------------- 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** ** 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 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 ASN ** C 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 93 ASN ** D 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 234 ASN ** D 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 234 ASN ** E 395 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** G 36 ASN ** G 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 234 ASN ** G 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 625 ASN ** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 234 ASN ** 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** ** J 126 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** ** K 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** ** 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 36 ASN ** O 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 234 ASN ** P 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.100 77344 Z= 0.265 Angle : 0.586 15.462 105104 Z= 0.295 Chirality : 0.044 0.246 12160 Planarity : 0.005 0.069 13488 Dihedral : 4.510 22.737 10928 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 16.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 4.11 % Allowed : 18.86 % Favored : 77.04 % 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: -1.70 (0.08), residues: 9600 helix: 0.11 (0.10), residues: 2320 sheet: -1.47 (0.12), residues: 1824 loop : -1.58 (0.08), residues: 5456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 51 HIS 0.008 0.001 HIS A 204 PHE 0.026 0.002 PHE P 313 TYR 0.020 0.002 TYR B 593 ARG 0.013 0.001 ARG C 458 *********************** 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 1523 residues out of total 8544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 351 poor density : 1172 time to evaluate : 6.260 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: A 59 MET cc_start: 0.6775 (mmm) cc_final: 0.5890 (mmt) REVERT: A 169 LEU cc_start: 0.7313 (mt) cc_final: 0.6707 (mt) REVERT: A 400 LYS cc_start: 0.4955 (mmtp) cc_final: 0.4633 (mmtt) REVERT: A 492 GLN cc_start: 0.6426 (tt0) cc_final: 0.6000 (mm-40) REVERT: A 510 CYS cc_start: 0.6698 (m) cc_final: 0.6346 (m) REVERT: B 135 ARG cc_start: 0.8133 (ttp-110) cc_final: 0.7803 (mtm110) REVERT: B 154 ASN cc_start: 0.8545 (p0) cc_final: 0.8265 (p0) REVERT: B 314 ILE cc_start: 0.8450 (OUTLIER) cc_final: 0.7824 (mt) REVERT: B 335 GLU cc_start: 0.7396 (tp30) cc_final: 0.7083 (tp30) REVERT: B 510 CYS cc_start: 0.6215 (m) cc_final: 0.5703 (m) REVERT: C 189 MET cc_start: 0.8451 (tpp) cc_final: 0.8017 (tpp) REVERT: C 314 ILE cc_start: 0.8631 (OUTLIER) cc_final: 0.8070 (mt) REVERT: C 492 GLN cc_start: 0.6239 (tt0) cc_final: 0.5837 (mm-40) REVERT: D 169 LEU cc_start: 0.7290 (mt) cc_final: 0.6816 (mt) REVERT: D 335 GLU cc_start: 0.7656 (tp30) cc_final: 0.7215 (tp30) REVERT: D 399 GLN cc_start: 0.7001 (pp30) cc_final: 0.5901 (pp30) REVERT: D 492 GLN cc_start: 0.6702 (tt0) cc_final: 0.6038 (mm-40) REVERT: E 59 MET cc_start: 0.6551 (mmm) cc_final: 0.6039 (mmt) REVERT: E 140 GLN cc_start: 0.7015 (tt0) cc_final: 0.6749 (mt0) REVERT: E 169 LEU cc_start: 0.7348 (mt) cc_final: 0.6717 (mt) REVERT: E 218 GLU cc_start: 0.7388 (mt-10) cc_final: 0.7161 (mt-10) REVERT: E 492 GLN cc_start: 0.6498 (tt0) cc_final: 0.5810 (mm-40) REVERT: E 510 CYS cc_start: 0.6806 (m) cc_final: 0.6210 (m) REVERT: F 59 MET cc_start: 0.6500 (mmm) cc_final: 0.6253 (mmt) REVERT: F 135 ARG cc_start: 0.8204 (ttp-110) cc_final: 0.7813 (mtm110) REVERT: F 189 MET cc_start: 0.8763 (tpp) cc_final: 0.8399 (tpp) REVERT: F 364 MET cc_start: 0.7702 (mtp) cc_final: 0.7485 (mtp) REVERT: F 492 GLN cc_start: 0.6601 (tt0) cc_final: 0.6054 (mm-40) REVERT: F 510 CYS cc_start: 0.6911 (m) cc_final: 0.6661 (m) REVERT: G 105 MET cc_start: 0.7832 (mmm) cc_final: 0.7625 (mmm) REVERT: G 169 LEU cc_start: 0.7493 (mt) cc_final: 0.6932 (mt) REVERT: G 314 ILE cc_start: 0.8730 (OUTLIER) cc_final: 0.8190 (mt) REVERT: G 492 GLN cc_start: 0.6389 (tt0) cc_final: 0.5917 (mm-40) REVERT: H 78 TYR cc_start: 0.8309 (m-80) cc_final: 0.7977 (m-80) REVERT: H 139 LEU cc_start: 0.8340 (mt) cc_final: 0.8090 (mt) REVERT: H 169 LEU cc_start: 0.7389 (mt) cc_final: 0.6828 (mt) REVERT: H 335 GLU cc_start: 0.7245 (tp30) cc_final: 0.6888 (tp30) REVERT: H 492 GLN cc_start: 0.6842 (tt0) cc_final: 0.6144 (mm-40) REVERT: I 44 GLU cc_start: 0.8512 (tt0) cc_final: 0.8283 (tt0) REVERT: I 57 VAL cc_start: 0.8692 (m) cc_final: 0.8443 (m) REVERT: I 59 MET cc_start: 0.6521 (mmm) cc_final: 0.5864 (mmt) REVERT: I 96 MET cc_start: 0.8272 (mpp) cc_final: 0.7646 (mmt) REVERT: I 169 LEU cc_start: 0.7487 (mt) cc_final: 0.6813 (mt) REVERT: I 335 GLU cc_start: 0.7162 (tp30) cc_final: 0.6953 (tp30) REVERT: I 492 GLN cc_start: 0.6775 (tt0) cc_final: 0.6009 (mm-40) REVERT: J 59 MET cc_start: 0.6686 (mmm) cc_final: 0.6368 (mmt) REVERT: J 135 ARG cc_start: 0.8231 (ttp-110) cc_final: 0.7852 (mtm110) REVERT: J 189 MET cc_start: 0.8641 (tpp) cc_final: 0.8294 (tpp) REVERT: J 492 GLN cc_start: 0.6546 (tt0) cc_final: 0.6139 (mm-40) REVERT: J 510 CYS cc_start: 0.6643 (m) cc_final: 0.6397 (m) REVERT: K 492 GLN cc_start: 0.6420 (tt0) cc_final: 0.5898 (mm-40) REVERT: L 59 MET cc_start: 0.6714 (mmm) cc_final: 0.6404 (mmt) REVERT: L 169 LEU cc_start: 0.7448 (mt) cc_final: 0.6838 (mt) REVERT: L 335 GLU cc_start: 0.7243 (tp30) cc_final: 0.6932 (tp30) REVERT: L 492 GLN cc_start: 0.6807 (tt0) cc_final: 0.6118 (mm-40) REVERT: M 44 GLU cc_start: 0.8462 (tt0) cc_final: 0.8227 (tt0) REVERT: M 57 VAL cc_start: 0.8594 (m) cc_final: 0.8392 (m) REVERT: M 59 MET cc_start: 0.6617 (mmm) cc_final: 0.6021 (mmt) REVERT: M 96 MET cc_start: 0.8236 (mpp) cc_final: 0.7640 (mmt) REVERT: M 169 LEU cc_start: 0.7514 (mt) cc_final: 0.6853 (mt) REVERT: M 335 GLU cc_start: 0.7133 (tp30) cc_final: 0.6801 (tp30) REVERT: M 492 GLN cc_start: 0.6324 (tt0) cc_final: 0.5518 (mm-40) REVERT: M 510 CYS cc_start: 0.6828 (m) cc_final: 0.6264 (m) REVERT: N 59 MET cc_start: 0.6789 (mmm) cc_final: 0.6449 (mmt) REVERT: N 135 ARG cc_start: 0.8155 (ttp-110) cc_final: 0.7776 (mtm110) REVERT: N 399 GLN cc_start: 0.7149 (pp30) cc_final: 0.6073 (pp30) REVERT: N 400 LYS cc_start: 0.5282 (mmtp) cc_final: 0.4374 (mmtp) REVERT: N 492 GLN cc_start: 0.6405 (tt0) cc_final: 0.5994 (mm-40) REVERT: N 510 CYS cc_start: 0.6739 (m) cc_final: 0.6480 (m) REVERT: O 189 MET cc_start: 0.8666 (tpp) cc_final: 0.8229 (tpp) REVERT: O 322 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.8027 (mp) REVERT: O 399 GLN cc_start: 0.6715 (pp30) cc_final: 0.6488 (pp30) REVERT: O 492 GLN cc_start: 0.6351 (tt0) cc_final: 0.5875 (mm-40) REVERT: P 169 LEU cc_start: 0.7490 (mt) cc_final: 0.6897 (mt) REVERT: P 322 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8231 (mp) REVERT: P 335 GLU cc_start: 0.7165 (tp30) cc_final: 0.6897 (tp30) REVERT: P 492 GLN cc_start: 0.6853 (tt0) cc_final: 0.6077 (mm-40) outliers start: 351 outliers final: 230 residues processed: 1422 average time/residue: 0.6421 time to fit residues: 1624.7011 Evaluate side-chains 1322 residues out of total 8544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 235 poor density : 1087 time to evaluate : 6.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 499 ILE Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 594 THR Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 366 ASP Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain C residue 422 THR Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain C residue 610 THR Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 143 ASP Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 195 GLU Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 366 ASP Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 499 ILE Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 610 THR Chi-restraints excluded: chain D residue 617 SER Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 151 GLN Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain E residue 303 ILE Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 366 ASP Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain E residue 503 LEU Chi-restraints excluded: chain E residue 538 VAL Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 277 SER Chi-restraints excluded: chain F residue 290 GLU Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 366 ASP Chi-restraints excluded: chain F residue 499 ILE Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain G residue 147 THR Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 234 ASN Chi-restraints excluded: chain G residue 277 SER Chi-restraints excluded: chain G residue 314 ILE Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 366 ASP Chi-restraints excluded: chain G residue 416 VAL Chi-restraints excluded: chain G residue 538 VAL Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 113 LEU Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain H residue 147 THR Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 195 GLU Chi-restraints excluded: chain H residue 277 SER Chi-restraints excluded: chain H residue 333 THR Chi-restraints excluded: chain H residue 366 ASP Chi-restraints excluded: chain H residue 416 VAL Chi-restraints excluded: chain H residue 499 ILE Chi-restraints excluded: chain H residue 503 LEU Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain H residue 628 LYS Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 147 THR Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 277 SER Chi-restraints excluded: chain I residue 322 LEU Chi-restraints excluded: chain I residue 333 THR Chi-restraints excluded: chain I residue 366 ASP Chi-restraints excluded: chain I residue 416 VAL Chi-restraints excluded: chain I residue 538 VAL Chi-restraints excluded: chain J residue 45 VAL Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 151 GLN Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 277 SER Chi-restraints excluded: chain J residue 290 GLU Chi-restraints excluded: chain J residue 308 LEU Chi-restraints excluded: chain J residue 333 THR Chi-restraints excluded: chain J residue 366 ASP Chi-restraints excluded: chain J residue 416 VAL Chi-restraints excluded: chain J residue 499 ILE Chi-restraints excluded: chain J residue 538 VAL Chi-restraints excluded: chain J residue 594 THR Chi-restraints excluded: chain K residue 38 LEU Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain K residue 93 ASN Chi-restraints excluded: chain K residue 113 LEU Chi-restraints excluded: chain K residue 147 THR Chi-restraints excluded: chain K residue 159 VAL Chi-restraints excluded: chain K residue 234 ASN Chi-restraints excluded: chain K residue 277 SER Chi-restraints excluded: chain K residue 333 THR Chi-restraints excluded: chain K residue 366 ASP Chi-restraints excluded: chain K residue 406 ASP Chi-restraints excluded: chain K residue 416 VAL Chi-restraints excluded: chain K residue 499 ILE Chi-restraints excluded: chain K residue 538 VAL Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 66 THR Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 113 LEU Chi-restraints excluded: chain L residue 147 THR Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 195 GLU Chi-restraints excluded: chain L residue 235 THR Chi-restraints excluded: chain L residue 247 ILE Chi-restraints excluded: chain L residue 277 SER Chi-restraints excluded: chain L residue 333 THR Chi-restraints excluded: chain L residue 366 ASP Chi-restraints excluded: chain L residue 416 VAL Chi-restraints excluded: chain L residue 499 ILE Chi-restraints excluded: chain L residue 503 LEU Chi-restraints excluded: chain L residue 538 VAL Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 86 THR Chi-restraints excluded: chain M residue 119 LEU Chi-restraints excluded: chain M residue 147 THR Chi-restraints excluded: chain M residue 159 VAL Chi-restraints excluded: chain M residue 193 LEU Chi-restraints excluded: chain M residue 277 SER Chi-restraints excluded: chain M residue 303 ILE Chi-restraints excluded: chain M residue 322 LEU Chi-restraints excluded: chain M residue 333 THR Chi-restraints excluded: chain M residue 366 ASP Chi-restraints excluded: chain M residue 416 VAL Chi-restraints excluded: chain M residue 499 ILE Chi-restraints excluded: chain M residue 503 LEU Chi-restraints excluded: chain M residue 538 VAL Chi-restraints excluded: chain N residue 38 LEU Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 86 THR Chi-restraints excluded: chain N residue 131 THR Chi-restraints excluded: chain N residue 147 THR Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain N residue 234 ASN Chi-restraints excluded: chain N residue 277 SER Chi-restraints excluded: chain N residue 308 LEU Chi-restraints excluded: chain N residue 333 THR Chi-restraints excluded: chain N residue 366 ASP Chi-restraints excluded: chain N residue 416 VAL Chi-restraints excluded: chain N residue 538 VAL Chi-restraints excluded: chain N residue 594 THR Chi-restraints excluded: chain O residue 84 VAL Chi-restraints excluded: chain O residue 86 THR Chi-restraints excluded: chain O residue 93 ASN Chi-restraints excluded: chain O residue 113 LEU Chi-restraints excluded: chain O residue 147 THR Chi-restraints excluded: chain O residue 159 VAL Chi-restraints excluded: chain O residue 175 LEU Chi-restraints excluded: chain O residue 234 ASN Chi-restraints excluded: chain O residue 277 SER Chi-restraints excluded: chain O residue 322 LEU Chi-restraints excluded: chain O residue 333 THR Chi-restraints excluded: chain O residue 366 ASP Chi-restraints excluded: chain O residue 406 ASP Chi-restraints excluded: chain O residue 416 VAL Chi-restraints excluded: chain O residue 538 VAL Chi-restraints excluded: chain O residue 571 VAL Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain P residue 84 VAL Chi-restraints excluded: chain P residue 86 THR Chi-restraints excluded: chain P residue 143 ASP Chi-restraints excluded: chain P residue 147 THR Chi-restraints excluded: chain P residue 159 VAL Chi-restraints excluded: chain P residue 195 GLU Chi-restraints excluded: chain P residue 277 SER Chi-restraints excluded: chain P residue 291 THR Chi-restraints excluded: chain P residue 322 LEU Chi-restraints excluded: chain P residue 327 VAL Chi-restraints excluded: chain P residue 333 THR Chi-restraints excluded: chain P residue 343 THR Chi-restraints excluded: chain P residue 366 ASP Chi-restraints excluded: chain P residue 416 VAL Chi-restraints excluded: chain P residue 503 LEU Chi-restraints excluded: chain P residue 538 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 960 random chunks: chunk 772 optimal weight: 5.9990 chunk 526 optimal weight: 0.9980 chunk 13 optimal weight: 0.0980 chunk 690 optimal weight: 3.9990 chunk 382 optimal weight: 0.2980 chunk 791 optimal weight: 5.9990 chunk 641 optimal weight: 20.0000 chunk 1 optimal weight: 2.9990 chunk 473 optimal weight: 9.9990 chunk 832 optimal weight: 10.0000 chunk 234 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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** ** 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 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 ASN ** C 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 234 ASN ** D 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 234 ASN ** E 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 234 ASN ** 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 230 GLN G 234 ASN ** G 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 234 ASN ** H 395 GLN ** 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** ** J 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 234 ASN ** M 395 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 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 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 234 ASN ** P 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 77344 Z= 0.230 Angle : 0.565 16.116 105104 Z= 0.281 Chirality : 0.043 0.258 12160 Planarity : 0.005 0.072 13488 Dihedral : 4.402 19.395 10928 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 4.53 % Allowed : 19.99 % Favored : 75.48 % 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: -1.64 (0.08), residues: 9600 helix: 0.13 (0.10), residues: 2352 sheet: -1.47 (0.12), residues: 1824 loop : -1.51 (0.08), residues: 5424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP P 51 HIS 0.006 0.001 HIS E 311 PHE 0.030 0.002 PHE H 313 TYR 0.019 0.002 TYR P 341 ARG 0.006 0.000 ARG N 339 *********************** 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 1502 residues out of total 8544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 387 poor density : 1115 time to evaluate : 6.250 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: A 59 MET cc_start: 0.6738 (mmm) cc_final: 0.5923 (mmt) REVERT: A 169 LEU cc_start: 0.7244 (mt) cc_final: 0.6597 (mt) REVERT: A 218 GLU cc_start: 0.7463 (mt-10) cc_final: 0.7256 (mt-10) REVERT: A 335 GLU cc_start: 0.7094 (tp30) cc_final: 0.6641 (tp30) REVERT: A 492 GLN cc_start: 0.6635 (tt0) cc_final: 0.5998 (mm-40) REVERT: A 510 CYS cc_start: 0.6931 (m) cc_final: 0.6664 (m) REVERT: B 59 MET cc_start: 0.6638 (mmm) cc_final: 0.6416 (mmt) REVERT: B 135 ARG cc_start: 0.8196 (ttp-110) cc_final: 0.7672 (mtm110) REVERT: B 314 ILE cc_start: 0.8417 (OUTLIER) cc_final: 0.7870 (mt) REVERT: B 510 CYS cc_start: 0.6522 (m) cc_final: 0.6137 (m) REVERT: B 593 TYR cc_start: 0.7852 (m-80) cc_final: 0.7558 (m-80) REVERT: C 169 LEU cc_start: 0.7561 (mt) cc_final: 0.7158 (mt) REVERT: C 189 MET cc_start: 0.8472 (tpp) cc_final: 0.8018 (tpp) REVERT: C 314 ILE cc_start: 0.8709 (OUTLIER) cc_final: 0.8264 (mt) REVERT: C 399 GLN cc_start: 0.6439 (pp30) cc_final: 0.6112 (pp30) REVERT: C 458 ARG cc_start: 0.7344 (ptp90) cc_final: 0.7137 (ptp90) REVERT: C 492 GLN cc_start: 0.6226 (tt0) cc_final: 0.5790 (mm-40) REVERT: D 154 ASN cc_start: 0.8478 (p0) cc_final: 0.8256 (p0) REVERT: D 169 LEU cc_start: 0.7389 (mt) cc_final: 0.6840 (mt) REVERT: D 335 GLU cc_start: 0.7575 (tp30) cc_final: 0.7180 (tp30) REVERT: D 399 GLN cc_start: 0.7003 (pp30) cc_final: 0.5974 (pp30) REVERT: D 492 GLN cc_start: 0.6744 (tt0) cc_final: 0.5974 (mm-40) REVERT: E 59 MET cc_start: 0.6479 (mmm) cc_final: 0.6007 (mmt) REVERT: E 140 GLN cc_start: 0.7219 (tt0) cc_final: 0.6885 (mt0) REVERT: E 169 LEU cc_start: 0.7328 (mt) cc_final: 0.6715 (mt) REVERT: E 218 GLU cc_start: 0.7378 (mt-10) cc_final: 0.7167 (mt-10) REVERT: E 492 GLN cc_start: 0.6320 (tt0) cc_final: 0.5568 (mm-40) REVERT: E 510 CYS cc_start: 0.6970 (m) cc_final: 0.6466 (m) REVERT: F 59 MET cc_start: 0.6554 (mmm) cc_final: 0.6294 (mmt) REVERT: F 135 ARG cc_start: 0.8228 (ttp-110) cc_final: 0.7854 (mtm110) REVERT: F 169 LEU cc_start: 0.7455 (mt) cc_final: 0.7002 (mt) REVERT: F 314 ILE cc_start: 0.8244 (OUTLIER) cc_final: 0.7774 (mt) REVERT: F 335 GLU cc_start: 0.7293 (tp30) cc_final: 0.6944 (tp30) REVERT: F 364 MET cc_start: 0.7582 (mtp) cc_final: 0.7324 (mtp) REVERT: F 492 GLN cc_start: 0.6612 (tt0) cc_final: 0.6031 (mm-40) REVERT: F 510 CYS cc_start: 0.7006 (m) cc_final: 0.6794 (m) REVERT: G 189 MET cc_start: 0.8643 (tpp) cc_final: 0.8246 (tpp) REVERT: G 399 GLN cc_start: 0.6606 (pp30) cc_final: 0.6373 (pp30) REVERT: G 492 GLN cc_start: 0.6388 (tt0) cc_final: 0.5898 (mm-40) REVERT: H 78 TYR cc_start: 0.8288 (m-80) cc_final: 0.8060 (m-80) REVERT: H 169 LEU cc_start: 0.7449 (mt) cc_final: 0.6894 (mt) REVERT: H 313 PHE cc_start: 0.7252 (t80) cc_final: 0.6956 (m-80) REVERT: H 342 TYR cc_start: 0.8304 (m-80) cc_final: 0.7742 (m-80) REVERT: H 492 GLN cc_start: 0.6826 (tt0) cc_final: 0.6075 (mm-40) REVERT: I 44 GLU cc_start: 0.8514 (tt0) cc_final: 0.8291 (tt0) REVERT: I 57 VAL cc_start: 0.8684 (m) cc_final: 0.8451 (m) REVERT: I 59 MET cc_start: 0.6454 (mmm) cc_final: 0.5794 (mmt) REVERT: I 96 MET cc_start: 0.8249 (mpp) cc_final: 0.7627 (mmt) REVERT: I 105 MET cc_start: 0.7712 (mmm) cc_final: 0.7504 (mmm) REVERT: I 169 LEU cc_start: 0.7469 (mt) cc_final: 0.6823 (mt) REVERT: I 335 GLU cc_start: 0.7152 (tp30) cc_final: 0.6934 (tp30) REVERT: I 492 GLN cc_start: 0.6862 (tt0) cc_final: 0.5993 (mm-40) REVERT: I 510 CYS cc_start: 0.6941 (m) cc_final: 0.6408 (m) REVERT: I 639 MET cc_start: 0.5370 (ttm) cc_final: 0.4980 (tpp) REVERT: J 59 MET cc_start: 0.6669 (mmm) cc_final: 0.6351 (mmt) REVERT: J 135 ARG cc_start: 0.8238 (ttp-110) cc_final: 0.7998 (mtm110) REVERT: J 189 MET cc_start: 0.8530 (tpp) cc_final: 0.8310 (tpp) REVERT: J 492 GLN cc_start: 0.6576 (tt0) cc_final: 0.6139 (mm-40) REVERT: K 189 MET cc_start: 0.8746 (tpp) cc_final: 0.8315 (tpp) REVERT: K 460 TYR cc_start: 0.7221 (m-80) cc_final: 0.6972 (m-80) REVERT: K 492 GLN cc_start: 0.6371 (tt0) cc_final: 0.5810 (mm-40) REVERT: L 59 MET cc_start: 0.6649 (mmm) cc_final: 0.6399 (mmt) REVERT: L 169 LEU cc_start: 0.7519 (mt) cc_final: 0.6888 (mt) REVERT: L 314 ILE cc_start: 0.8456 (OUTLIER) cc_final: 0.7830 (mt) REVERT: L 335 GLU cc_start: 0.7299 (tp30) cc_final: 0.6981 (tp30) REVERT: L 342 TYR cc_start: 0.8322 (m-80) cc_final: 0.7742 (m-80) REVERT: L 492 GLN cc_start: 0.6891 (tt0) cc_final: 0.6121 (mm-40) REVERT: M 44 GLU cc_start: 0.8455 (tt0) cc_final: 0.8225 (tt0) REVERT: M 59 MET cc_start: 0.6500 (mmm) cc_final: 0.5922 (mmt) REVERT: M 96 MET cc_start: 0.8254 (mpp) cc_final: 0.8000 (mmt) REVERT: M 169 LEU cc_start: 0.7480 (mt) cc_final: 0.6816 (mt) REVERT: M 335 GLU cc_start: 0.7005 (tp30) cc_final: 0.6716 (tp30) REVERT: M 492 GLN cc_start: 0.6332 (tt0) cc_final: 0.5492 (mm-40) REVERT: M 510 CYS cc_start: 0.6837 (m) cc_final: 0.6367 (m) REVERT: N 59 MET cc_start: 0.6691 (mmm) cc_final: 0.6364 (mmt) REVERT: N 135 ARG cc_start: 0.8234 (ttp-110) cc_final: 0.7975 (mtm110) REVERT: N 193 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8537 (mt) REVERT: N 314 ILE cc_start: 0.8272 (OUTLIER) cc_final: 0.7793 (mt) REVERT: N 399 GLN cc_start: 0.7256 (pp30) cc_final: 0.6216 (pp30) REVERT: N 400 LYS cc_start: 0.5361 (mmtp) cc_final: 0.4398 (mmtp) REVERT: N 492 GLN cc_start: 0.6591 (tt0) cc_final: 0.5979 (mm-40) REVERT: O 169 LEU cc_start: 0.7542 (mt) cc_final: 0.7144 (mt) REVERT: O 189 MET cc_start: 0.8688 (tpp) cc_final: 0.8238 (tpp) REVERT: O 218 GLU cc_start: 0.7472 (mt-10) cc_final: 0.7176 (mt-10) REVERT: O 492 GLN cc_start: 0.6416 (tt0) cc_final: 0.5906 (mm-40) REVERT: P 335 GLU cc_start: 0.7236 (tp30) cc_final: 0.6907 (tp30) REVERT: P 492 GLN cc_start: 0.6820 (tt0) cc_final: 0.6002 (mm-40) outliers start: 387 outliers final: 279 residues processed: 1389 average time/residue: 0.6730 time to fit residues: 1670.5666 Evaluate side-chains 1352 residues out of total 8544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 285 poor density : 1067 time to evaluate : 6.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 143 ASP Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 442 CYS Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 442 CYS Chi-restraints excluded: chain B residue 499 ILE Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 594 THR Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 366 ASP Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain C residue 422 THR Chi-restraints excluded: chain C residue 442 CYS Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 195 GLU Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 366 ASP Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 442 CYS Chi-restraints excluded: chain D residue 481 THR Chi-restraints excluded: chain D residue 499 ILE Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 63 MET Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain E residue 303 ILE Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 366 ASP Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain E residue 442 CYS Chi-restraints excluded: chain E residue 481 THR Chi-restraints excluded: chain E residue 499 ILE Chi-restraints excluded: chain E residue 503 LEU Chi-restraints excluded: chain E residue 538 VAL Chi-restraints excluded: chain E residue 554 CYS Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 277 SER Chi-restraints excluded: chain F residue 290 GLU Chi-restraints excluded: chain F residue 314 ILE Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 366 ASP Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 442 CYS Chi-restraints excluded: chain F residue 499 ILE Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain F residue 594 THR Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain G residue 147 THR Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 199 LEU Chi-restraints excluded: chain G residue 277 SER Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 366 ASP Chi-restraints excluded: chain G residue 416 VAL Chi-restraints excluded: chain G residue 442 CYS Chi-restraints excluded: chain G residue 538 VAL Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 113 LEU Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain H residue 147 THR Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 195 GLU Chi-restraints excluded: chain H residue 234 ASN Chi-restraints excluded: chain H residue 235 THR Chi-restraints excluded: chain H residue 277 SER Chi-restraints excluded: chain H residue 303 ILE Chi-restraints excluded: chain H residue 333 THR Chi-restraints excluded: chain H residue 366 ASP Chi-restraints excluded: chain H residue 416 VAL Chi-restraints excluded: chain H residue 442 CYS Chi-restraints excluded: chain H residue 499 ILE Chi-restraints excluded: chain H residue 503 LEU Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain H residue 554 CYS Chi-restraints excluded: chain H residue 628 LYS Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 147 THR Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 193 LEU Chi-restraints excluded: chain I residue 247 ILE Chi-restraints excluded: chain I residue 277 SER Chi-restraints excluded: chain I residue 322 LEU Chi-restraints excluded: chain I residue 333 THR Chi-restraints excluded: chain I residue 366 ASP Chi-restraints excluded: chain I residue 416 VAL Chi-restraints excluded: chain I residue 442 CYS Chi-restraints excluded: chain I residue 538 VAL Chi-restraints excluded: chain J residue 45 VAL Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 113 LEU Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 277 SER Chi-restraints excluded: chain J residue 303 ILE Chi-restraints excluded: chain J residue 308 LEU Chi-restraints excluded: chain J residue 333 THR Chi-restraints excluded: chain J residue 366 ASP Chi-restraints excluded: chain J residue 406 ASP Chi-restraints excluded: chain J residue 416 VAL Chi-restraints excluded: chain J residue 442 CYS Chi-restraints excluded: chain J residue 499 ILE Chi-restraints excluded: chain J residue 503 LEU Chi-restraints excluded: chain J residue 538 VAL Chi-restraints excluded: chain J residue 594 THR Chi-restraints excluded: chain K residue 38 LEU Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain K residue 93 ASN Chi-restraints excluded: chain K residue 113 LEU Chi-restraints excluded: chain K residue 147 THR Chi-restraints excluded: chain K residue 159 VAL Chi-restraints excluded: chain K residue 175 LEU Chi-restraints excluded: chain K residue 277 SER Chi-restraints excluded: chain K residue 333 THR Chi-restraints excluded: chain K residue 366 ASP Chi-restraints excluded: chain K residue 416 VAL Chi-restraints excluded: chain K residue 442 CYS Chi-restraints excluded: chain K residue 499 ILE Chi-restraints excluded: chain K residue 538 VAL Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 66 THR Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 113 LEU Chi-restraints excluded: chain L residue 115 ILE Chi-restraints excluded: chain L residue 147 THR Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 195 GLU Chi-restraints excluded: chain L residue 235 THR Chi-restraints excluded: chain L residue 247 ILE Chi-restraints excluded: chain L residue 277 SER Chi-restraints excluded: chain L residue 290 GLU Chi-restraints excluded: chain L residue 314 ILE Chi-restraints excluded: chain L residue 322 LEU Chi-restraints excluded: chain L residue 333 THR Chi-restraints excluded: chain L residue 366 ASP Chi-restraints excluded: chain L residue 416 VAL Chi-restraints excluded: chain L residue 481 THR Chi-restraints excluded: chain L residue 499 ILE Chi-restraints excluded: chain L residue 503 LEU Chi-restraints excluded: chain L residue 538 VAL Chi-restraints excluded: chain L residue 610 THR Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 86 THR Chi-restraints excluded: chain M residue 147 THR Chi-restraints excluded: chain M residue 159 VAL Chi-restraints excluded: chain M residue 193 LEU Chi-restraints excluded: chain M residue 247 ILE Chi-restraints excluded: chain M residue 277 SER Chi-restraints excluded: chain M residue 322 LEU Chi-restraints excluded: chain M residue 333 THR Chi-restraints excluded: chain M residue 366 ASP Chi-restraints excluded: chain M residue 416 VAL Chi-restraints excluded: chain M residue 442 CYS Chi-restraints excluded: chain M residue 499 ILE Chi-restraints excluded: chain M residue 503 LEU Chi-restraints excluded: chain M residue 538 VAL Chi-restraints excluded: chain N residue 38 LEU Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 86 THR Chi-restraints excluded: chain N residue 131 THR Chi-restraints excluded: chain N residue 147 THR Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain N residue 193 LEU Chi-restraints excluded: chain N residue 247 ILE Chi-restraints excluded: chain N residue 277 SER Chi-restraints excluded: chain N residue 314 ILE Chi-restraints excluded: chain N residue 322 LEU Chi-restraints excluded: chain N residue 333 THR Chi-restraints excluded: chain N residue 366 ASP Chi-restraints excluded: chain N residue 416 VAL Chi-restraints excluded: chain N residue 442 CYS Chi-restraints excluded: chain N residue 538 VAL Chi-restraints excluded: chain N residue 594 THR Chi-restraints excluded: chain O residue 84 VAL Chi-restraints excluded: chain O residue 86 THR Chi-restraints excluded: chain O residue 93 ASN Chi-restraints excluded: chain O residue 113 LEU Chi-restraints excluded: chain O residue 119 LEU Chi-restraints excluded: chain O residue 143 ASP Chi-restraints excluded: chain O residue 147 THR Chi-restraints excluded: chain O residue 159 VAL Chi-restraints excluded: chain O residue 175 LEU Chi-restraints excluded: chain O residue 176 MET Chi-restraints excluded: chain O residue 277 SER Chi-restraints excluded: chain O residue 333 THR Chi-restraints excluded: chain O residue 366 ASP Chi-restraints excluded: chain O residue 416 VAL Chi-restraints excluded: chain O residue 442 CYS Chi-restraints excluded: chain O residue 538 VAL Chi-restraints excluded: chain O residue 554 CYS Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain P residue 84 VAL Chi-restraints excluded: chain P residue 86 THR Chi-restraints excluded: chain P residue 115 ILE Chi-restraints excluded: chain P residue 143 ASP Chi-restraints excluded: chain P residue 147 THR Chi-restraints excluded: chain P residue 159 VAL Chi-restraints excluded: chain P residue 195 GLU Chi-restraints excluded: chain P residue 209 VAL Chi-restraints excluded: chain P residue 234 ASN Chi-restraints excluded: chain P residue 247 ILE Chi-restraints excluded: chain P residue 277 SER Chi-restraints excluded: chain P residue 290 GLU Chi-restraints excluded: chain P residue 291 THR Chi-restraints excluded: chain P residue 303 ILE Chi-restraints excluded: chain P residue 327 VAL Chi-restraints excluded: chain P residue 333 THR Chi-restraints excluded: chain P residue 366 ASP Chi-restraints excluded: chain P residue 416 VAL Chi-restraints excluded: chain P residue 499 ILE Chi-restraints excluded: chain P residue 503 LEU Chi-restraints excluded: chain P residue 538 VAL Chi-restraints excluded: chain P residue 554 CYS Chi-restraints excluded: chain P residue 610 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 63.5207 > 50: distance: 106 - 111: 10.583 distance: 111 - 112: 14.241 distance: 112 - 113: 38.636 distance: 112 - 115: 6.697 distance: 113 - 114: 37.536 distance: 113 - 118: 19.790 distance: 115 - 116: 11.234 distance: 115 - 117: 12.643 distance: 118 - 119: 8.560 distance: 119 - 120: 21.534 distance: 119 - 122: 5.346 distance: 120 - 121: 38.605 distance: 120 - 129: 15.366 distance: 122 - 123: 22.759 distance: 123 - 124: 15.768 distance: 124 - 125: 8.867 distance: 125 - 126: 4.485 distance: 126 - 127: 5.963 distance: 126 - 128: 5.525 distance: 129 - 130: 15.097 distance: 130 - 131: 10.187 distance: 130 - 133: 26.998 distance: 131 - 132: 7.128 distance: 131 - 137: 5.928 distance: 133 - 134: 6.051 distance: 134 - 135: 10.754 distance: 134 - 136: 20.209 distance: 137 - 138: 11.256 distance: 137 - 143: 5.359 distance: 138 - 139: 5.695 distance: 138 - 141: 9.868 distance: 139 - 140: 24.364 distance: 141 - 142: 6.892 distance: 142 - 143: 15.456 distance: 144 - 145: 5.691 distance: 144 - 150: 10.501 distance: 145 - 146: 10.172 distance: 145 - 148: 10.544 distance: 146 - 147: 13.741 distance: 146 - 151: 11.407 distance: 148 - 149: 9.514 distance: 149 - 150: 7.183 distance: 151 - 152: 9.311 distance: 152 - 153: 11.213 distance: 152 - 155: 13.465 distance: 153 - 154: 14.764 distance: 153 - 163: 14.171 distance: 155 - 156: 5.414 distance: 156 - 157: 7.119 distance: 156 - 158: 7.941 distance: 157 - 159: 4.334 distance: 159 - 161: 8.429 distance: 160 - 161: 7.324 distance: 161 - 162: 13.066 distance: 163 - 164: 12.680 distance: 164 - 167: 13.849 distance: 165 - 166: 3.105 distance: 165 - 170: 7.060 distance: 167 - 168: 10.220 distance: 167 - 169: 10.439 distance: 170 - 171: 9.157 distance: 171 - 172: 20.927 distance: 171 - 174: 14.692 distance: 172 - 173: 14.669 distance: 172 - 179: 17.080 distance: 174 - 175: 4.548 distance: 175 - 176: 5.997 distance: 176 - 177: 10.774 distance: 177 - 178: 9.897 distance: 179 - 180: 25.471 distance: 179 - 185: 13.491 distance: 180 - 181: 26.143 distance: 180 - 183: 18.177 distance: 181 - 182: 24.226 distance: 181 - 186: 18.590 distance: 183 - 184: 7.172 distance: 184 - 185: 23.824 distance: 186 - 187: 10.027 distance: 186 - 192: 20.724 distance: 187 - 188: 3.735 distance: 187 - 190: 14.225 distance: 188 - 189: 7.245 distance: 188 - 193: 5.977 distance: 190 - 191: 24.900 distance: 191 - 192: 24.089