Starting phenix.real_space_refine (version: 1.21rc1) on Thu Jul 6 18:37:24 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3los_5137/07_2023/3los_5137.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3los_5137/07_2023/3los_5137.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3los_5137/07_2023/3los_5137.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3los_5137/07_2023/3los_5137.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3los_5137/07_2023/3los_5137.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3los_5137/07_2023/3los_5137.pdb" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.014 sd= 0.098 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 448 5.16 5 C 39488 2.51 5 N 11024 2.21 5 O 12752 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 18": "NH1" <-> "NH2" Residue "A ASP 50": "OD1" <-> "OD2" Residue "A ASP 51": "OD1" <-> "OD2" Residue "A GLU 71": "OE1" <-> "OE2" Residue "A GLU 86": "OE1" <-> "OE2" Residue "A ARG 105": "NH1" <-> "NH2" Residue "A TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 146": "OD1" <-> "OD2" Residue "A GLU 148": "OE1" <-> "OE2" Residue "A GLU 164": "OE1" <-> "OE2" Residue "A GLU 176": "OE1" <-> "OE2" Residue "A ASP 183": "OD1" <-> "OD2" Residue "A GLU 185": "OE1" <-> "OE2" Residue "A ASP 189": "OD1" <-> "OD2" Residue "A GLU 196": "OE1" <-> "OE2" Residue "A ASP 204": "OD1" <-> "OD2" Residue "A ASP 215": "OD1" <-> "OD2" Residue "A ARG 218": "NH1" <-> "NH2" Residue "A ASP 229": "OD1" <-> "OD2" Residue "A GLU 240": "OE1" <-> "OE2" Residue "A GLU 245": "OE1" <-> "OE2" Residue "A ASP 247": "OD1" <-> "OD2" Residue "A ARG 251": "NH1" <-> "NH2" Residue "A ASP 254": "OD1" <-> "OD2" Residue "A GLU 263": "OE1" <-> "OE2" Residue "A GLU 265": "OE1" <-> "OE2" Residue "A GLU 266": "OE1" <-> "OE2" Residue "A PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 292": "OD1" <-> "OD2" Residue "A TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 331": "OD1" <-> "OD2" Residue "A PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 378": "OE1" <-> "OE2" Residue "A GLU 379": "OE1" <-> "OE2" Residue "A GLU 396": "OE1" <-> "OE2" Residue "A ASP 397": "OD1" <-> "OD2" Residue "A GLU 408": "OE1" <-> "OE2" Residue "A GLU 426": "OE1" <-> "OE2" Residue "A PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 435": "OD1" <-> "OD2" Residue "A PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 481": "OE1" <-> "OE2" Residue "A GLU 485": "OE1" <-> "OE2" Residue "A GLU 504": "OE1" <-> "OE2" Residue "A ASP 514": "OD1" <-> "OD2" Residue "A ARG 522": "NH1" <-> "NH2" Residue "B ARG 18": "NH1" <-> "NH2" Residue "B ASP 50": "OD1" <-> "OD2" Residue "B ASP 51": "OD1" <-> "OD2" Residue "B GLU 71": "OE1" <-> "OE2" Residue "B GLU 86": "OE1" <-> "OE2" Residue "B ARG 105": "NH1" <-> "NH2" Residue "B TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 146": "OD1" <-> "OD2" Residue "B GLU 148": "OE1" <-> "OE2" Residue "B GLU 164": "OE1" <-> "OE2" Residue "B GLU 176": "OE1" <-> "OE2" Residue "B ASP 183": "OD1" <-> "OD2" Residue "B GLU 185": "OE1" <-> "OE2" Residue "B ASP 189": "OD1" <-> "OD2" Residue "B GLU 196": "OE1" <-> "OE2" Residue "B ASP 204": "OD1" <-> "OD2" Residue "B ASP 215": "OD1" <-> "OD2" Residue "B ARG 218": "NH1" <-> "NH2" Residue "B ASP 229": "OD1" <-> "OD2" Residue "B GLU 240": "OE1" <-> "OE2" Residue "B GLU 245": "OE1" <-> "OE2" Residue "B ASP 247": "OD1" <-> "OD2" Residue "B ARG 251": "NH1" <-> "NH2" Residue "B ASP 254": "OD1" <-> "OD2" Residue "B GLU 263": "OE1" <-> "OE2" Residue "B GLU 265": "OE1" <-> "OE2" Residue "B GLU 266": "OE1" <-> "OE2" Residue "B PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 292": "OD1" <-> "OD2" Residue "B TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 331": "OD1" <-> "OD2" Residue "B PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 378": "OE1" <-> "OE2" Residue "B GLU 379": "OE1" <-> "OE2" Residue "B GLU 396": "OE1" <-> "OE2" Residue "B GLU 408": "OE1" <-> "OE2" Residue "B GLU 426": "OE1" <-> "OE2" Residue "B PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 435": "OD1" <-> "OD2" Residue "B PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 481": "OE1" <-> "OE2" Residue "B GLU 485": "OE1" <-> "OE2" Residue "B GLU 504": "OE1" <-> "OE2" Residue "B ASP 514": "OD1" <-> "OD2" Residue "B ARG 522": "NH1" <-> "NH2" Residue "C ARG 18": "NH1" <-> "NH2" Residue "C ASP 50": "OD1" <-> "OD2" Residue "C ASP 51": "OD1" <-> "OD2" Residue "C GLU 71": "OE1" <-> "OE2" Residue "C GLU 86": "OE1" <-> "OE2" Residue "C ARG 105": "NH1" <-> "NH2" Residue "C TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 146": "OD1" <-> "OD2" Residue "C GLU 148": "OE1" <-> "OE2" Residue "C GLU 164": "OE1" <-> "OE2" Residue "C GLU 176": "OE1" <-> "OE2" Residue "C ASP 183": "OD1" <-> "OD2" Residue "C GLU 185": "OE1" <-> "OE2" Residue "C ASP 189": "OD1" <-> "OD2" Residue "C GLU 196": "OE1" <-> "OE2" Residue "C ASP 204": "OD1" <-> "OD2" Residue "C ASP 215": "OD1" <-> "OD2" Residue "C ARG 218": "NH1" <-> "NH2" Residue "C ASP 229": "OD1" <-> "OD2" Residue "C GLU 240": "OE1" <-> "OE2" Residue "C GLU 245": "OE1" <-> "OE2" Residue "C ASP 247": "OD1" <-> "OD2" Residue "C ARG 251": "NH1" <-> "NH2" Residue "C ASP 254": "OD1" <-> "OD2" Residue "C GLU 263": "OE1" <-> "OE2" Residue "C GLU 265": "OE1" <-> "OE2" Residue "C GLU 266": "OE1" <-> "OE2" Residue "C PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 292": "OD1" <-> "OD2" Residue "C TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 331": "OD1" <-> "OD2" Residue "C PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 378": "OE1" <-> "OE2" Residue "C GLU 379": "OE1" <-> "OE2" Residue "C GLU 396": "OE1" <-> "OE2" Residue "C ASP 397": "OD1" <-> "OD2" Residue "C GLU 408": "OE1" <-> "OE2" Residue "C GLU 426": "OE1" <-> "OE2" Residue "C PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 435": "OD1" <-> "OD2" Residue "C PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 481": "OE1" <-> "OE2" Residue "C GLU 485": "OE1" <-> "OE2" Residue "C GLU 504": "OE1" <-> "OE2" Residue "C ASP 514": "OD1" <-> "OD2" Residue "C ARG 522": "NH1" <-> "NH2" Residue "D ARG 18": "NH1" <-> "NH2" Residue "D ASP 50": "OD1" <-> "OD2" Residue "D ASP 51": "OD1" <-> "OD2" Residue "D GLU 71": "OE1" <-> "OE2" Residue "D GLU 86": "OE1" <-> "OE2" Residue "D ARG 105": "NH1" <-> "NH2" Residue "D TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 146": "OD1" <-> "OD2" Residue "D GLU 148": "OE1" <-> "OE2" Residue "D GLU 164": "OE1" <-> "OE2" Residue "D GLU 176": "OE1" <-> "OE2" Residue "D ASP 183": "OD1" <-> "OD2" Residue "D GLU 185": "OE1" <-> "OE2" Residue "D ASP 189": "OD1" <-> "OD2" Residue "D GLU 196": "OE1" <-> "OE2" Residue "D ASP 204": "OD1" <-> "OD2" Residue "D ASP 215": "OD1" <-> "OD2" Residue "D ARG 218": "NH1" <-> "NH2" Residue "D ASP 229": "OD1" <-> "OD2" Residue "D GLU 240": "OE1" <-> "OE2" Residue "D GLU 245": "OE1" <-> "OE2" Residue "D ASP 247": "OD1" <-> "OD2" Residue "D ARG 251": "NH1" <-> "NH2" Residue "D ASP 254": "OD1" <-> "OD2" Residue "D GLU 263": "OE1" <-> "OE2" Residue "D GLU 265": "OE1" <-> "OE2" Residue "D GLU 266": "OE1" <-> "OE2" Residue "D PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 292": "OD1" <-> "OD2" Residue "D TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 331": "OD1" <-> "OD2" Residue "D PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 378": "OE1" <-> "OE2" Residue "D GLU 379": "OE1" <-> "OE2" Residue "D GLU 396": "OE1" <-> "OE2" Residue "D ASP 397": "OD1" <-> "OD2" Residue "D GLU 408": "OE1" <-> "OE2" Residue "D GLU 426": "OE1" <-> "OE2" Residue "D PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 435": "OD1" <-> "OD2" Residue "D PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 481": "OE1" <-> "OE2" Residue "D GLU 485": "OE1" <-> "OE2" Residue "D GLU 504": "OE1" <-> "OE2" Residue "D ASP 514": "OD1" <-> "OD2" Residue "D ARG 522": "NH1" <-> "NH2" Residue "E ARG 18": "NH1" <-> "NH2" Residue "E ASP 50": "OD1" <-> "OD2" Residue "E ASP 51": "OD1" <-> "OD2" Residue "E GLU 71": "OE1" <-> "OE2" Residue "E GLU 86": "OE1" <-> "OE2" Residue "E ARG 105": "NH1" <-> "NH2" Residue "E TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 146": "OD1" <-> "OD2" Residue "E GLU 148": "OE1" <-> "OE2" Residue "E GLU 164": "OE1" <-> "OE2" Residue "E GLU 176": "OE1" <-> "OE2" Residue "E ASP 183": "OD1" <-> "OD2" Residue "E GLU 185": "OE1" <-> "OE2" Residue "E ASP 189": "OD1" <-> "OD2" Residue "E GLU 196": "OE1" <-> "OE2" Residue "E ASP 204": "OD1" <-> "OD2" Residue "E ASP 215": "OD1" <-> "OD2" Residue "E ARG 218": "NH1" <-> "NH2" Residue "E ASP 229": "OD1" <-> "OD2" Residue "E GLU 240": "OE1" <-> "OE2" Residue "E GLU 245": "OE1" <-> "OE2" Residue "E ASP 247": "OD1" <-> "OD2" Residue "E ARG 251": "NH1" <-> "NH2" Residue "E ASP 254": "OD1" <-> "OD2" Residue "E GLU 263": "OE1" <-> "OE2" Residue "E GLU 265": "OE1" <-> "OE2" Residue "E GLU 266": "OE1" <-> "OE2" Residue "E PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 292": "OD1" <-> "OD2" Residue "E TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 331": "OD1" <-> "OD2" Residue "E PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 378": "OE1" <-> "OE2" Residue "E GLU 379": "OE1" <-> "OE2" Residue "E GLU 396": "OE1" <-> "OE2" Residue "E ASP 397": "OD1" <-> "OD2" Residue "E GLU 408": "OE1" <-> "OE2" Residue "E GLU 426": "OE1" <-> "OE2" Residue "E PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 435": "OD1" <-> "OD2" Residue "E PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 481": "OE1" <-> "OE2" Residue "E GLU 485": "OE1" <-> "OE2" Residue "E GLU 504": "OE1" <-> "OE2" Residue "E ASP 514": "OD1" <-> "OD2" Residue "E ARG 522": "NH1" <-> "NH2" Residue "F ARG 18": "NH1" <-> "NH2" Residue "F ASP 50": "OD1" <-> "OD2" Residue "F ASP 51": "OD1" <-> "OD2" Residue "F GLU 71": "OE1" <-> "OE2" Residue "F GLU 86": "OE1" <-> "OE2" Residue "F ARG 105": "NH1" <-> "NH2" Residue "F TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 146": "OD1" <-> "OD2" Residue "F GLU 148": "OE1" <-> "OE2" Residue "F GLU 164": "OE1" <-> "OE2" Residue "F GLU 176": "OE1" <-> "OE2" Residue "F ASP 183": "OD1" <-> "OD2" Residue "F GLU 185": "OE1" <-> "OE2" Residue "F ASP 189": "OD1" <-> "OD2" Residue "F GLU 196": "OE1" <-> "OE2" Residue "F ASP 204": "OD1" <-> "OD2" Residue "F ASP 215": "OD1" <-> "OD2" Residue "F ARG 218": "NH1" <-> "NH2" Residue "F ASP 229": "OD1" <-> "OD2" Residue "F GLU 240": "OE1" <-> "OE2" Residue "F GLU 245": "OE1" <-> "OE2" Residue "F ASP 247": "OD1" <-> "OD2" Residue "F ARG 251": "NH1" <-> "NH2" Residue "F ASP 254": "OD1" <-> "OD2" Residue "F GLU 263": "OE1" <-> "OE2" Residue "F GLU 265": "OE1" <-> "OE2" Residue "F GLU 266": "OE1" <-> "OE2" Residue "F PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 292": "OD1" <-> "OD2" Residue "F TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 331": "OD1" <-> "OD2" Residue "F PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 378": "OE1" <-> "OE2" Residue "F GLU 379": "OE1" <-> "OE2" Residue "F GLU 396": "OE1" <-> "OE2" Residue "F ASP 397": "OD1" <-> "OD2" Residue "F GLU 408": "OE1" <-> "OE2" Residue "F GLU 426": "OE1" <-> "OE2" Residue "F PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 435": "OD1" <-> "OD2" Residue "F PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 481": "OE1" <-> "OE2" Residue "F GLU 485": "OE1" <-> "OE2" Residue "F GLU 504": "OE1" <-> "OE2" Residue "F ASP 514": "OD1" <-> "OD2" Residue "F ARG 522": "NH1" <-> "NH2" Residue "G ARG 18": "NH1" <-> "NH2" Residue "G ASP 50": "OD1" <-> "OD2" Residue "G ASP 51": "OD1" <-> "OD2" Residue "G GLU 71": "OE1" <-> "OE2" Residue "G GLU 86": "OE1" <-> "OE2" Residue "G ARG 105": "NH1" <-> "NH2" Residue "G TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 146": "OD1" <-> "OD2" Residue "G GLU 148": "OE1" <-> "OE2" Residue "G GLU 164": "OE1" <-> "OE2" Residue "G GLU 176": "OE1" <-> "OE2" Residue "G ASP 183": "OD1" <-> "OD2" Residue "G GLU 185": "OE1" <-> "OE2" Residue "G ASP 189": "OD1" <-> "OD2" Residue "G GLU 196": "OE1" <-> "OE2" Residue "G ASP 204": "OD1" <-> "OD2" Residue "G ASP 215": "OD1" <-> "OD2" Residue "G ARG 218": "NH1" <-> "NH2" Residue "G ASP 229": "OD1" <-> "OD2" Residue "G GLU 240": "OE1" <-> "OE2" Residue "G GLU 245": "OE1" <-> "OE2" Residue "G ASP 247": "OD1" <-> "OD2" Residue "G ARG 251": "NH1" <-> "NH2" Residue "G ASP 254": "OD1" <-> "OD2" Residue "G GLU 263": "OE1" <-> "OE2" Residue "G GLU 265": "OE1" <-> "OE2" Residue "G GLU 266": "OE1" <-> "OE2" Residue "G PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 292": "OD1" <-> "OD2" Residue "G TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 331": "OD1" <-> "OD2" Residue "G PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 378": "OE1" <-> "OE2" Residue "G GLU 379": "OE1" <-> "OE2" Residue "G GLU 396": "OE1" <-> "OE2" Residue "G ASP 397": "OD1" <-> "OD2" Residue "G GLU 408": "OE1" <-> "OE2" Residue "G GLU 426": "OE1" <-> "OE2" Residue "G PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 435": "OD1" <-> "OD2" Residue "G PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 481": "OE1" <-> "OE2" Residue "G GLU 485": "OE1" <-> "OE2" Residue "G GLU 504": "OE1" <-> "OE2" Residue "G ASP 514": "OD1" <-> "OD2" Residue "G ARG 522": "NH1" <-> "NH2" Residue "H ARG 18": "NH1" <-> "NH2" Residue "H ASP 50": "OD1" <-> "OD2" Residue "H ASP 51": "OD1" <-> "OD2" Residue "H GLU 71": "OE1" <-> "OE2" Residue "H GLU 86": "OE1" <-> "OE2" Residue "H ARG 105": "NH1" <-> "NH2" Residue "H TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 146": "OD1" <-> "OD2" Residue "H GLU 148": "OE1" <-> "OE2" Residue "H GLU 164": "OE1" <-> "OE2" Residue "H GLU 176": "OE1" <-> "OE2" Residue "H ASP 183": "OD1" <-> "OD2" Residue "H GLU 185": "OE1" <-> "OE2" Residue "H ASP 189": "OD1" <-> "OD2" Residue "H GLU 196": "OE1" <-> "OE2" Residue "H ASP 204": "OD1" <-> "OD2" Residue "H ASP 215": "OD1" <-> "OD2" Residue "H ARG 218": "NH1" <-> "NH2" Residue "H ASP 229": "OD1" <-> "OD2" Residue "H GLU 240": "OE1" <-> "OE2" Residue "H GLU 245": "OE1" <-> "OE2" Residue "H ASP 247": "OD1" <-> "OD2" Residue "H ARG 251": "NH1" <-> "NH2" Residue "H ASP 254": "OD1" <-> "OD2" Residue "H GLU 263": "OE1" <-> "OE2" Residue "H GLU 265": "OE1" <-> "OE2" Residue "H GLU 266": "OE1" <-> "OE2" Residue "H PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 292": "OD1" <-> "OD2" Residue "H TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 331": "OD1" <-> "OD2" Residue "H PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 378": "OE1" <-> "OE2" Residue "H GLU 379": "OE1" <-> "OE2" Residue "H GLU 396": "OE1" <-> "OE2" Residue "H ASP 397": "OD1" <-> "OD2" Residue "H GLU 408": "OE1" <-> "OE2" Residue "H GLU 426": "OE1" <-> "OE2" Residue "H PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 435": "OD1" <-> "OD2" Residue "H PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 481": "OE1" <-> "OE2" Residue "H GLU 485": "OE1" <-> "OE2" Residue "H GLU 504": "OE1" <-> "OE2" Residue "H ASP 514": "OD1" <-> "OD2" Residue "H ARG 522": "NH1" <-> "NH2" Residue "I ARG 18": "NH1" <-> "NH2" Residue "I ASP 50": "OD1" <-> "OD2" Residue "I ASP 51": "OD1" <-> "OD2" Residue "I GLU 71": "OE1" <-> "OE2" Residue "I GLU 86": "OE1" <-> "OE2" Residue "I ARG 105": "NH1" <-> "NH2" Residue "I TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 146": "OD1" <-> "OD2" Residue "I GLU 148": "OE1" <-> "OE2" Residue "I GLU 164": "OE1" <-> "OE2" Residue "I GLU 176": "OE1" <-> "OE2" Residue "I ASP 183": "OD1" <-> "OD2" Residue "I GLU 185": "OE1" <-> "OE2" Residue "I ASP 189": "OD1" <-> "OD2" Residue "I GLU 196": "OE1" <-> "OE2" Residue "I ASP 204": "OD1" <-> "OD2" Residue "I ASP 215": "OD1" <-> "OD2" Residue "I ARG 218": "NH1" <-> "NH2" Residue "I ASP 229": "OD1" <-> "OD2" Residue "I GLU 240": "OE1" <-> "OE2" Residue "I GLU 245": "OE1" <-> "OE2" Residue "I ASP 247": "OD1" <-> "OD2" Residue "I ARG 251": "NH1" <-> "NH2" Residue "I ASP 254": "OD1" <-> "OD2" Residue "I GLU 263": "OE1" <-> "OE2" Residue "I GLU 265": "OE1" <-> "OE2" Residue "I GLU 266": "OE1" <-> "OE2" Residue "I PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 292": "OD1" <-> "OD2" Residue "I TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 331": "OD1" <-> "OD2" Residue "I PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 378": "OE1" <-> "OE2" Residue "I GLU 379": "OE1" <-> "OE2" Residue "I GLU 396": "OE1" <-> "OE2" Residue "I ASP 397": "OD1" <-> "OD2" Residue "I GLU 408": "OE1" <-> "OE2" Residue "I GLU 426": "OE1" <-> "OE2" Residue "I PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 435": "OD1" <-> "OD2" Residue "I PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 481": "OE1" <-> "OE2" Residue "I GLU 485": "OE1" <-> "OE2" Residue "I GLU 504": "OE1" <-> "OE2" Residue "I ASP 514": "OD1" <-> "OD2" Residue "I ARG 522": "NH1" <-> "NH2" Residue "J ARG 18": "NH1" <-> "NH2" Residue "J ASP 50": "OD1" <-> "OD2" Residue "J ASP 51": "OD1" <-> "OD2" Residue "J GLU 71": "OE1" <-> "OE2" Residue "J GLU 86": "OE1" <-> "OE2" Residue "J ARG 105": "NH1" <-> "NH2" Residue "J TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 146": "OD1" <-> "OD2" Residue "J GLU 148": "OE1" <-> "OE2" Residue "J GLU 164": "OE1" <-> "OE2" Residue "J GLU 176": "OE1" <-> "OE2" Residue "J ASP 183": "OD1" <-> "OD2" Residue "J GLU 185": "OE1" <-> "OE2" Residue "J ASP 189": "OD1" <-> "OD2" Residue "J GLU 196": "OE1" <-> "OE2" Residue "J ASP 204": "OD1" <-> "OD2" Residue "J ASP 215": "OD1" <-> "OD2" Residue "J ARG 218": "NH1" <-> "NH2" Residue "J ASP 229": "OD1" <-> "OD2" Residue "J GLU 240": "OE1" <-> "OE2" Residue "J GLU 245": "OE1" <-> "OE2" Residue "J ASP 247": "OD1" <-> "OD2" Residue "J ARG 251": "NH1" <-> "NH2" Residue "J ASP 254": "OD1" <-> "OD2" Residue "J GLU 263": "OE1" <-> "OE2" Residue "J GLU 265": "OE1" <-> "OE2" Residue "J GLU 266": "OE1" <-> "OE2" Residue "J PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 292": "OD1" <-> "OD2" Residue "J TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 331": "OD1" <-> "OD2" Residue "J PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 378": "OE1" <-> "OE2" Residue "J GLU 379": "OE1" <-> "OE2" Residue "J GLU 396": "OE1" <-> "OE2" Residue "J ASP 397": "OD1" <-> "OD2" Residue "J GLU 408": "OE1" <-> "OE2" Residue "J GLU 426": "OE1" <-> "OE2" Residue "J PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 435": "OD1" <-> "OD2" Residue "J PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 481": "OE1" <-> "OE2" Residue "J GLU 485": "OE1" <-> "OE2" Residue "J GLU 504": "OE1" <-> "OE2" Residue "J ASP 514": "OD1" <-> "OD2" Residue "J ARG 522": "NH1" <-> "NH2" Residue "K ARG 18": "NH1" <-> "NH2" Residue "K ASP 50": "OD1" <-> "OD2" Residue "K ASP 51": "OD1" <-> "OD2" Residue "K GLU 71": "OE1" <-> "OE2" Residue "K GLU 86": "OE1" <-> "OE2" Residue "K ARG 105": "NH1" <-> "NH2" Residue "K TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 146": "OD1" <-> "OD2" Residue "K GLU 148": "OE1" <-> "OE2" Residue "K GLU 164": "OE1" <-> "OE2" Residue "K GLU 176": "OE1" <-> "OE2" Residue "K ASP 183": "OD1" <-> "OD2" Residue "K GLU 185": "OE1" <-> "OE2" Residue "K ASP 189": "OD1" <-> "OD2" Residue "K GLU 196": "OE1" <-> "OE2" Residue "K ASP 204": "OD1" <-> "OD2" Residue "K ASP 215": "OD1" <-> "OD2" Residue "K ARG 218": "NH1" <-> "NH2" Residue "K ASP 229": "OD1" <-> "OD2" Residue "K GLU 240": "OE1" <-> "OE2" Residue "K GLU 245": "OE1" <-> "OE2" Residue "K ASP 247": "OD1" <-> "OD2" Residue "K ARG 251": "NH1" <-> "NH2" Residue "K ASP 254": "OD1" <-> "OD2" Residue "K GLU 263": "OE1" <-> "OE2" Residue "K GLU 265": "OE1" <-> "OE2" Residue "K GLU 266": "OE1" <-> "OE2" Residue "K PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 292": "OD1" <-> "OD2" Residue "K TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 331": "OD1" <-> "OD2" Residue "K PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 378": "OE1" <-> "OE2" Residue "K GLU 379": "OE1" <-> "OE2" Residue "K GLU 396": "OE1" <-> "OE2" Residue "K ASP 397": "OD1" <-> "OD2" Residue "K GLU 408": "OE1" <-> "OE2" Residue "K GLU 426": "OE1" <-> "OE2" Residue "K PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 435": "OD1" <-> "OD2" Residue "K PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 481": "OE1" <-> "OE2" Residue "K GLU 485": "OE1" <-> "OE2" Residue "K GLU 504": "OE1" <-> "OE2" Residue "K ASP 514": "OD1" <-> "OD2" Residue "K ARG 522": "NH1" <-> "NH2" Residue "L ARG 18": "NH1" <-> "NH2" Residue "L ASP 50": "OD1" <-> "OD2" Residue "L ASP 51": "OD1" <-> "OD2" Residue "L GLU 71": "OE1" <-> "OE2" Residue "L GLU 86": "OE1" <-> "OE2" Residue "L ARG 105": "NH1" <-> "NH2" Residue "L TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 146": "OD1" <-> "OD2" Residue "L GLU 148": "OE1" <-> "OE2" Residue "L GLU 164": "OE1" <-> "OE2" Residue "L GLU 176": "OE1" <-> "OE2" Residue "L ASP 183": "OD1" <-> "OD2" Residue "L GLU 185": "OE1" <-> "OE2" Residue "L ASP 189": "OD1" <-> "OD2" Residue "L GLU 196": "OE1" <-> "OE2" Residue "L ASP 204": "OD1" <-> "OD2" Residue "L ASP 215": "OD1" <-> "OD2" Residue "L ARG 218": "NH1" <-> "NH2" Residue "L ASP 229": "OD1" <-> "OD2" Residue "L GLU 240": "OE1" <-> "OE2" Residue "L GLU 245": "OE1" <-> "OE2" Residue "L ASP 247": "OD1" <-> "OD2" Residue "L ARG 251": "NH1" <-> "NH2" Residue "L ASP 254": "OD1" <-> "OD2" Residue "L GLU 263": "OE1" <-> "OE2" Residue "L GLU 265": "OE1" <-> "OE2" Residue "L GLU 266": "OE1" <-> "OE2" Residue "L PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 292": "OD1" <-> "OD2" Residue "L TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 331": "OD1" <-> "OD2" Residue "L PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 378": "OE1" <-> "OE2" Residue "L GLU 379": "OE1" <-> "OE2" Residue "L GLU 396": "OE1" <-> "OE2" Residue "L ASP 397": "OD1" <-> "OD2" Residue "L GLU 408": "OE1" <-> "OE2" Residue "L GLU 426": "OE1" <-> "OE2" Residue "L PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 435": "OD1" <-> "OD2" Residue "L PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 481": "OE1" <-> "OE2" Residue "L GLU 485": "OE1" <-> "OE2" Residue "L GLU 504": "OE1" <-> "OE2" Residue "L ASP 514": "OD1" <-> "OD2" Residue "L ARG 522": "NH1" <-> "NH2" Residue "M ARG 18": "NH1" <-> "NH2" Residue "M ASP 50": "OD1" <-> "OD2" Residue "M ASP 51": "OD1" <-> "OD2" Residue "M GLU 71": "OE1" <-> "OE2" Residue "M GLU 86": "OE1" <-> "OE2" Residue "M ARG 105": "NH1" <-> "NH2" Residue "M TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 146": "OD1" <-> "OD2" Residue "M GLU 148": "OE1" <-> "OE2" Residue "M GLU 164": "OE1" <-> "OE2" Residue "M GLU 176": "OE1" <-> "OE2" Residue "M ASP 183": "OD1" <-> "OD2" Residue "M GLU 185": "OE1" <-> "OE2" Residue "M ASP 189": "OD1" <-> "OD2" Residue "M GLU 196": "OE1" <-> "OE2" Residue "M ASP 204": "OD1" <-> "OD2" Residue "M ASP 215": "OD1" <-> "OD2" Residue "M ARG 218": "NH1" <-> "NH2" Residue "M ASP 229": "OD1" <-> "OD2" Residue "M GLU 240": "OE1" <-> "OE2" Residue "M GLU 245": "OE1" <-> "OE2" Residue "M ASP 247": "OD1" <-> "OD2" Residue "M ARG 251": "NH1" <-> "NH2" Residue "M ASP 254": "OD1" <-> "OD2" Residue "M GLU 263": "OE1" <-> "OE2" Residue "M GLU 265": "OE1" <-> "OE2" Residue "M GLU 266": "OE1" <-> "OE2" Residue "M PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 292": "OD1" <-> "OD2" Residue "M TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 331": "OD1" <-> "OD2" Residue "M PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 378": "OE1" <-> "OE2" Residue "M GLU 379": "OE1" <-> "OE2" Residue "M GLU 396": "OE1" <-> "OE2" Residue "M ASP 397": "OD1" <-> "OD2" Residue "M GLU 408": "OE1" <-> "OE2" Residue "M GLU 426": "OE1" <-> "OE2" Residue "M PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 435": "OD1" <-> "OD2" Residue "M PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 481": "OE1" <-> "OE2" Residue "M GLU 485": "OE1" <-> "OE2" Residue "M GLU 504": "OE1" <-> "OE2" Residue "M ASP 514": "OD1" <-> "OD2" Residue "M ARG 522": "NH1" <-> "NH2" Residue "N ARG 18": "NH1" <-> "NH2" Residue "N ASP 50": "OD1" <-> "OD2" Residue "N ASP 51": "OD1" <-> "OD2" Residue "N GLU 71": "OE1" <-> "OE2" Residue "N GLU 86": "OE1" <-> "OE2" Residue "N ARG 105": "NH1" <-> "NH2" Residue "N TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 146": "OD1" <-> "OD2" Residue "N GLU 148": "OE1" <-> "OE2" Residue "N GLU 164": "OE1" <-> "OE2" Residue "N GLU 176": "OE1" <-> "OE2" Residue "N ASP 183": "OD1" <-> "OD2" Residue "N GLU 185": "OE1" <-> "OE2" Residue "N ASP 189": "OD1" <-> "OD2" Residue "N GLU 196": "OE1" <-> "OE2" Residue "N ASP 204": "OD1" <-> "OD2" Residue "N ASP 215": "OD1" <-> "OD2" Residue "N ARG 218": "NH1" <-> "NH2" Residue "N ASP 229": "OD1" <-> "OD2" Residue "N GLU 240": "OE1" <-> "OE2" Residue "N GLU 245": "OE1" <-> "OE2" Residue "N ASP 247": "OD1" <-> "OD2" Residue "N ARG 251": "NH1" <-> "NH2" Residue "N ASP 254": "OD1" <-> "OD2" Residue "N GLU 263": "OE1" <-> "OE2" Residue "N GLU 265": "OE1" <-> "OE2" Residue "N GLU 266": "OE1" <-> "OE2" Residue "N PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 292": "OD1" <-> "OD2" Residue "N TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 331": "OD1" <-> "OD2" Residue "N PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 378": "OE1" <-> "OE2" Residue "N GLU 379": "OE1" <-> "OE2" Residue "N GLU 396": "OE1" <-> "OE2" Residue "N ASP 397": "OD1" <-> "OD2" Residue "N GLU 408": "OE1" <-> "OE2" Residue "N GLU 426": "OE1" <-> "OE2" Residue "N PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 435": "OD1" <-> "OD2" Residue "N PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 481": "OE1" <-> "OE2" Residue "N GLU 485": "OE1" <-> "OE2" Residue "N GLU 504": "OE1" <-> "OE2" Residue "N ASP 514": "OD1" <-> "OD2" Residue "N ARG 522": "NH1" <-> "NH2" Residue "O ARG 18": "NH1" <-> "NH2" Residue "O ASP 50": "OD1" <-> "OD2" Residue "O ASP 51": "OD1" <-> "OD2" Residue "O GLU 71": "OE1" <-> "OE2" Residue "O GLU 86": "OE1" <-> "OE2" Residue "O ARG 105": "NH1" <-> "NH2" Residue "O TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 146": "OD1" <-> "OD2" Residue "O GLU 148": "OE1" <-> "OE2" Residue "O GLU 164": "OE1" <-> "OE2" Residue "O GLU 176": "OE1" <-> "OE2" Residue "O ASP 183": "OD1" <-> "OD2" Residue "O GLU 185": "OE1" <-> "OE2" Residue "O ASP 189": "OD1" <-> "OD2" Residue "O GLU 196": "OE1" <-> "OE2" Residue "O ASP 204": "OD1" <-> "OD2" Residue "O ASP 215": "OD1" <-> "OD2" Residue "O ARG 218": "NH1" <-> "NH2" Residue "O ASP 229": "OD1" <-> "OD2" Residue "O GLU 240": "OE1" <-> "OE2" Residue "O GLU 245": "OE1" <-> "OE2" Residue "O ASP 247": "OD1" <-> "OD2" Residue "O ARG 251": "NH1" <-> "NH2" Residue "O ASP 254": "OD1" <-> "OD2" Residue "O GLU 263": "OE1" <-> "OE2" Residue "O GLU 265": "OE1" <-> "OE2" Residue "O GLU 266": "OE1" <-> "OE2" Residue "O PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 292": "OD1" <-> "OD2" Residue "O TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 331": "OD1" <-> "OD2" Residue "O PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 378": "OE1" <-> "OE2" Residue "O GLU 379": "OE1" <-> "OE2" Residue "O GLU 396": "OE1" <-> "OE2" Residue "O ASP 397": "OD1" <-> "OD2" Residue "O GLU 408": "OE1" <-> "OE2" Residue "O GLU 426": "OE1" <-> "OE2" Residue "O PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 435": "OD1" <-> "OD2" Residue "O PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 481": "OE1" <-> "OE2" Residue "O GLU 485": "OE1" <-> "OE2" Residue "O GLU 504": "OE1" <-> "OE2" Residue "O ASP 514": "OD1" <-> "OD2" Residue "O ARG 522": "NH1" <-> "NH2" Residue "P ARG 18": "NH1" <-> "NH2" Residue "P ASP 50": "OD1" <-> "OD2" Residue "P ASP 51": "OD1" <-> "OD2" Residue "P GLU 71": "OE1" <-> "OE2" Residue "P GLU 86": "OE1" <-> "OE2" Residue "P ARG 105": "NH1" <-> "NH2" Residue "P TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 146": "OD1" <-> "OD2" Residue "P GLU 148": "OE1" <-> "OE2" Residue "P GLU 164": "OE1" <-> "OE2" Residue "P GLU 176": "OE1" <-> "OE2" Residue "P ASP 183": "OD1" <-> "OD2" Residue "P GLU 185": "OE1" <-> "OE2" Residue "P ASP 189": "OD1" <-> "OD2" Residue "P GLU 196": "OE1" <-> "OE2" Residue "P ASP 204": "OD1" <-> "OD2" Residue "P ASP 215": "OD1" <-> "OD2" Residue "P ARG 218": "NH1" <-> "NH2" Residue "P ASP 229": "OD1" <-> "OD2" Residue "P GLU 240": "OE1" <-> "OE2" Residue "P GLU 245": "OE1" <-> "OE2" Residue "P ASP 247": "OD1" <-> "OD2" Residue "P ARG 251": "NH1" <-> "NH2" Residue "P ASP 254": "OD1" <-> "OD2" Residue "P GLU 263": "OE1" <-> "OE2" Residue "P GLU 265": "OE1" <-> "OE2" Residue "P GLU 266": "OE1" <-> "OE2" Residue "P PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 292": "OD1" <-> "OD2" Residue "P TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 331": "OD1" <-> "OD2" Residue "P PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 378": "OE1" <-> "OE2" Residue "P GLU 379": "OE1" <-> "OE2" Residue "P GLU 396": "OE1" <-> "OE2" Residue "P ASP 397": "OD1" <-> "OD2" Residue "P GLU 408": "OE1" <-> "OE2" Residue "P GLU 426": "OE1" <-> "OE2" Residue "P PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 435": "OD1" <-> "OD2" Residue "P PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 481": "OE1" <-> "OE2" Residue "P GLU 485": "OE1" <-> "OE2" Residue "P GLU 504": "OE1" <-> "OE2" Residue "P ASP 514": "OD1" <-> "OD2" Residue "P ARG 522": "NH1" <-> "NH2" Time to flip residues: 0.21s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 63712 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 3982 Classifications: {'peptide': 532} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 520} Chain: "B" Number of atoms: 3982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 3982 Classifications: {'peptide': 532} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 520} Chain: "C" Number of atoms: 3982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 3982 Classifications: {'peptide': 532} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 520} Chain: "D" Number of atoms: 3982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 3982 Classifications: {'peptide': 532} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 520} Chain: "E" Number of atoms: 3982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 3982 Classifications: {'peptide': 532} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 520} Chain: "F" Number of atoms: 3982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 3982 Classifications: {'peptide': 532} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 520} Chain: "G" Number of atoms: 3982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 3982 Classifications: {'peptide': 532} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 520} Chain: "H" Number of atoms: 3982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 3982 Classifications: {'peptide': 532} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 520} Chain: "I" Number of atoms: 3982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 3982 Classifications: {'peptide': 532} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 520} Chain: "J" Number of atoms: 3982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 3982 Classifications: {'peptide': 532} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 520} Chain: "K" Number of atoms: 3982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 3982 Classifications: {'peptide': 532} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 520} Chain: "L" Number of atoms: 3982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 3982 Classifications: {'peptide': 532} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 520} Chain: "M" Number of atoms: 3982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 3982 Classifications: {'peptide': 532} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 520} Chain: "N" Number of atoms: 3982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 3982 Classifications: {'peptide': 532} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 520} Chain: "O" Number of atoms: 3982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 3982 Classifications: {'peptide': 532} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 520} Chain: "P" Number of atoms: 3982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 3982 Classifications: {'peptide': 532} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 520} Residues with excluded nonbonded symmetry interactions: 15 residue: pdb=" N MET B 1 " occ=0.00 ... (6 atoms not shown) pdb=" CE MET B 1 " occ=0.00 residue: pdb=" N MET C 1 " occ=0.00 ... (6 atoms not shown) pdb=" CE MET C 1 " occ=0.00 residue: pdb=" N MET D 1 " occ=0.00 ... (6 atoms not shown) pdb=" CE MET D 1 " occ=0.00 residue: pdb=" N MET E 1 " occ=0.00 ... (6 atoms not shown) pdb=" CE MET E 1 " occ=0.00 residue: pdb=" N MET F 1 " occ=0.00 ... (6 atoms not shown) pdb=" CE MET F 1 " occ=0.00 residue: pdb=" N MET G 1 " occ=0.00 ... (6 atoms not shown) pdb=" CE MET G 1 " occ=0.00 residue: pdb=" N MET H 1 " occ=0.00 ... (6 atoms not shown) pdb=" CE MET H 1 " occ=0.00 residue: pdb=" N MET I 1 " occ=0.00 ... (6 atoms not shown) pdb=" CE MET I 1 " occ=0.00 residue: pdb=" N MET J 1 " occ=0.00 ... (6 atoms not shown) pdb=" CE MET J 1 " occ=0.00 residue: pdb=" N MET K 1 " occ=0.00 ... (6 atoms not shown) pdb=" CE MET K 1 " occ=0.00 residue: pdb=" N MET L 1 " occ=0.00 ... (6 atoms not shown) pdb=" CE MET L 1 " occ=0.00 residue: pdb=" N MET M 1 " occ=0.00 ... (6 atoms not shown) pdb=" CE MET M 1 " occ=0.00 ... (remaining 3 not shown) Time building chain proxies: 22.64, per 1000 atoms: 0.36 Number of scatterers: 63712 At special positions: 0 Unit cell: (176.89, 176.89, 174.23, 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 448 16.00 O 12752 8.00 N 11024 7.00 C 39488 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=32, symmetry=0 Simple disulfide: pdb=" SG CYS A 237 " - pdb=" SG CYS A 286 " distance=2.03 Simple disulfide: pdb=" SG CYS A 470 " - pdb=" SG CYS A 484 " distance=2.02 Simple disulfide: pdb=" SG CYS B 237 " - pdb=" SG CYS B 286 " distance=2.03 Simple disulfide: pdb=" SG CYS B 470 " - pdb=" SG CYS B 484 " distance=2.02 Simple disulfide: pdb=" SG CYS C 237 " - pdb=" SG CYS C 286 " distance=2.03 Simple disulfide: pdb=" SG CYS C 470 " - pdb=" SG CYS C 484 " distance=2.02 Simple disulfide: pdb=" SG CYS D 237 " - pdb=" SG CYS D 286 " distance=2.03 Simple disulfide: pdb=" SG CYS D 470 " - pdb=" SG CYS D 484 " distance=2.02 Simple disulfide: pdb=" SG CYS E 237 " - pdb=" SG CYS E 286 " distance=2.03 Simple disulfide: pdb=" SG CYS E 470 " - pdb=" SG CYS E 484 " distance=2.02 Simple disulfide: pdb=" SG CYS F 237 " - pdb=" SG CYS F 286 " distance=2.03 Simple disulfide: pdb=" SG CYS F 470 " - pdb=" SG CYS F 484 " distance=2.02 Simple disulfide: pdb=" SG CYS G 237 " - pdb=" SG CYS G 286 " distance=2.03 Simple disulfide: pdb=" SG CYS G 470 " - pdb=" SG CYS G 484 " distance=2.02 Simple disulfide: pdb=" SG CYS H 237 " - pdb=" SG CYS H 286 " distance=2.03 Simple disulfide: pdb=" SG CYS H 470 " - pdb=" SG CYS H 484 " distance=2.02 Simple disulfide: pdb=" SG CYS I 237 " - pdb=" SG CYS I 286 " distance=2.03 Simple disulfide: pdb=" SG CYS I 470 " - pdb=" SG CYS I 484 " distance=2.02 Simple disulfide: pdb=" SG CYS J 237 " - pdb=" SG CYS J 286 " distance=2.03 Simple disulfide: pdb=" SG CYS J 470 " - pdb=" SG CYS J 484 " distance=2.02 Simple disulfide: pdb=" SG CYS K 237 " - pdb=" SG CYS K 286 " distance=2.03 Simple disulfide: pdb=" SG CYS K 470 " - pdb=" SG CYS K 484 " distance=2.02 Simple disulfide: pdb=" SG CYS L 237 " - pdb=" SG CYS L 286 " distance=2.03 Simple disulfide: pdb=" SG CYS L 470 " - pdb=" SG CYS L 484 " distance=2.02 Simple disulfide: pdb=" SG CYS M 237 " - pdb=" SG CYS M 286 " distance=2.03 Simple disulfide: pdb=" SG CYS M 470 " - pdb=" SG CYS M 484 " distance=2.02 Simple disulfide: pdb=" SG CYS N 237 " - pdb=" SG CYS N 286 " distance=2.03 Simple disulfide: pdb=" SG CYS N 470 " - pdb=" SG CYS N 484 " distance=2.02 Simple disulfide: pdb=" SG CYS O 237 " - pdb=" SG CYS O 286 " distance=2.03 Simple disulfide: pdb=" SG CYS O 470 " - pdb=" SG CYS O 484 " distance=2.02 Simple disulfide: pdb=" SG CYS P 237 " - pdb=" SG CYS P 286 " distance=2.03 Simple disulfide: pdb=" SG CYS P 470 " - pdb=" SG CYS P 484 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 21.26 Conformation dependent library (CDL) restraints added in 7.2 seconds 16960 Ramachandran restraints generated. 8480 Oldfield, 0 Emsley, 8480 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15680 Finding SS restraints... Secondary structure from input PDB file: 272 helices and 16 sheets defined 46.6% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.44 Creating SS restraints... Processing helix chain 'A' and resid 17 through 37 removed outlier: 3.571A pdb=" N GLN A 21 " --> pdb=" O GLY A 17 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N ARG A 22 " --> pdb=" O ARG A 18 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE A 31 " --> pdb=" O ALA A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 43 Processing helix chain 'A' and resid 60 through 67 removed outlier: 3.974A pdb=" N ILE A 64 " --> pdb=" O ASP A 60 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU A 67 " --> pdb=" O THR A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 87 removed outlier: 3.965A pdb=" N GLU A 80 " --> pdb=" O LYS A 76 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N VAL A 81 " --> pdb=" O MET A 77 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ALA A 82 " --> pdb=" O LEU A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 110 removed outlier: 3.967A pdb=" N THR A 95 " --> pdb=" O ASP A 91 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU A 103 " --> pdb=" O VAL A 99 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU A 104 " --> pdb=" O ALA A 100 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N ARG A 105 " --> pdb=" O GLY A 101 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LYS A 106 " --> pdb=" O GLU A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 136 removed outlier: 4.877A pdb=" N VAL A 120 " --> pdb=" O HIS A 116 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS A 122 " --> pdb=" O THR A 118 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LYS A 136 " --> pdb=" O GLN A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 159 removed outlier: 3.554A pdb=" N THR A 151 " --> pdb=" O LYS A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 184 removed outlier: 5.187A pdb=" N GLU A 172 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU A 176 " --> pdb=" O GLU A 172 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL A 182 " --> pdb=" O VAL A 178 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASP A 183 " --> pdb=" O SER A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 194 removed outlier: 3.785A pdb=" N ILE A 193 " --> pdb=" O ASP A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 280 removed outlier: 4.089A pdb=" N GLU A 263 " --> pdb=" O MET A 259 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU A 266 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N MET A 272 " --> pdb=" O MET A 268 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE A 276 " --> pdb=" O MET A 272 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N SER A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N GLY A 280 " --> pdb=" O ILE A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 301 Processing helix chain 'A' and resid 310 through 319 removed outlier: 3.862A pdb=" N MET A 314 " --> pdb=" O LYS A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 396 removed outlier: 4.154A pdb=" N GLU A 379 " --> pdb=" O HIS A 375 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL A 380 " --> pdb=" O VAL A 376 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASP A 385 " --> pdb=" O ALA A 381 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL A 391 " --> pdb=" O ALA A 387 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY A 392 " --> pdb=" O VAL A 388 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N GLU A 396 " --> pdb=" O GLY A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 419 removed outlier: 3.612A pdb=" N GLU A 410 " --> pdb=" O SER A 406 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N MET A 413 " --> pdb=" O VAL A 409 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA A 419 " --> pdb=" O LEU A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 445 removed outlier: 3.698A pdb=" N ALA A 436 " --> pdb=" O ALA A 432 " (cutoff:3.500A) Proline residue: A 441 - end of helix removed outlier: 3.587A pdb=" N ALA A 445 " --> pdb=" O PRO A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 461 removed outlier: 3.802A pdb=" N VAL A 457 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LYS A 458 " --> pdb=" O GLU A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 510 removed outlier: 4.284A pdb=" N ALA A 502 " --> pdb=" O ALA A 498 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA A 503 " --> pdb=" O ILE A 499 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU A 507 " --> pdb=" O ALA A 503 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N MET A 508 " --> pdb=" O GLU A 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 37 removed outlier: 3.575A pdb=" N GLN B 21 " --> pdb=" O GLY B 17 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N ARG B 22 " --> pdb=" O ARG B 18 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE B 31 " --> pdb=" O ALA B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 43 Processing helix chain 'B' and resid 60 through 67 removed outlier: 3.976A pdb=" N ILE B 64 " --> pdb=" O ASP B 60 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU B 67 " --> pdb=" O THR B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 87 removed outlier: 3.963A pdb=" N GLU B 80 " --> pdb=" O LYS B 76 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N VAL B 81 " --> pdb=" O MET B 77 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA B 82 " --> pdb=" O LEU B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 110 removed outlier: 3.965A pdb=" N THR B 95 " --> pdb=" O ASP B 91 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU B 103 " --> pdb=" O VAL B 99 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU B 104 " --> pdb=" O ALA B 100 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N ARG B 105 " --> pdb=" O GLY B 101 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LYS B 106 " --> pdb=" O GLU B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 136 removed outlier: 4.874A pdb=" N VAL B 120 " --> pdb=" O HIS B 116 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS B 122 " --> pdb=" O THR B 118 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LYS B 136 " --> pdb=" O GLN B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 159 removed outlier: 3.557A pdb=" N THR B 151 " --> pdb=" O LYS B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 184 removed outlier: 5.191A pdb=" N GLU B 172 " --> pdb=" O GLU B 168 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU B 176 " --> pdb=" O GLU B 172 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL B 182 " --> pdb=" O VAL B 178 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASP B 183 " --> pdb=" O SER B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 194 removed outlier: 3.786A pdb=" N ILE B 193 " --> pdb=" O ASP B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 280 removed outlier: 4.089A pdb=" N GLU B 263 " --> pdb=" O MET B 259 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU B 266 " --> pdb=" O ILE B 262 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N MET B 272 " --> pdb=" O MET B 268 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE B 276 " --> pdb=" O MET B 272 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N SER B 279 " --> pdb=" O GLU B 275 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N GLY B 280 " --> pdb=" O ILE B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 301 Processing helix chain 'B' and resid 310 through 319 removed outlier: 3.854A pdb=" N MET B 314 " --> pdb=" O LYS B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 396 removed outlier: 4.147A pdb=" N GLU B 379 " --> pdb=" O HIS B 375 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL B 380 " --> pdb=" O VAL B 376 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASP B 385 " --> pdb=" O ALA B 381 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL B 391 " --> pdb=" O ALA B 387 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLY B 392 " --> pdb=" O VAL B 388 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR B 394 " --> pdb=" O VAL B 390 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N GLU B 396 " --> pdb=" O GLY B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 419 removed outlier: 3.608A pdb=" N GLU B 410 " --> pdb=" O SER B 406 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N MET B 413 " --> pdb=" O VAL B 409 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA B 419 " --> pdb=" O LEU B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 445 removed outlier: 3.695A pdb=" N ALA B 436 " --> pdb=" O ALA B 432 " (cutoff:3.500A) Proline residue: B 441 - end of helix removed outlier: 3.588A pdb=" N ALA B 445 " --> pdb=" O PRO B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 461 removed outlier: 3.802A pdb=" N VAL B 457 " --> pdb=" O ILE B 453 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LYS B 458 " --> pdb=" O GLU B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 510 removed outlier: 4.287A pdb=" N ALA B 502 " --> pdb=" O ALA B 498 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA B 503 " --> pdb=" O ILE B 499 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU B 507 " --> pdb=" O ALA B 503 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N MET B 508 " --> pdb=" O GLU B 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 37 removed outlier: 3.574A pdb=" N GLN C 21 " --> pdb=" O GLY C 17 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N ARG C 22 " --> pdb=" O ARG C 18 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE C 31 " --> pdb=" O ALA C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 43 Processing helix chain 'C' and resid 60 through 67 removed outlier: 3.977A pdb=" N ILE C 64 " --> pdb=" O ASP C 60 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU C 67 " --> pdb=" O THR C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 87 removed outlier: 3.960A pdb=" N GLU C 80 " --> pdb=" O LYS C 76 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N VAL C 81 " --> pdb=" O MET C 77 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA C 82 " --> pdb=" O LEU C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 110 removed outlier: 3.965A pdb=" N THR C 95 " --> pdb=" O ASP C 91 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU C 103 " --> pdb=" O VAL C 99 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU C 104 " --> pdb=" O ALA C 100 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N ARG C 105 " --> pdb=" O GLY C 101 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LYS C 106 " --> pdb=" O GLU C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 136 removed outlier: 4.878A pdb=" N VAL C 120 " --> pdb=" O HIS C 116 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS C 122 " --> pdb=" O THR C 118 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYS C 136 " --> pdb=" O GLN C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 159 removed outlier: 3.554A pdb=" N THR C 151 " --> pdb=" O LYS C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 184 removed outlier: 5.190A pdb=" N GLU C 172 " --> pdb=" O GLU C 168 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU C 176 " --> pdb=" O GLU C 172 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL C 182 " --> pdb=" O VAL C 178 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASP C 183 " --> pdb=" O SER C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 194 removed outlier: 3.788A pdb=" N ILE C 193 " --> pdb=" O ASP C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 280 removed outlier: 4.096A pdb=" N GLU C 263 " --> pdb=" O MET C 259 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU C 266 " --> pdb=" O ILE C 262 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N MET C 272 " --> pdb=" O MET C 268 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE C 276 " --> pdb=" O MET C 272 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N SER C 279 " --> pdb=" O GLU C 275 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N GLY C 280 " --> pdb=" O ILE C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 301 Processing helix chain 'C' and resid 310 through 319 removed outlier: 3.853A pdb=" N MET C 314 " --> pdb=" O LYS C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 396 removed outlier: 4.150A pdb=" N GLU C 379 " --> pdb=" O HIS C 375 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL C 380 " --> pdb=" O VAL C 376 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP C 385 " --> pdb=" O ALA C 381 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL C 391 " --> pdb=" O ALA C 387 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY C 392 " --> pdb=" O VAL C 388 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N GLU C 396 " --> pdb=" O GLY C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 419 removed outlier: 3.610A pdb=" N GLU C 410 " --> pdb=" O SER C 406 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N MET C 413 " --> pdb=" O VAL C 409 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA C 419 " --> pdb=" O LEU C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 428 through 445 removed outlier: 3.693A pdb=" N ALA C 436 " --> pdb=" O ALA C 432 " (cutoff:3.500A) Proline residue: C 441 - end of helix removed outlier: 3.587A pdb=" N ALA C 445 " --> pdb=" O PRO C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 453 through 461 removed outlier: 3.803A pdb=" N VAL C 457 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS C 458 " --> pdb=" O GLU C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 510 removed outlier: 4.285A pdb=" N ALA C 502 " --> pdb=" O ALA C 498 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA C 503 " --> pdb=" O ILE C 499 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU C 507 " --> pdb=" O ALA C 503 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N MET C 508 " --> pdb=" O GLU C 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 37 removed outlier: 3.572A pdb=" N GLN D 21 " --> pdb=" O GLY D 17 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N ARG D 22 " --> pdb=" O ARG D 18 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE D 31 " --> pdb=" O ALA D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 43 Processing helix chain 'D' and resid 60 through 67 removed outlier: 3.976A pdb=" N ILE D 64 " --> pdb=" O ASP D 60 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU D 67 " --> pdb=" O THR D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 87 removed outlier: 3.958A pdb=" N GLU D 80 " --> pdb=" O LYS D 76 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N VAL D 81 " --> pdb=" O MET D 77 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA D 82 " --> pdb=" O LEU D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 110 removed outlier: 3.965A pdb=" N THR D 95 " --> pdb=" O ASP D 91 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU D 103 " --> pdb=" O VAL D 99 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU D 104 " --> pdb=" O ALA D 100 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ARG D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LYS D 106 " --> pdb=" O GLU D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 136 removed outlier: 4.874A pdb=" N VAL D 120 " --> pdb=" O HIS D 116 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS D 122 " --> pdb=" O THR D 118 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LYS D 136 " --> pdb=" O GLN D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 159 removed outlier: 3.556A pdb=" N THR D 151 " --> pdb=" O LYS D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 184 removed outlier: 5.191A pdb=" N GLU D 172 " --> pdb=" O GLU D 168 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU D 176 " --> pdb=" O GLU D 172 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL D 182 " --> pdb=" O VAL D 178 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP D 183 " --> pdb=" O SER D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 194 removed outlier: 3.786A pdb=" N ILE D 193 " --> pdb=" O ASP D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 280 removed outlier: 4.090A pdb=" N GLU D 263 " --> pdb=" O MET D 259 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU D 266 " --> pdb=" O ILE D 262 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N MET D 272 " --> pdb=" O MET D 268 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE D 276 " --> pdb=" O MET D 272 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N SER D 279 " --> pdb=" O GLU D 275 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N GLY D 280 " --> pdb=" O ILE D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 301 Processing helix chain 'D' and resid 310 through 319 removed outlier: 3.850A pdb=" N MET D 314 " --> pdb=" O LYS D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 396 removed outlier: 4.148A pdb=" N GLU D 379 " --> pdb=" O HIS D 375 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL D 380 " --> pdb=" O VAL D 376 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASP D 385 " --> pdb=" O ALA D 381 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL D 391 " --> pdb=" O ALA D 387 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY D 392 " --> pdb=" O VAL D 388 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N GLU D 396 " --> pdb=" O GLY D 392 " (cutoff:3.500A) Processing helix chain 'D' and resid 406 through 419 removed outlier: 3.612A pdb=" N GLU D 410 " --> pdb=" O SER D 406 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N MET D 413 " --> pdb=" O VAL D 409 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA D 419 " --> pdb=" O LEU D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 428 through 445 removed outlier: 3.693A pdb=" N ALA D 436 " --> pdb=" O ALA D 432 " (cutoff:3.500A) Proline residue: D 441 - end of helix removed outlier: 3.587A pdb=" N ALA D 445 " --> pdb=" O PRO D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 453 through 461 removed outlier: 3.802A pdb=" N VAL D 457 " --> pdb=" O ILE D 453 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LYS D 458 " --> pdb=" O GLU D 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 494 through 510 removed outlier: 4.285A pdb=" N ALA D 502 " --> pdb=" O ALA D 498 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA D 503 " --> pdb=" O ILE D 499 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU D 507 " --> pdb=" O ALA D 503 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N MET D 508 " --> pdb=" O GLU D 504 " (cutoff:3.500A) Processing helix chain 'E' and resid 17 through 37 removed outlier: 3.574A pdb=" N GLN E 21 " --> pdb=" O GLY E 17 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N ARG E 22 " --> pdb=" O ARG E 18 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE E 31 " --> pdb=" O ALA E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 43 Processing helix chain 'E' and resid 60 through 67 removed outlier: 3.977A pdb=" N ILE E 64 " --> pdb=" O ASP E 60 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU E 67 " --> pdb=" O THR E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 87 removed outlier: 3.960A pdb=" N GLU E 80 " --> pdb=" O LYS E 76 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N VAL E 81 " --> pdb=" O MET E 77 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA E 82 " --> pdb=" O LEU E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 110 removed outlier: 3.965A pdb=" N THR E 95 " --> pdb=" O ASP E 91 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU E 103 " --> pdb=" O VAL E 99 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU E 104 " --> pdb=" O ALA E 100 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N ARG E 105 " --> pdb=" O GLY E 101 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LYS E 106 " --> pdb=" O GLU E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 116 through 136 removed outlier: 4.878A pdb=" N VAL E 120 " --> pdb=" O HIS E 116 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS E 122 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYS E 136 " --> pdb=" O GLN E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 159 removed outlier: 3.554A pdb=" N THR E 151 " --> pdb=" O LYS E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 184 removed outlier: 5.190A pdb=" N GLU E 172 " --> pdb=" O GLU E 168 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU E 176 " --> pdb=" O GLU E 172 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL E 182 " --> pdb=" O VAL E 178 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASP E 183 " --> pdb=" O SER E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 194 removed outlier: 3.788A pdb=" N ILE E 193 " --> pdb=" O ASP E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 280 removed outlier: 4.096A pdb=" N GLU E 263 " --> pdb=" O MET E 259 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU E 266 " --> pdb=" O ILE E 262 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N MET E 272 " --> pdb=" O MET E 268 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE E 276 " --> pdb=" O MET E 272 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N SER E 279 " --> pdb=" O GLU E 275 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N GLY E 280 " --> pdb=" O ILE E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 301 Processing helix chain 'E' and resid 310 through 319 removed outlier: 3.853A pdb=" N MET E 314 " --> pdb=" O LYS E 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 374 through 396 removed outlier: 4.150A pdb=" N GLU E 379 " --> pdb=" O HIS E 375 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL E 380 " --> pdb=" O VAL E 376 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP E 385 " --> pdb=" O ALA E 381 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL E 391 " --> pdb=" O ALA E 387 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY E 392 " --> pdb=" O VAL E 388 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N GLU E 396 " --> pdb=" O GLY E 392 " (cutoff:3.500A) Processing helix chain 'E' and resid 406 through 419 removed outlier: 3.610A pdb=" N GLU E 410 " --> pdb=" O SER E 406 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N MET E 413 " --> pdb=" O VAL E 409 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA E 419 " --> pdb=" O LEU E 415 " (cutoff:3.500A) Processing helix chain 'E' and resid 428 through 445 removed outlier: 3.693A pdb=" N ALA E 436 " --> pdb=" O ALA E 432 " (cutoff:3.500A) Proline residue: E 441 - end of helix removed outlier: 3.587A pdb=" N ALA E 445 " --> pdb=" O PRO E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 453 through 461 removed outlier: 3.803A pdb=" N VAL E 457 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS E 458 " --> pdb=" O GLU E 454 " (cutoff:3.500A) Processing helix chain 'E' and resid 494 through 510 removed outlier: 4.285A pdb=" N ALA E 502 " --> pdb=" O ALA E 498 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA E 503 " --> pdb=" O ILE E 499 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU E 507 " --> pdb=" O ALA E 503 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N MET E 508 " --> pdb=" O GLU E 504 " (cutoff:3.500A) Processing helix chain 'F' and resid 17 through 37 removed outlier: 3.572A pdb=" N GLN F 21 " --> pdb=" O GLY F 17 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N ARG F 22 " --> pdb=" O ARG F 18 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE F 31 " --> pdb=" O ALA F 27 " (cutoff:3.500A) Processing helix chain 'F' and resid 39 through 43 Processing helix chain 'F' and resid 60 through 67 removed outlier: 3.976A pdb=" N ILE F 64 " --> pdb=" O ASP F 60 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU F 67 " --> pdb=" O THR F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 87 removed outlier: 3.958A pdb=" N GLU F 80 " --> pdb=" O LYS F 76 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N VAL F 81 " --> pdb=" O MET F 77 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA F 82 " --> pdb=" O LEU F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 110 removed outlier: 3.965A pdb=" N THR F 95 " --> pdb=" O ASP F 91 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU F 103 " --> pdb=" O VAL F 99 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU F 104 " --> pdb=" O ALA F 100 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ARG F 105 " --> pdb=" O GLY F 101 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LYS F 106 " --> pdb=" O GLU F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 136 removed outlier: 4.874A pdb=" N VAL F 120 " --> pdb=" O HIS F 116 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS F 122 " --> pdb=" O THR F 118 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LYS F 136 " --> pdb=" O GLN F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 147 through 159 removed outlier: 3.556A pdb=" N THR F 151 " --> pdb=" O LYS F 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 184 removed outlier: 5.191A pdb=" N GLU F 172 " --> pdb=" O GLU F 168 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU F 176 " --> pdb=" O GLU F 172 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL F 182 " --> pdb=" O VAL F 178 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP F 183 " --> pdb=" O SER F 179 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 194 removed outlier: 3.786A pdb=" N ILE F 193 " --> pdb=" O ASP F 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 280 removed outlier: 4.090A pdb=" N GLU F 263 " --> pdb=" O MET F 259 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU F 266 " --> pdb=" O ILE F 262 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N MET F 272 " --> pdb=" O MET F 268 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE F 276 " --> pdb=" O MET F 272 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N SER F 279 " --> pdb=" O GLU F 275 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N GLY F 280 " --> pdb=" O ILE F 276 " (cutoff:3.500A) Processing helix chain 'F' and resid 295 through 301 Processing helix chain 'F' and resid 310 through 319 removed outlier: 3.850A pdb=" N MET F 314 " --> pdb=" O LYS F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 374 through 396 removed outlier: 4.148A pdb=" N GLU F 379 " --> pdb=" O HIS F 375 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL F 380 " --> pdb=" O VAL F 376 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASP F 385 " --> pdb=" O ALA F 381 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL F 391 " --> pdb=" O ALA F 387 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY F 392 " --> pdb=" O VAL F 388 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N GLU F 396 " --> pdb=" O GLY F 392 " (cutoff:3.500A) Processing helix chain 'F' and resid 406 through 419 removed outlier: 3.612A pdb=" N GLU F 410 " --> pdb=" O SER F 406 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N MET F 413 " --> pdb=" O VAL F 409 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA F 419 " --> pdb=" O LEU F 415 " (cutoff:3.500A) Processing helix chain 'F' and resid 428 through 445 removed outlier: 3.693A pdb=" N ALA F 436 " --> pdb=" O ALA F 432 " (cutoff:3.500A) Proline residue: F 441 - end of helix removed outlier: 3.587A pdb=" N ALA F 445 " --> pdb=" O PRO F 441 " (cutoff:3.500A) Processing helix chain 'F' and resid 453 through 461 removed outlier: 3.802A pdb=" N VAL F 457 " --> pdb=" O ILE F 453 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LYS F 458 " --> pdb=" O GLU F 454 " (cutoff:3.500A) Processing helix chain 'F' and resid 494 through 510 removed outlier: 4.285A pdb=" N ALA F 502 " --> pdb=" O ALA F 498 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA F 503 " --> pdb=" O ILE F 499 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU F 507 " --> pdb=" O ALA F 503 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N MET F 508 " --> pdb=" O GLU F 504 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 37 removed outlier: 3.574A pdb=" N GLN G 21 " --> pdb=" O GLY G 17 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N ARG G 22 " --> pdb=" O ARG G 18 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE G 31 " --> pdb=" O ALA G 27 " (cutoff:3.500A) Processing helix chain 'G' and resid 39 through 43 Processing helix chain 'G' and resid 60 through 67 removed outlier: 3.977A pdb=" N ILE G 64 " --> pdb=" O ASP G 60 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU G 67 " --> pdb=" O THR G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 87 removed outlier: 3.960A pdb=" N GLU G 80 " --> pdb=" O LYS G 76 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N VAL G 81 " --> pdb=" O MET G 77 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA G 82 " --> pdb=" O LEU G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 110 removed outlier: 3.965A pdb=" N THR G 95 " --> pdb=" O ASP G 91 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU G 103 " --> pdb=" O VAL G 99 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU G 104 " --> pdb=" O ALA G 100 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N ARG G 105 " --> pdb=" O GLY G 101 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LYS G 106 " --> pdb=" O GLU G 102 " (cutoff:3.500A) Processing helix chain 'G' and resid 116 through 136 removed outlier: 4.878A pdb=" N VAL G 120 " --> pdb=" O HIS G 116 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS G 122 " --> pdb=" O THR G 118 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYS G 136 " --> pdb=" O GLN G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 147 through 159 removed outlier: 3.554A pdb=" N THR G 151 " --> pdb=" O LYS G 147 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 184 removed outlier: 5.190A pdb=" N GLU G 172 " --> pdb=" O GLU G 168 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU G 176 " --> pdb=" O GLU G 172 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL G 182 " --> pdb=" O VAL G 178 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASP G 183 " --> pdb=" O SER G 179 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 194 removed outlier: 3.788A pdb=" N ILE G 193 " --> pdb=" O ASP G 189 " (cutoff:3.500A) Processing helix chain 'G' and resid 258 through 280 removed outlier: 4.096A pdb=" N GLU G 263 " --> pdb=" O MET G 259 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU G 266 " --> pdb=" O ILE G 262 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N MET G 272 " --> pdb=" O MET G 268 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE G 276 " --> pdb=" O MET G 272 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N SER G 279 " --> pdb=" O GLU G 275 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N GLY G 280 " --> pdb=" O ILE G 276 " (cutoff:3.500A) Processing helix chain 'G' and resid 295 through 301 Processing helix chain 'G' and resid 310 through 319 removed outlier: 3.853A pdb=" N MET G 314 " --> pdb=" O LYS G 310 " (cutoff:3.500A) Processing helix chain 'G' and resid 374 through 396 removed outlier: 4.150A pdb=" N GLU G 379 " --> pdb=" O HIS G 375 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL G 380 " --> pdb=" O VAL G 376 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP G 385 " --> pdb=" O ALA G 381 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL G 391 " --> pdb=" O ALA G 387 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY G 392 " --> pdb=" O VAL G 388 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N GLU G 396 " --> pdb=" O GLY G 392 " (cutoff:3.500A) Processing helix chain 'G' and resid 406 through 419 removed outlier: 3.610A pdb=" N GLU G 410 " --> pdb=" O SER G 406 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N MET G 413 " --> pdb=" O VAL G 409 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA G 419 " --> pdb=" O LEU G 415 " (cutoff:3.500A) Processing helix chain 'G' and resid 428 through 445 removed outlier: 3.693A pdb=" N ALA G 436 " --> pdb=" O ALA G 432 " (cutoff:3.500A) Proline residue: G 441 - end of helix removed outlier: 3.587A pdb=" N ALA G 445 " --> pdb=" O PRO G 441 " (cutoff:3.500A) Processing helix chain 'G' and resid 453 through 461 removed outlier: 3.803A pdb=" N VAL G 457 " --> pdb=" O ILE G 453 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS G 458 " --> pdb=" O GLU G 454 " (cutoff:3.500A) Processing helix chain 'G' and resid 494 through 510 removed outlier: 4.285A pdb=" N ALA G 502 " --> pdb=" O ALA G 498 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA G 503 " --> pdb=" O ILE G 499 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU G 507 " --> pdb=" O ALA G 503 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N MET G 508 " --> pdb=" O GLU G 504 " (cutoff:3.500A) Processing helix chain 'H' and resid 17 through 37 removed outlier: 3.572A pdb=" N GLN H 21 " --> pdb=" O GLY H 17 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N ARG H 22 " --> pdb=" O ARG H 18 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE H 31 " --> pdb=" O ALA H 27 " (cutoff:3.500A) Processing helix chain 'H' and resid 39 through 43 Processing helix chain 'H' and resid 60 through 67 removed outlier: 3.976A pdb=" N ILE H 64 " --> pdb=" O ASP H 60 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU H 67 " --> pdb=" O THR H 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 87 removed outlier: 3.958A pdb=" N GLU H 80 " --> pdb=" O LYS H 76 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N VAL H 81 " --> pdb=" O MET H 77 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA H 82 " --> pdb=" O LEU H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 91 through 110 removed outlier: 3.965A pdb=" N THR H 95 " --> pdb=" O ASP H 91 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU H 103 " --> pdb=" O VAL H 99 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU H 104 " --> pdb=" O ALA H 100 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ARG H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LYS H 106 " --> pdb=" O GLU H 102 " (cutoff:3.500A) Processing helix chain 'H' and resid 116 through 136 removed outlier: 4.874A pdb=" N VAL H 120 " --> pdb=" O HIS H 116 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS H 122 " --> pdb=" O THR H 118 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LYS H 136 " --> pdb=" O GLN H 132 " (cutoff:3.500A) Processing helix chain 'H' and resid 147 through 159 removed outlier: 3.556A pdb=" N THR H 151 " --> pdb=" O LYS H 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 168 through 184 removed outlier: 5.191A pdb=" N GLU H 172 " --> pdb=" O GLU H 168 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU H 176 " --> pdb=" O GLU H 172 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL H 182 " --> pdb=" O VAL H 178 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP H 183 " --> pdb=" O SER H 179 " (cutoff:3.500A) Processing helix chain 'H' and resid 187 through 194 removed outlier: 3.786A pdb=" N ILE H 193 " --> pdb=" O ASP H 189 " (cutoff:3.500A) Processing helix chain 'H' and resid 258 through 280 removed outlier: 4.092A pdb=" N GLU H 263 " --> pdb=" O MET H 259 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU H 266 " --> pdb=" O ILE H 262 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N MET H 272 " --> pdb=" O MET H 268 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE H 276 " --> pdb=" O MET H 272 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N SER H 279 " --> pdb=" O GLU H 275 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N GLY H 280 " --> pdb=" O ILE H 276 " (cutoff:3.500A) Processing helix chain 'H' and resid 295 through 301 Processing helix chain 'H' and resid 310 through 319 removed outlier: 3.850A pdb=" N MET H 314 " --> pdb=" O LYS H 310 " (cutoff:3.500A) Processing helix chain 'H' and resid 374 through 396 removed outlier: 4.148A pdb=" N GLU H 379 " --> pdb=" O HIS H 375 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL H 380 " --> pdb=" O VAL H 376 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASP H 385 " --> pdb=" O ALA H 381 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL H 391 " --> pdb=" O ALA H 387 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY H 392 " --> pdb=" O VAL H 388 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N GLU H 396 " --> pdb=" O GLY H 392 " (cutoff:3.500A) Processing helix chain 'H' and resid 406 through 419 removed outlier: 3.612A pdb=" N GLU H 410 " --> pdb=" O SER H 406 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N MET H 413 " --> pdb=" O VAL H 409 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA H 419 " --> pdb=" O LEU H 415 " (cutoff:3.500A) Processing helix chain 'H' and resid 428 through 445 removed outlier: 3.693A pdb=" N ALA H 436 " --> pdb=" O ALA H 432 " (cutoff:3.500A) Proline residue: H 441 - end of helix removed outlier: 3.587A pdb=" N ALA H 445 " --> pdb=" O PRO H 441 " (cutoff:3.500A) Processing helix chain 'H' and resid 453 through 461 removed outlier: 3.802A pdb=" N VAL H 457 " --> pdb=" O ILE H 453 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LYS H 458 " --> pdb=" O GLU H 454 " (cutoff:3.500A) Processing helix chain 'H' and resid 494 through 510 removed outlier: 4.284A pdb=" N ALA H 502 " --> pdb=" O ALA H 498 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA H 503 " --> pdb=" O ILE H 499 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU H 507 " --> pdb=" O ALA H 503 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N MET H 508 " --> pdb=" O GLU H 504 " (cutoff:3.500A) Processing helix chain 'I' and resid 17 through 37 removed outlier: 3.572A pdb=" N GLN I 21 " --> pdb=" O GLY I 17 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N ARG I 22 " --> pdb=" O ARG I 18 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE I 31 " --> pdb=" O ALA I 27 " (cutoff:3.500A) Processing helix chain 'I' and resid 39 through 43 Processing helix chain 'I' and resid 60 through 67 removed outlier: 3.976A pdb=" N ILE I 64 " --> pdb=" O ASP I 60 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU I 67 " --> pdb=" O THR I 63 " (cutoff:3.500A) Processing helix chain 'I' and resid 74 through 87 removed outlier: 3.958A pdb=" N GLU I 80 " --> pdb=" O LYS I 76 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N VAL I 81 " --> pdb=" O MET I 77 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA I 82 " --> pdb=" O LEU I 78 " (cutoff:3.500A) Processing helix chain 'I' and resid 91 through 110 removed outlier: 3.965A pdb=" N THR I 95 " --> pdb=" O ASP I 91 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU I 103 " --> pdb=" O VAL I 99 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU I 104 " --> pdb=" O ALA I 100 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ARG I 105 " --> pdb=" O GLY I 101 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LYS I 106 " --> pdb=" O GLU I 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 116 through 136 removed outlier: 4.874A pdb=" N VAL I 120 " --> pdb=" O HIS I 116 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS I 122 " --> pdb=" O THR I 118 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LYS I 136 " --> pdb=" O GLN I 132 " (cutoff:3.500A) Processing helix chain 'I' and resid 147 through 159 removed outlier: 3.556A pdb=" N THR I 151 " --> pdb=" O LYS I 147 " (cutoff:3.500A) Processing helix chain 'I' and resid 168 through 184 removed outlier: 5.191A pdb=" N GLU I 172 " --> pdb=" O GLU I 168 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU I 176 " --> pdb=" O GLU I 172 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL I 182 " --> pdb=" O VAL I 178 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP I 183 " --> pdb=" O SER I 179 " (cutoff:3.500A) Processing helix chain 'I' and resid 187 through 194 removed outlier: 3.786A pdb=" N ILE I 193 " --> pdb=" O ASP I 189 " (cutoff:3.500A) Processing helix chain 'I' and resid 258 through 280 removed outlier: 4.089A pdb=" N GLU I 263 " --> pdb=" O MET I 259 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU I 266 " --> pdb=" O ILE I 262 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N MET I 272 " --> pdb=" O MET I 268 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE I 276 " --> pdb=" O MET I 272 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N SER I 279 " --> pdb=" O GLU I 275 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N GLY I 280 " --> pdb=" O ILE I 276 " (cutoff:3.500A) Processing helix chain 'I' and resid 295 through 301 Processing helix chain 'I' and resid 310 through 319 removed outlier: 3.850A pdb=" N MET I 314 " --> pdb=" O LYS I 310 " (cutoff:3.500A) Processing helix chain 'I' and resid 374 through 396 removed outlier: 4.148A pdb=" N GLU I 379 " --> pdb=" O HIS I 375 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL I 380 " --> pdb=" O VAL I 376 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASP I 385 " --> pdb=" O ALA I 381 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL I 391 " --> pdb=" O ALA I 387 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY I 392 " --> pdb=" O VAL I 388 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N GLU I 396 " --> pdb=" O GLY I 392 " (cutoff:3.500A) Processing helix chain 'I' and resid 406 through 419 removed outlier: 3.612A pdb=" N GLU I 410 " --> pdb=" O SER I 406 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N MET I 413 " --> pdb=" O VAL I 409 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA I 419 " --> pdb=" O LEU I 415 " (cutoff:3.500A) Processing helix chain 'I' and resid 428 through 445 removed outlier: 3.693A pdb=" N ALA I 436 " --> pdb=" O ALA I 432 " (cutoff:3.500A) Proline residue: I 441 - end of helix removed outlier: 3.587A pdb=" N ALA I 445 " --> pdb=" O PRO I 441 " (cutoff:3.500A) Processing helix chain 'I' and resid 453 through 461 removed outlier: 3.802A pdb=" N VAL I 457 " --> pdb=" O ILE I 453 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LYS I 458 " --> pdb=" O GLU I 454 " (cutoff:3.500A) Processing helix chain 'I' and resid 494 through 510 removed outlier: 4.285A pdb=" N ALA I 502 " --> pdb=" O ALA I 498 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA I 503 " --> pdb=" O ILE I 499 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU I 507 " --> pdb=" O ALA I 503 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N MET I 508 " --> pdb=" O GLU I 504 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 37 removed outlier: 3.574A pdb=" N GLN J 21 " --> pdb=" O GLY J 17 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N ARG J 22 " --> pdb=" O ARG J 18 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE J 31 " --> pdb=" O ALA J 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 39 through 43 Processing helix chain 'J' and resid 60 through 67 removed outlier: 3.977A pdb=" N ILE J 64 " --> pdb=" O ASP J 60 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU J 67 " --> pdb=" O THR J 63 " (cutoff:3.500A) Processing helix chain 'J' and resid 74 through 87 removed outlier: 3.960A pdb=" N GLU J 80 " --> pdb=" O LYS J 76 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N VAL J 81 " --> pdb=" O MET J 77 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA J 82 " --> pdb=" O LEU J 78 " (cutoff:3.500A) Processing helix chain 'J' and resid 91 through 110 removed outlier: 3.965A pdb=" N THR J 95 " --> pdb=" O ASP J 91 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU J 103 " --> pdb=" O VAL J 99 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU J 104 " --> pdb=" O ALA J 100 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N ARG J 105 " --> pdb=" O GLY J 101 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LYS J 106 " --> pdb=" O GLU J 102 " (cutoff:3.500A) Processing helix chain 'J' and resid 116 through 136 removed outlier: 4.878A pdb=" N VAL J 120 " --> pdb=" O HIS J 116 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS J 122 " --> pdb=" O THR J 118 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYS J 136 " --> pdb=" O GLN J 132 " (cutoff:3.500A) Processing helix chain 'J' and resid 147 through 159 removed outlier: 3.554A pdb=" N THR J 151 " --> pdb=" O LYS J 147 " (cutoff:3.500A) Processing helix chain 'J' and resid 168 through 184 removed outlier: 5.190A pdb=" N GLU J 172 " --> pdb=" O GLU J 168 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU J 176 " --> pdb=" O GLU J 172 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL J 182 " --> pdb=" O VAL J 178 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASP J 183 " --> pdb=" O SER J 179 " (cutoff:3.500A) Processing helix chain 'J' and resid 187 through 194 removed outlier: 3.788A pdb=" N ILE J 193 " --> pdb=" O ASP J 189 " (cutoff:3.500A) Processing helix chain 'J' and resid 258 through 280 removed outlier: 4.095A pdb=" N GLU J 263 " --> pdb=" O MET J 259 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU J 266 " --> pdb=" O ILE J 262 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N MET J 272 " --> pdb=" O MET J 268 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE J 276 " --> pdb=" O MET J 272 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N SER J 279 " --> pdb=" O GLU J 275 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N GLY J 280 " --> pdb=" O ILE J 276 " (cutoff:3.500A) Processing helix chain 'J' and resid 295 through 301 Processing helix chain 'J' and resid 310 through 319 removed outlier: 3.853A pdb=" N MET J 314 " --> pdb=" O LYS J 310 " (cutoff:3.500A) Processing helix chain 'J' and resid 374 through 396 removed outlier: 4.150A pdb=" N GLU J 379 " --> pdb=" O HIS J 375 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL J 380 " --> pdb=" O VAL J 376 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP J 385 " --> pdb=" O ALA J 381 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL J 391 " --> pdb=" O ALA J 387 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY J 392 " --> pdb=" O VAL J 388 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N GLU J 396 " --> pdb=" O GLY J 392 " (cutoff:3.500A) Processing helix chain 'J' and resid 406 through 419 removed outlier: 3.610A pdb=" N GLU J 410 " --> pdb=" O SER J 406 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N MET J 413 " --> pdb=" O VAL J 409 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA J 419 " --> pdb=" O LEU J 415 " (cutoff:3.500A) Processing helix chain 'J' and resid 428 through 445 removed outlier: 3.693A pdb=" N ALA J 436 " --> pdb=" O ALA J 432 " (cutoff:3.500A) Proline residue: J 441 - end of helix removed outlier: 3.587A pdb=" N ALA J 445 " --> pdb=" O PRO J 441 " (cutoff:3.500A) Processing helix chain 'J' and resid 453 through 461 removed outlier: 3.803A pdb=" N VAL J 457 " --> pdb=" O ILE J 453 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS J 458 " --> pdb=" O GLU J 454 " (cutoff:3.500A) Processing helix chain 'J' and resid 494 through 510 removed outlier: 4.285A pdb=" N ALA J 502 " --> pdb=" O ALA J 498 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA J 503 " --> pdb=" O ILE J 499 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU J 507 " --> pdb=" O ALA J 503 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N MET J 508 " --> pdb=" O GLU J 504 " (cutoff:3.500A) Processing helix chain 'K' and resid 17 through 37 removed outlier: 3.572A pdb=" N GLN K 21 " --> pdb=" O GLY K 17 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N ARG K 22 " --> pdb=" O ARG K 18 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE K 31 " --> pdb=" O ALA K 27 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 43 Processing helix chain 'K' and resid 60 through 67 removed outlier: 3.976A pdb=" N ILE K 64 " --> pdb=" O ASP K 60 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU K 67 " --> pdb=" O THR K 63 " (cutoff:3.500A) Processing helix chain 'K' and resid 74 through 87 removed outlier: 3.958A pdb=" N GLU K 80 " --> pdb=" O LYS K 76 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N VAL K 81 " --> pdb=" O MET K 77 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA K 82 " --> pdb=" O LEU K 78 " (cutoff:3.500A) Processing helix chain 'K' and resid 91 through 110 removed outlier: 3.965A pdb=" N THR K 95 " --> pdb=" O ASP K 91 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU K 103 " --> pdb=" O VAL K 99 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU K 104 " --> pdb=" O ALA K 100 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ARG K 105 " --> pdb=" O GLY K 101 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LYS K 106 " --> pdb=" O GLU K 102 " (cutoff:3.500A) Processing helix chain 'K' and resid 116 through 136 removed outlier: 4.874A pdb=" N VAL K 120 " --> pdb=" O HIS K 116 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS K 122 " --> pdb=" O THR K 118 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LYS K 136 " --> pdb=" O GLN K 132 " (cutoff:3.500A) Processing helix chain 'K' and resid 147 through 159 removed outlier: 3.556A pdb=" N THR K 151 " --> pdb=" O LYS K 147 " (cutoff:3.500A) Processing helix chain 'K' and resid 168 through 184 removed outlier: 5.191A pdb=" N GLU K 172 " --> pdb=" O GLU K 168 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU K 176 " --> pdb=" O GLU K 172 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL K 182 " --> pdb=" O VAL K 178 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP K 183 " --> pdb=" O SER K 179 " (cutoff:3.500A) Processing helix chain 'K' and resid 187 through 194 removed outlier: 3.786A pdb=" N ILE K 193 " --> pdb=" O ASP K 189 " (cutoff:3.500A) Processing helix chain 'K' and resid 258 through 280 removed outlier: 4.089A pdb=" N GLU K 263 " --> pdb=" O MET K 259 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU K 266 " --> pdb=" O ILE K 262 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N MET K 272 " --> pdb=" O MET K 268 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE K 276 " --> pdb=" O MET K 272 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N SER K 279 " --> pdb=" O GLU K 275 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N GLY K 280 " --> pdb=" O ILE K 276 " (cutoff:3.500A) Processing helix chain 'K' and resid 295 through 301 Processing helix chain 'K' and resid 310 through 319 removed outlier: 3.850A pdb=" N MET K 314 " --> pdb=" O LYS K 310 " (cutoff:3.500A) Processing helix chain 'K' and resid 374 through 396 removed outlier: 4.148A pdb=" N GLU K 379 " --> pdb=" O HIS K 375 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL K 380 " --> pdb=" O VAL K 376 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASP K 385 " --> pdb=" O ALA K 381 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL K 391 " --> pdb=" O ALA K 387 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY K 392 " --> pdb=" O VAL K 388 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N GLU K 396 " --> pdb=" O GLY K 392 " (cutoff:3.500A) Processing helix chain 'K' and resid 406 through 419 removed outlier: 3.612A pdb=" N GLU K 410 " --> pdb=" O SER K 406 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N MET K 413 " --> pdb=" O VAL K 409 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA K 419 " --> pdb=" O LEU K 415 " (cutoff:3.500A) Processing helix chain 'K' and resid 428 through 445 removed outlier: 3.693A pdb=" N ALA K 436 " --> pdb=" O ALA K 432 " (cutoff:3.500A) Proline residue: K 441 - end of helix removed outlier: 3.587A pdb=" N ALA K 445 " --> pdb=" O PRO K 441 " (cutoff:3.500A) Processing helix chain 'K' and resid 453 through 461 removed outlier: 3.802A pdb=" N VAL K 457 " --> pdb=" O ILE K 453 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LYS K 458 " --> pdb=" O GLU K 454 " (cutoff:3.500A) Processing helix chain 'K' and resid 494 through 510 removed outlier: 4.285A pdb=" N ALA K 502 " --> pdb=" O ALA K 498 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA K 503 " --> pdb=" O ILE K 499 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU K 507 " --> pdb=" O ALA K 503 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N MET K 508 " --> pdb=" O GLU K 504 " (cutoff:3.500A) Processing helix chain 'L' and resid 17 through 37 removed outlier: 3.574A pdb=" N GLN L 21 " --> pdb=" O GLY L 17 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N ARG L 22 " --> pdb=" O ARG L 18 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE L 31 " --> pdb=" O ALA L 27 " (cutoff:3.500A) Processing helix chain 'L' and resid 39 through 43 Processing helix chain 'L' and resid 60 through 67 removed outlier: 3.977A pdb=" N ILE L 64 " --> pdb=" O ASP L 60 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU L 67 " --> pdb=" O THR L 63 " (cutoff:3.500A) Processing helix chain 'L' and resid 74 through 87 removed outlier: 3.960A pdb=" N GLU L 80 " --> pdb=" O LYS L 76 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N VAL L 81 " --> pdb=" O MET L 77 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA L 82 " --> pdb=" O LEU L 78 " (cutoff:3.500A) Processing helix chain 'L' and resid 91 through 110 removed outlier: 3.965A pdb=" N THR L 95 " --> pdb=" O ASP L 91 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU L 103 " --> pdb=" O VAL L 99 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU L 104 " --> pdb=" O ALA L 100 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N ARG L 105 " --> pdb=" O GLY L 101 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LYS L 106 " --> pdb=" O GLU L 102 " (cutoff:3.500A) Processing helix chain 'L' and resid 116 through 136 removed outlier: 4.878A pdb=" N VAL L 120 " --> pdb=" O HIS L 116 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS L 122 " --> pdb=" O THR L 118 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYS L 136 " --> pdb=" O GLN L 132 " (cutoff:3.500A) Processing helix chain 'L' and resid 147 through 159 removed outlier: 3.554A pdb=" N THR L 151 " --> pdb=" O LYS L 147 " (cutoff:3.500A) Processing helix chain 'L' and resid 168 through 184 removed outlier: 5.190A pdb=" N GLU L 172 " --> pdb=" O GLU L 168 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU L 176 " --> pdb=" O GLU L 172 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL L 182 " --> pdb=" O VAL L 178 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASP L 183 " --> pdb=" O SER L 179 " (cutoff:3.500A) Processing helix chain 'L' and resid 187 through 194 removed outlier: 3.788A pdb=" N ILE L 193 " --> pdb=" O ASP L 189 " (cutoff:3.500A) Processing helix chain 'L' and resid 258 through 280 removed outlier: 4.095A pdb=" N GLU L 263 " --> pdb=" O MET L 259 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU L 266 " --> pdb=" O ILE L 262 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N MET L 272 " --> pdb=" O MET L 268 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE L 276 " --> pdb=" O MET L 272 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N SER L 279 " --> pdb=" O GLU L 275 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N GLY L 280 " --> pdb=" O ILE L 276 " (cutoff:3.500A) Processing helix chain 'L' and resid 295 through 301 Processing helix chain 'L' and resid 310 through 319 removed outlier: 3.853A pdb=" N MET L 314 " --> pdb=" O LYS L 310 " (cutoff:3.500A) Processing helix chain 'L' and resid 374 through 396 removed outlier: 4.150A pdb=" N GLU L 379 " --> pdb=" O HIS L 375 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL L 380 " --> pdb=" O VAL L 376 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP L 385 " --> pdb=" O ALA L 381 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL L 391 " --> pdb=" O ALA L 387 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY L 392 " --> pdb=" O VAL L 388 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N GLU L 396 " --> pdb=" O GLY L 392 " (cutoff:3.500A) Processing helix chain 'L' and resid 406 through 419 removed outlier: 3.610A pdb=" N GLU L 410 " --> pdb=" O SER L 406 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N MET L 413 " --> pdb=" O VAL L 409 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA L 419 " --> pdb=" O LEU L 415 " (cutoff:3.500A) Processing helix chain 'L' and resid 428 through 445 removed outlier: 3.693A pdb=" N ALA L 436 " --> pdb=" O ALA L 432 " (cutoff:3.500A) Proline residue: L 441 - end of helix removed outlier: 3.587A pdb=" N ALA L 445 " --> pdb=" O PRO L 441 " (cutoff:3.500A) Processing helix chain 'L' and resid 453 through 461 removed outlier: 3.803A pdb=" N VAL L 457 " --> pdb=" O ILE L 453 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS L 458 " --> pdb=" O GLU L 454 " (cutoff:3.500A) Processing helix chain 'L' and resid 494 through 510 removed outlier: 4.285A pdb=" N ALA L 502 " --> pdb=" O ALA L 498 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA L 503 " --> pdb=" O ILE L 499 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU L 507 " --> pdb=" O ALA L 503 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N MET L 508 " --> pdb=" O GLU L 504 " (cutoff:3.500A) Processing helix chain 'M' and resid 17 through 37 removed outlier: 3.572A pdb=" N GLN M 21 " --> pdb=" O GLY M 17 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N ARG M 22 " --> pdb=" O ARG M 18 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE M 31 " --> pdb=" O ALA M 27 " (cutoff:3.500A) Processing helix chain 'M' and resid 39 through 43 Processing helix chain 'M' and resid 60 through 67 removed outlier: 3.976A pdb=" N ILE M 64 " --> pdb=" O ASP M 60 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU M 67 " --> pdb=" O THR M 63 " (cutoff:3.500A) Processing helix chain 'M' and resid 74 through 87 removed outlier: 3.958A pdb=" N GLU M 80 " --> pdb=" O LYS M 76 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N VAL M 81 " --> pdb=" O MET M 77 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA M 82 " --> pdb=" O LEU M 78 " (cutoff:3.500A) Processing helix chain 'M' and resid 91 through 110 removed outlier: 3.965A pdb=" N THR M 95 " --> pdb=" O ASP M 91 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU M 103 " --> pdb=" O VAL M 99 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU M 104 " --> pdb=" O ALA M 100 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ARG M 105 " --> pdb=" O GLY M 101 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LYS M 106 " --> pdb=" O GLU M 102 " (cutoff:3.500A) Processing helix chain 'M' and resid 116 through 136 removed outlier: 4.874A pdb=" N VAL M 120 " --> pdb=" O HIS M 116 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS M 122 " --> pdb=" O THR M 118 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LYS M 136 " --> pdb=" O GLN M 132 " (cutoff:3.500A) Processing helix chain 'M' and resid 147 through 159 removed outlier: 3.556A pdb=" N THR M 151 " --> pdb=" O LYS M 147 " (cutoff:3.500A) Processing helix chain 'M' and resid 168 through 184 removed outlier: 5.191A pdb=" N GLU M 172 " --> pdb=" O GLU M 168 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU M 176 " --> pdb=" O GLU M 172 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL M 182 " --> pdb=" O VAL M 178 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP M 183 " --> pdb=" O SER M 179 " (cutoff:3.500A) Processing helix chain 'M' and resid 187 through 194 removed outlier: 3.786A pdb=" N ILE M 193 " --> pdb=" O ASP M 189 " (cutoff:3.500A) Processing helix chain 'M' and resid 258 through 280 removed outlier: 4.089A pdb=" N GLU M 263 " --> pdb=" O MET M 259 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU M 266 " --> pdb=" O ILE M 262 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N MET M 272 " --> pdb=" O MET M 268 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE M 276 " --> pdb=" O MET M 272 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N SER M 279 " --> pdb=" O GLU M 275 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N GLY M 280 " --> pdb=" O ILE M 276 " (cutoff:3.500A) Processing helix chain 'M' and resid 295 through 301 Processing helix chain 'M' and resid 310 through 319 removed outlier: 3.850A pdb=" N MET M 314 " --> pdb=" O LYS M 310 " (cutoff:3.500A) Processing helix chain 'M' and resid 374 through 396 removed outlier: 4.148A pdb=" N GLU M 379 " --> pdb=" O HIS M 375 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL M 380 " --> pdb=" O VAL M 376 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASP M 385 " --> pdb=" O ALA M 381 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL M 391 " --> pdb=" O ALA M 387 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY M 392 " --> pdb=" O VAL M 388 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N GLU M 396 " --> pdb=" O GLY M 392 " (cutoff:3.500A) Processing helix chain 'M' and resid 406 through 419 removed outlier: 3.612A pdb=" N GLU M 410 " --> pdb=" O SER M 406 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N MET M 413 " --> pdb=" O VAL M 409 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA M 419 " --> pdb=" O LEU M 415 " (cutoff:3.500A) Processing helix chain 'M' and resid 428 through 445 removed outlier: 3.693A pdb=" N ALA M 436 " --> pdb=" O ALA M 432 " (cutoff:3.500A) Proline residue: M 441 - end of helix removed outlier: 3.587A pdb=" N ALA M 445 " --> pdb=" O PRO M 441 " (cutoff:3.500A) Processing helix chain 'M' and resid 453 through 461 removed outlier: 3.802A pdb=" N VAL M 457 " --> pdb=" O ILE M 453 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LYS M 458 " --> pdb=" O GLU M 454 " (cutoff:3.500A) Processing helix chain 'M' and resid 494 through 510 removed outlier: 4.285A pdb=" N ALA M 502 " --> pdb=" O ALA M 498 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA M 503 " --> pdb=" O ILE M 499 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU M 507 " --> pdb=" O ALA M 503 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N MET M 508 " --> pdb=" O GLU M 504 " (cutoff:3.500A) Processing helix chain 'N' and resid 17 through 37 removed outlier: 3.574A pdb=" N GLN N 21 " --> pdb=" O GLY N 17 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N ARG N 22 " --> pdb=" O ARG N 18 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE N 31 " --> pdb=" O ALA N 27 " (cutoff:3.500A) Processing helix chain 'N' and resid 39 through 43 Processing helix chain 'N' and resid 60 through 67 removed outlier: 3.977A pdb=" N ILE N 64 " --> pdb=" O ASP N 60 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU N 67 " --> pdb=" O THR N 63 " (cutoff:3.500A) Processing helix chain 'N' and resid 74 through 87 removed outlier: 3.960A pdb=" N GLU N 80 " --> pdb=" O LYS N 76 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N VAL N 81 " --> pdb=" O MET N 77 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA N 82 " --> pdb=" O LEU N 78 " (cutoff:3.500A) Processing helix chain 'N' and resid 91 through 110 removed outlier: 3.965A pdb=" N THR N 95 " --> pdb=" O ASP N 91 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU N 103 " --> pdb=" O VAL N 99 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU N 104 " --> pdb=" O ALA N 100 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N ARG N 105 " --> pdb=" O GLY N 101 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LYS N 106 " --> pdb=" O GLU N 102 " (cutoff:3.500A) Processing helix chain 'N' and resid 116 through 136 removed outlier: 4.878A pdb=" N VAL N 120 " --> pdb=" O HIS N 116 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS N 122 " --> pdb=" O THR N 118 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYS N 136 " --> pdb=" O GLN N 132 " (cutoff:3.500A) Processing helix chain 'N' and resid 147 through 159 removed outlier: 3.554A pdb=" N THR N 151 " --> pdb=" O LYS N 147 " (cutoff:3.500A) Processing helix chain 'N' and resid 168 through 184 removed outlier: 5.190A pdb=" N GLU N 172 " --> pdb=" O GLU N 168 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU N 176 " --> pdb=" O GLU N 172 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL N 182 " --> pdb=" O VAL N 178 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASP N 183 " --> pdb=" O SER N 179 " (cutoff:3.500A) Processing helix chain 'N' and resid 187 through 194 removed outlier: 3.788A pdb=" N ILE N 193 " --> pdb=" O ASP N 189 " (cutoff:3.500A) Processing helix chain 'N' and resid 258 through 280 removed outlier: 4.095A pdb=" N GLU N 263 " --> pdb=" O MET N 259 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU N 266 " --> pdb=" O ILE N 262 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N MET N 272 " --> pdb=" O MET N 268 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE N 276 " --> pdb=" O MET N 272 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N SER N 279 " --> pdb=" O GLU N 275 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N GLY N 280 " --> pdb=" O ILE N 276 " (cutoff:3.500A) Processing helix chain 'N' and resid 295 through 301 Processing helix chain 'N' and resid 310 through 319 removed outlier: 3.853A pdb=" N MET N 314 " --> pdb=" O LYS N 310 " (cutoff:3.500A) Processing helix chain 'N' and resid 374 through 396 removed outlier: 4.150A pdb=" N GLU N 379 " --> pdb=" O HIS N 375 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL N 380 " --> pdb=" O VAL N 376 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP N 385 " --> pdb=" O ALA N 381 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL N 391 " --> pdb=" O ALA N 387 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY N 392 " --> pdb=" O VAL N 388 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N GLU N 396 " --> pdb=" O GLY N 392 " (cutoff:3.500A) Processing helix chain 'N' and resid 406 through 419 removed outlier: 3.610A pdb=" N GLU N 410 " --> pdb=" O SER N 406 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N MET N 413 " --> pdb=" O VAL N 409 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA N 419 " --> pdb=" O LEU N 415 " (cutoff:3.500A) Processing helix chain 'N' and resid 428 through 445 removed outlier: 3.693A pdb=" N ALA N 436 " --> pdb=" O ALA N 432 " (cutoff:3.500A) Proline residue: N 441 - end of helix removed outlier: 3.587A pdb=" N ALA N 445 " --> pdb=" O PRO N 441 " (cutoff:3.500A) Processing helix chain 'N' and resid 453 through 461 removed outlier: 3.803A pdb=" N VAL N 457 " --> pdb=" O ILE N 453 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS N 458 " --> pdb=" O GLU N 454 " (cutoff:3.500A) Processing helix chain 'N' and resid 494 through 510 removed outlier: 4.285A pdb=" N ALA N 502 " --> pdb=" O ALA N 498 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA N 503 " --> pdb=" O ILE N 499 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU N 507 " --> pdb=" O ALA N 503 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N MET N 508 " --> pdb=" O GLU N 504 " (cutoff:3.500A) Processing helix chain 'O' and resid 17 through 37 removed outlier: 3.572A pdb=" N GLN O 21 " --> pdb=" O GLY O 17 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N ARG O 22 " --> pdb=" O ARG O 18 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE O 31 " --> pdb=" O ALA O 27 " (cutoff:3.500A) Processing helix chain 'O' and resid 39 through 43 Processing helix chain 'O' and resid 60 through 67 removed outlier: 3.976A pdb=" N ILE O 64 " --> pdb=" O ASP O 60 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU O 67 " --> pdb=" O THR O 63 " (cutoff:3.500A) Processing helix chain 'O' and resid 74 through 87 removed outlier: 3.958A pdb=" N GLU O 80 " --> pdb=" O LYS O 76 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N VAL O 81 " --> pdb=" O MET O 77 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA O 82 " --> pdb=" O LEU O 78 " (cutoff:3.500A) Processing helix chain 'O' and resid 91 through 110 removed outlier: 3.965A pdb=" N THR O 95 " --> pdb=" O ASP O 91 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU O 103 " --> pdb=" O VAL O 99 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU O 104 " --> pdb=" O ALA O 100 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ARG O 105 " --> pdb=" O GLY O 101 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LYS O 106 " --> pdb=" O GLU O 102 " (cutoff:3.500A) Processing helix chain 'O' and resid 116 through 136 removed outlier: 4.874A pdb=" N VAL O 120 " --> pdb=" O HIS O 116 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS O 122 " --> pdb=" O THR O 118 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LYS O 136 " --> pdb=" O GLN O 132 " (cutoff:3.500A) Processing helix chain 'O' and resid 147 through 159 removed outlier: 3.556A pdb=" N THR O 151 " --> pdb=" O LYS O 147 " (cutoff:3.500A) Processing helix chain 'O' and resid 168 through 184 removed outlier: 5.191A pdb=" N GLU O 172 " --> pdb=" O GLU O 168 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU O 176 " --> pdb=" O GLU O 172 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL O 182 " --> pdb=" O VAL O 178 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP O 183 " --> pdb=" O SER O 179 " (cutoff:3.500A) Processing helix chain 'O' and resid 187 through 194 removed outlier: 3.786A pdb=" N ILE O 193 " --> pdb=" O ASP O 189 " (cutoff:3.500A) Processing helix chain 'O' and resid 258 through 280 removed outlier: 4.089A pdb=" N GLU O 263 " --> pdb=" O MET O 259 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU O 266 " --> pdb=" O ILE O 262 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N MET O 272 " --> pdb=" O MET O 268 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE O 276 " --> pdb=" O MET O 272 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N SER O 279 " --> pdb=" O GLU O 275 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N GLY O 280 " --> pdb=" O ILE O 276 " (cutoff:3.500A) Processing helix chain 'O' and resid 295 through 301 Processing helix chain 'O' and resid 310 through 319 removed outlier: 3.850A pdb=" N MET O 314 " --> pdb=" O LYS O 310 " (cutoff:3.500A) Processing helix chain 'O' and resid 374 through 396 removed outlier: 4.148A pdb=" N GLU O 379 " --> pdb=" O HIS O 375 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL O 380 " --> pdb=" O VAL O 376 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASP O 385 " --> pdb=" O ALA O 381 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL O 391 " --> pdb=" O ALA O 387 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY O 392 " --> pdb=" O VAL O 388 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N GLU O 396 " --> pdb=" O GLY O 392 " (cutoff:3.500A) Processing helix chain 'O' and resid 406 through 419 removed outlier: 3.612A pdb=" N GLU O 410 " --> pdb=" O SER O 406 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N MET O 413 " --> pdb=" O VAL O 409 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA O 419 " --> pdb=" O LEU O 415 " (cutoff:3.500A) Processing helix chain 'O' and resid 428 through 445 removed outlier: 3.693A pdb=" N ALA O 436 " --> pdb=" O ALA O 432 " (cutoff:3.500A) Proline residue: O 441 - end of helix removed outlier: 3.587A pdb=" N ALA O 445 " --> pdb=" O PRO O 441 " (cutoff:3.500A) Processing helix chain 'O' and resid 453 through 461 removed outlier: 3.801A pdb=" N VAL O 457 " --> pdb=" O ILE O 453 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LYS O 458 " --> pdb=" O GLU O 454 " (cutoff:3.500A) Processing helix chain 'O' and resid 494 through 510 removed outlier: 4.285A pdb=" N ALA O 502 " --> pdb=" O ALA O 498 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA O 503 " --> pdb=" O ILE O 499 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU O 507 " --> pdb=" O ALA O 503 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N MET O 508 " --> pdb=" O GLU O 504 " (cutoff:3.500A) Processing helix chain 'P' and resid 17 through 37 removed outlier: 3.574A pdb=" N GLN P 21 " --> pdb=" O GLY P 17 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N ARG P 22 " --> pdb=" O ARG P 18 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE P 31 " --> pdb=" O ALA P 27 " (cutoff:3.500A) Processing helix chain 'P' and resid 39 through 43 Processing helix chain 'P' and resid 60 through 67 removed outlier: 3.977A pdb=" N ILE P 64 " --> pdb=" O ASP P 60 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU P 67 " --> pdb=" O THR P 63 " (cutoff:3.500A) Processing helix chain 'P' and resid 74 through 87 removed outlier: 3.960A pdb=" N GLU P 80 " --> pdb=" O LYS P 76 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N VAL P 81 " --> pdb=" O MET P 77 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA P 82 " --> pdb=" O LEU P 78 " (cutoff:3.500A) Processing helix chain 'P' and resid 91 through 110 removed outlier: 3.965A pdb=" N THR P 95 " --> pdb=" O ASP P 91 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU P 103 " --> pdb=" O VAL P 99 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU P 104 " --> pdb=" O ALA P 100 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N ARG P 105 " --> pdb=" O GLY P 101 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LYS P 106 " --> pdb=" O GLU P 102 " (cutoff:3.500A) Processing helix chain 'P' and resid 116 through 136 removed outlier: 4.878A pdb=" N VAL P 120 " --> pdb=" O HIS P 116 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS P 122 " --> pdb=" O THR P 118 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYS P 136 " --> pdb=" O GLN P 132 " (cutoff:3.500A) Processing helix chain 'P' and resid 147 through 159 removed outlier: 3.554A pdb=" N THR P 151 " --> pdb=" O LYS P 147 " (cutoff:3.500A) Processing helix chain 'P' and resid 168 through 184 removed outlier: 5.190A pdb=" N GLU P 172 " --> pdb=" O GLU P 168 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU P 176 " --> pdb=" O GLU P 172 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL P 182 " --> pdb=" O VAL P 178 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASP P 183 " --> pdb=" O SER P 179 " (cutoff:3.500A) Processing helix chain 'P' and resid 187 through 194 removed outlier: 3.788A pdb=" N ILE P 193 " --> pdb=" O ASP P 189 " (cutoff:3.500A) Processing helix chain 'P' and resid 258 through 280 removed outlier: 4.095A pdb=" N GLU P 263 " --> pdb=" O MET P 259 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU P 266 " --> pdb=" O ILE P 262 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N MET P 272 " --> pdb=" O MET P 268 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE P 276 " --> pdb=" O MET P 272 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N SER P 279 " --> pdb=" O GLU P 275 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N GLY P 280 " --> pdb=" O ILE P 276 " (cutoff:3.500A) Processing helix chain 'P' and resid 295 through 301 Processing helix chain 'P' and resid 310 through 319 removed outlier: 3.853A pdb=" N MET P 314 " --> pdb=" O LYS P 310 " (cutoff:3.500A) Processing helix chain 'P' and resid 374 through 396 removed outlier: 4.150A pdb=" N GLU P 379 " --> pdb=" O HIS P 375 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL P 380 " --> pdb=" O VAL P 376 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP P 385 " --> pdb=" O ALA P 381 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL P 391 " --> pdb=" O ALA P 387 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY P 392 " --> pdb=" O VAL P 388 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N GLU P 396 " --> pdb=" O GLY P 392 " (cutoff:3.500A) Processing helix chain 'P' and resid 406 through 419 removed outlier: 3.610A pdb=" N GLU P 410 " --> pdb=" O SER P 406 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N MET P 413 " --> pdb=" O VAL P 409 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA P 419 " --> pdb=" O LEU P 415 " (cutoff:3.500A) Processing helix chain 'P' and resid 428 through 445 removed outlier: 3.693A pdb=" N ALA P 436 " --> pdb=" O ALA P 432 " (cutoff:3.500A) Proline residue: P 441 - end of helix removed outlier: 3.587A pdb=" N ALA P 445 " --> pdb=" O PRO P 441 " (cutoff:3.500A) Processing helix chain 'P' and resid 453 through 461 removed outlier: 3.803A pdb=" N VAL P 457 " --> pdb=" O ILE P 453 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS P 458 " --> pdb=" O GLU P 454 " (cutoff:3.500A) Processing helix chain 'P' and resid 494 through 510 removed outlier: 4.285A pdb=" N ALA P 502 " --> pdb=" O ALA P 498 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA P 503 " --> pdb=" O ILE P 499 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU P 507 " --> pdb=" O ALA P 503 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N MET P 508 " --> pdb=" O GLU P 504 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 46 through 47 removed outlier: 4.104A pdb=" N LYS A 46 " --> pdb=" O VAL A 57 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N VAL A 57 " --> pdb=" O LYS A 46 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'B' and resid 46 through 47 removed outlier: 4.104A pdb=" N LYS B 46 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N VAL B 57 " --> pdb=" O LYS B 46 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'C' and resid 46 through 47 removed outlier: 4.108A pdb=" N LYS C 46 " --> pdb=" O VAL C 57 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N VAL C 57 " --> pdb=" O LYS C 46 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'D' and resid 46 through 47 removed outlier: 4.108A pdb=" N LYS D 46 " --> pdb=" O VAL D 57 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N VAL D 57 " --> pdb=" O LYS D 46 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'E' and resid 46 through 47 removed outlier: 4.109A pdb=" N LYS E 46 " --> pdb=" O VAL E 57 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N VAL E 57 " --> pdb=" O LYS E 46 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'F' and resid 46 through 47 removed outlier: 4.108A pdb=" N LYS F 46 " --> pdb=" O VAL F 57 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N VAL F 57 " --> pdb=" O LYS F 46 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'G' and resid 46 through 47 removed outlier: 4.109A pdb=" N LYS G 46 " --> pdb=" O VAL G 57 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N VAL G 57 " --> pdb=" O LYS G 46 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'H' and resid 46 through 47 removed outlier: 4.108A pdb=" N LYS H 46 " --> pdb=" O VAL H 57 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N VAL H 57 " --> pdb=" O LYS H 46 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'I' and resid 46 through 47 removed outlier: 4.108A pdb=" N LYS I 46 " --> pdb=" O VAL I 57 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N VAL I 57 " --> pdb=" O LYS I 46 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'J' and resid 46 through 47 removed outlier: 4.109A pdb=" N LYS J 46 " --> pdb=" O VAL J 57 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N VAL J 57 " --> pdb=" O LYS J 46 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'K' and resid 46 through 47 removed outlier: 4.108A pdb=" N LYS K 46 " --> pdb=" O VAL K 57 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N VAL K 57 " --> pdb=" O LYS K 46 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'L' and resid 46 through 47 removed outlier: 4.109A pdb=" N LYS L 46 " --> pdb=" O VAL L 57 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N VAL L 57 " --> pdb=" O LYS L 46 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'M' and resid 46 through 47 removed outlier: 4.108A pdb=" N LYS M 46 " --> pdb=" O VAL M 57 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N VAL M 57 " --> pdb=" O LYS M 46 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'N' and resid 46 through 47 removed outlier: 4.109A pdb=" N LYS N 46 " --> pdb=" O VAL N 57 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N VAL N 57 " --> pdb=" O LYS N 46 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'O' and resid 46 through 47 removed outlier: 4.108A pdb=" N LYS O 46 " --> pdb=" O VAL O 57 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N VAL O 57 " --> pdb=" O LYS O 46 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'P' and resid 46 through 47 removed outlier: 4.109A pdb=" N LYS P 46 " --> pdb=" O VAL P 57 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N VAL P 57 " --> pdb=" O LYS P 46 " (cutoff:3.500A) No H-bonds generated for sheet with id= P 2111 hydrogen bonds defined for protein. 6237 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: 17.19 Time building geometry restraints manager: 23.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 22009 1.34 - 1.46: 9232 1.46 - 1.58: 32071 1.58 - 1.71: 16 1.71 - 1.83: 784 Bond restraints: 64112 Sorted by residual: bond pdb=" CA VAL C 7 " pdb=" CB VAL C 7 " ideal model delta sigma weight residual 1.540 1.592 -0.052 1.36e-02 5.41e+03 1.46e+01 bond pdb=" CA VAL O 7 " pdb=" CB VAL O 7 " ideal model delta sigma weight residual 1.540 1.592 -0.052 1.36e-02 5.41e+03 1.44e+01 bond pdb=" CA VAL A 7 " pdb=" CB VAL A 7 " ideal model delta sigma weight residual 1.540 1.591 -0.051 1.36e-02 5.41e+03 1.43e+01 bond pdb=" CA VAL L 7 " pdb=" CB VAL L 7 " ideal model delta sigma weight residual 1.540 1.591 -0.051 1.36e-02 5.41e+03 1.42e+01 bond pdb=" CA VAL E 7 " pdb=" CB VAL E 7 " ideal model delta sigma weight residual 1.540 1.591 -0.051 1.36e-02 5.41e+03 1.42e+01 ... (remaining 64107 not shown) Histogram of bond angle deviations from ideal: 87.98 - 97.02: 80 97.02 - 106.07: 2382 106.07 - 115.11: 39197 115.11 - 124.15: 41568 124.15 - 133.19: 3013 Bond angle restraints: 86240 Sorted by residual: angle pdb=" N ARG L 308 " pdb=" CA ARG L 308 " pdb=" C ARG L 308 " ideal model delta sigma weight residual 108.99 129.83 -20.84 1.57e+00 4.06e-01 1.76e+02 angle pdb=" N ARG P 308 " pdb=" CA ARG P 308 " pdb=" C ARG P 308 " ideal model delta sigma weight residual 108.99 129.83 -20.84 1.57e+00 4.06e-01 1.76e+02 angle pdb=" N ARG E 308 " pdb=" CA ARG E 308 " pdb=" C ARG E 308 " ideal model delta sigma weight residual 108.99 129.83 -20.84 1.57e+00 4.06e-01 1.76e+02 angle pdb=" N ARG C 308 " pdb=" CA ARG C 308 " pdb=" C ARG C 308 " ideal model delta sigma weight residual 108.99 129.83 -20.84 1.57e+00 4.06e-01 1.76e+02 angle pdb=" N ARG G 308 " pdb=" CA ARG G 308 " pdb=" C ARG G 308 " ideal model delta sigma weight residual 108.99 129.83 -20.84 1.57e+00 4.06e-01 1.76e+02 ... (remaining 86235 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.14: 34547 18.14 - 36.27: 3807 36.27 - 54.41: 1391 54.41 - 72.55: 463 72.55 - 90.68: 288 Dihedral angle restraints: 40496 sinusoidal: 16256 harmonic: 24240 Sorted by residual: dihedral pdb=" C ILE B 195 " pdb=" N ILE B 195 " pdb=" CA ILE B 195 " pdb=" CB ILE B 195 " ideal model delta harmonic sigma weight residual -122.00 -142.38 20.38 0 2.50e+00 1.60e-01 6.64e+01 dihedral pdb=" C ILE H 195 " pdb=" N ILE H 195 " pdb=" CA ILE H 195 " pdb=" CB ILE H 195 " ideal model delta harmonic sigma weight residual -122.00 -142.36 20.36 0 2.50e+00 1.60e-01 6.63e+01 dihedral pdb=" C ILE K 195 " pdb=" N ILE K 195 " pdb=" CA ILE K 195 " pdb=" CB ILE K 195 " ideal model delta harmonic sigma weight residual -122.00 -142.34 20.34 0 2.50e+00 1.60e-01 6.62e+01 ... (remaining 40493 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.168: 7647 0.168 - 0.335: 1947 0.335 - 0.503: 518 0.503 - 0.671: 272 0.671 - 0.839: 64 Chirality restraints: 10448 Sorted by residual: chirality pdb=" CA ILE H 195 " pdb=" N ILE H 195 " pdb=" C ILE H 195 " pdb=" CB ILE H 195 " both_signs ideal model delta sigma weight residual False 2.43 1.59 0.84 2.00e-01 2.50e+01 1.76e+01 chirality pdb=" CA ILE G 195 " pdb=" N ILE G 195 " pdb=" C ILE G 195 " pdb=" CB ILE G 195 " both_signs ideal model delta sigma weight residual False 2.43 1.59 0.84 2.00e-01 2.50e+01 1.76e+01 chirality pdb=" CA ILE C 195 " pdb=" N ILE C 195 " pdb=" C ILE C 195 " pdb=" CB ILE C 195 " both_signs ideal model delta sigma weight residual False 2.43 1.59 0.84 2.00e-01 2.50e+01 1.76e+01 ... (remaining 10445 not shown) Planarity restraints: 11216 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN P 4 " 0.087 5.00e-02 4.00e+02 1.31e-01 2.73e+01 pdb=" N PRO P 5 " -0.226 5.00e-02 4.00e+02 pdb=" CA PRO P 5 " 0.072 5.00e-02 4.00e+02 pdb=" CD PRO P 5 " 0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN E 4 " 0.087 5.00e-02 4.00e+02 1.31e-01 2.73e+01 pdb=" N PRO E 5 " -0.226 5.00e-02 4.00e+02 pdb=" CA PRO E 5 " 0.072 5.00e-02 4.00e+02 pdb=" CD PRO E 5 " 0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN N 4 " -0.087 5.00e-02 4.00e+02 1.31e-01 2.73e+01 pdb=" N PRO N 5 " 0.226 5.00e-02 4.00e+02 pdb=" CA PRO N 5 " -0.072 5.00e-02 4.00e+02 pdb=" CD PRO N 5 " -0.067 5.00e-02 4.00e+02 ... (remaining 11213 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 14267 2.79 - 3.32: 80856 3.32 - 3.84: 109180 3.84 - 4.37: 130979 4.37 - 4.90: 190043 Nonbonded interactions: 525325 Sorted by model distance: nonbonded pdb=" N CYS L 484 " pdb=" N GLU L 485 " model vdw 2.259 2.560 nonbonded pdb=" N CYS E 484 " pdb=" N GLU E 485 " model vdw 2.259 2.560 nonbonded pdb=" N CYS P 484 " pdb=" N GLU P 485 " model vdw 2.259 2.560 nonbonded pdb=" N CYS C 484 " pdb=" N GLU C 485 " model vdw 2.259 2.560 nonbonded pdb=" N CYS J 484 " pdb=" N GLU J 485 " model vdw 2.259 2.560 ... (remaining 525320 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=0.00 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: 0.340 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: 0.050 Extract box with map and model: 6.450 Check model and map are aligned: 0.690 Set scattering table: 0.470 Process input model: 116.510 Find NCS groups from input model: 3.460 Set up NCS constraints: 0.410 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:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 130.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5064 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 : 0.008 0.080 64112 Z= 0.491 Angle : 2.440 24.374 86240 Z= 1.514 Chirality : 0.189 0.839 10448 Planarity : 0.011 0.131 11216 Dihedral : 19.869 90.683 24720 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 87.93 Ramachandran Plot: Outliers : 13.79 % Allowed : 17.36 % Favored : 68.86 % Rotamer Outliers : 23.89 % Cbeta Deviations : 2.86 % Peptide Plane: Cis-proline : 18.18 % 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: -6.57 (0.06), residues: 8480 helix: -3.70 (0.05), residues: 3152 sheet: None (None), residues: 0 loop : -5.15 (0.06), residues: 5328 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16960 Ramachandran restraints generated. 8480 Oldfield, 0 Emsley, 8480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16960 Ramachandran restraints generated. 8480 Oldfield, 0 Emsley, 8480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3358 residues out of total 6832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1632 poor density : 1726 time to evaluate : 5.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1632 outliers final: 750 residues processed: 2865 average time/residue: 0.6483 time to fit residues: 3039.3315 Evaluate side-chains 2052 residues out of total 6832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 750 poor density : 1302 time to evaluate : 5.574 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 750 outliers final: 48 residues processed: 750 average time/residue: 0.6086 time to fit residues: 763.9143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 848 random chunks: chunk 716 optimal weight: 2.9990 chunk 642 optimal weight: 6.9990 chunk 356 optimal weight: 2.9990 chunk 219 optimal weight: 6.9990 chunk 433 optimal weight: 10.0000 chunk 343 optimal weight: 7.9990 chunk 664 optimal weight: 5.9990 chunk 257 optimal weight: 10.0000 chunk 404 optimal weight: 10.0000 chunk 494 optimal weight: 1.9990 chunk 770 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 GLN A 114 ASN ** A 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 500 GLN B 4 GLN B 114 ASN ** B 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 324 ASN ** B 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 4 GLN C 114 ASN ** C 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 500 GLN D 4 GLN D 114 ASN ** D 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 324 ASN ** D 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 4 GLN E 114 ASN ** E 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 500 GLN F 4 GLN F 114 ASN ** F 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 324 ASN ** F 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 4 GLN G 114 ASN ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 500 GLN H 4 GLN H 114 ASN ** H 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 324 ASN ** H 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 4 GLN I 114 ASN ** I 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 324 ASN ** I 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 4 GLN J 114 ASN ** J 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 500 GLN K 4 GLN K 114 ASN ** K 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 324 ASN ** K 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 4 GLN L 114 ASN ** L 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 500 GLN M 4 GLN M 114 ASN ** M 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 324 ASN ** M 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 4 GLN N 114 ASN ** N 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 500 GLN O 4 GLN O 114 ASN ** O 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 324 ASN ** O 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 4 GLN P 114 ASN ** P 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 500 GLN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4958 moved from start: 0.5069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.082 64112 Z= 0.356 Angle : 1.459 14.616 86240 Z= 0.762 Chirality : 0.067 0.372 10448 Planarity : 0.008 0.132 11216 Dihedral : 9.743 33.144 8928 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 42.05 Ramachandran Plot: Outliers : 5.67 % Allowed : 22.23 % Favored : 72.10 % Rotamer Outliers : 2.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -5.80 (0.07), residues: 8480 helix: -2.43 (0.07), residues: 3312 sheet: None (None), residues: 0 loop : -5.21 (0.06), residues: 5168 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16960 Ramachandran restraints generated. 8480 Oldfield, 0 Emsley, 8480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16960 Ramachandran restraints generated. 8480 Oldfield, 0 Emsley, 8480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2067 residues out of total 6832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 1891 time to evaluate : 5.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 176 outliers final: 32 residues processed: 1979 average time/residue: 0.6418 time to fit residues: 2070.1321 Evaluate side-chains 1231 residues out of total 6832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 1199 time to evaluate : 5.565 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.4323 time to fit residues: 34.4165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 848 random chunks: chunk 427 optimal weight: 5.9990 chunk 238 optimal weight: 4.9990 chunk 640 optimal weight: 0.9990 chunk 524 optimal weight: 5.9990 chunk 212 optimal weight: 7.9990 chunk 771 optimal weight: 20.0000 chunk 833 optimal weight: 6.9990 chunk 687 optimal weight: 6.9990 chunk 765 optimal weight: 7.9990 chunk 263 optimal weight: 5.9990 chunk 618 optimal weight: 20.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 GLN ** B 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 222 GLN ** D 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 497 GLN ** E 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 4 GLN F 222 GLN ** F 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 497 GLN ** G 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 222 GLN ** H 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 497 GLN I 4 GLN I 222 GLN ** I 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 497 GLN ** J 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 4 GLN K 222 GLN ** K 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 497 GLN ** L 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 4 GLN M 222 GLN ** M 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 497 GLN ** N 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 4 GLN O 222 GLN ** O 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 497 GLN ** P 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5035 moved from start: 0.6751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.053 64112 Z= 0.329 Angle : 1.308 17.979 86240 Z= 0.678 Chirality : 0.060 0.239 10448 Planarity : 0.010 0.175 11216 Dihedral : 9.906 34.761 8928 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 38.81 Ramachandran Plot: Outliers : 6.01 % Allowed : 21.27 % Favored : 72.71 % Rotamer Outliers : 0.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.61 % 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: -5.26 (0.07), residues: 8480 helix: -1.87 (0.08), residues: 3312 sheet: None (None), residues: 0 loop : -4.98 (0.06), residues: 5168 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16960 Ramachandran restraints generated. 8480 Oldfield, 0 Emsley, 8480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16960 Ramachandran restraints generated. 8480 Oldfield, 0 Emsley, 8480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1663 residues out of total 6832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 1630 time to evaluate : 5.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 17 residues processed: 1663 average time/residue: 0.6296 time to fit residues: 1728.2841 Evaluate side-chains 1207 residues out of total 6832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 1190 time to evaluate : 5.595 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.4344 time to fit residues: 21.9997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 848 random chunks: chunk 762 optimal weight: 0.6980 chunk 580 optimal weight: 2.9990 chunk 400 optimal weight: 40.0000 chunk 85 optimal weight: 9.9990 chunk 368 optimal weight: 5.9990 chunk 518 optimal weight: 9.9990 chunk 774 optimal weight: 10.0000 chunk 819 optimal weight: 10.0000 chunk 404 optimal weight: 20.0000 chunk 733 optimal weight: 0.0060 chunk 220 optimal weight: 0.6980 overall best weight: 2.0800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4878 moved from start: 0.7625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 64112 Z= 0.250 Angle : 1.152 12.753 86240 Z= 0.591 Chirality : 0.054 0.238 10448 Planarity : 0.008 0.148 11216 Dihedral : 9.096 32.283 8928 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 30.33 Ramachandran Plot: Outliers : 5.08 % Allowed : 19.96 % Favored : 74.95 % Rotamer Outliers : 0.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: -4.93 (0.07), residues: 8480 helix: -1.43 (0.08), residues: 3440 sheet: None (None), residues: 0 loop : -5.00 (0.06), residues: 5040 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16960 Ramachandran restraints generated. 8480 Oldfield, 0 Emsley, 8480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16960 Ramachandran restraints generated. 8480 Oldfield, 0 Emsley, 8480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1620 residues out of total 6832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 1599 time to evaluate : 5.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 0 residues processed: 1620 average time/residue: 0.6376 time to fit residues: 1710.7643 Evaluate side-chains 1139 residues out of total 6832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1139 time to evaluate : 5.568 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.7719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 848 random chunks: chunk 682 optimal weight: 2.9990 chunk 465 optimal weight: 20.0000 chunk 11 optimal weight: 10.0000 chunk 610 optimal weight: 20.0000 chunk 338 optimal weight: 6.9990 chunk 699 optimal weight: 3.9990 chunk 566 optimal weight: 20.0000 chunk 0 optimal weight: 9.9990 chunk 418 optimal weight: 20.0000 chunk 735 optimal weight: 30.0000 chunk 206 optimal weight: 20.0000 overall best weight: 6.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 236 ASN ** C 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 236 ASN ** E 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 236 ASN ** G 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5157 moved from start: 0.8010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.062 64112 Z= 0.366 Angle : 1.269 19.644 86240 Z= 0.651 Chirality : 0.058 0.229 10448 Planarity : 0.009 0.177 11216 Dihedral : 9.543 33.223 8928 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 38.44 Ramachandran Plot: Outliers : 5.06 % Allowed : 23.83 % Favored : 71.11 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 5.11 % Twisted General : 0.60 % 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: -4.68 (0.08), residues: 8480 helix: -1.34 (0.09), residues: 3232 sheet: None (None), residues: 0 loop : -4.63 (0.07), residues: 5248 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16960 Ramachandran restraints generated. 8480 Oldfield, 0 Emsley, 8480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16960 Ramachandran restraints generated. 8480 Oldfield, 0 Emsley, 8480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1375 residues out of total 6832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1375 time to evaluate : 5.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 1375 average time/residue: 0.6787 time to fit residues: 1524.7794 Evaluate side-chains 1047 residues out of total 6832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1047 time to evaluate : 5.586 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.8099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 848 random chunks: chunk 275 optimal weight: 2.9990 chunk 738 optimal weight: 4.9990 chunk 162 optimal weight: 3.9990 chunk 481 optimal weight: 5.9990 chunk 202 optimal weight: 0.7980 chunk 820 optimal weight: 2.9990 chunk 681 optimal weight: 0.0470 chunk 379 optimal weight: 9.9990 chunk 68 optimal weight: 20.0000 chunk 271 optimal weight: 3.9990 chunk 430 optimal weight: 4.9990 overall best weight: 2.1684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 HIS ** A 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 497 GLN ** B 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 296 HIS ** B 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 HIS ** C 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 497 GLN ** D 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 296 HIS ** D 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 296 HIS ** E 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 497 GLN ** F 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 296 HIS ** F 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 296 HIS ** G 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 497 GLN ** H 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 296 HIS ** H 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 296 HIS ** I 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 296 HIS ** J 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 497 GLN ** K 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 296 HIS ** K 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 296 HIS ** L 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 497 GLN ** M 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 296 HIS ** M 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 296 HIS ** N 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 497 GLN ** O 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 296 HIS ** O 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 296 HIS ** P 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 497 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4936 moved from start: 0.8488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 64112 Z= 0.246 Angle : 1.110 12.546 86240 Z= 0.567 Chirality : 0.053 0.246 10448 Planarity : 0.008 0.151 11216 Dihedral : 8.926 32.407 8928 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 29.85 Ramachandran Plot: Outliers : 4.85 % Allowed : 20.77 % Favored : 74.39 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.30 % 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: -4.62 (0.08), residues: 8480 helix: -1.39 (0.08), residues: 3488 sheet: None (None), residues: 0 loop : -4.65 (0.07), residues: 4992 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16960 Ramachandran restraints generated. 8480 Oldfield, 0 Emsley, 8480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16960 Ramachandran restraints generated. 8480 Oldfield, 0 Emsley, 8480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1475 residues out of total 6832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1475 time to evaluate : 5.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 1475 average time/residue: 0.6468 time to fit residues: 1557.3757 Evaluate side-chains 1092 residues out of total 6832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1092 time to evaluate : 5.599 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.7217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 848 random chunks: chunk 791 optimal weight: 8.9990 chunk 92 optimal weight: 2.9990 chunk 467 optimal weight: 3.9990 chunk 599 optimal weight: 5.9990 chunk 464 optimal weight: 1.9990 chunk 690 optimal weight: 7.9990 chunk 458 optimal weight: 0.7980 chunk 817 optimal weight: 20.0000 chunk 511 optimal weight: 6.9990 chunk 498 optimal weight: 2.9990 chunk 377 optimal weight: 5.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 HIS ** A 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 HIS ** C 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 497 GLN ** D 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 296 HIS ** E 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 497 GLN ** F 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 296 HIS ** G 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 296 HIS ** J 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 296 HIS ** L 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 296 HIS ** N 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 296 HIS ** P 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4939 moved from start: 0.8838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 64112 Z= 0.247 Angle : 1.094 19.593 86240 Z= 0.554 Chirality : 0.053 0.235 10448 Planarity : 0.008 0.174 11216 Dihedral : 8.675 33.710 8928 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 29.88 Ramachandran Plot: Outliers : 4.68 % Allowed : 21.99 % Favored : 73.33 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.22 % 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: -4.43 (0.08), residues: 8480 helix: -1.06 (0.09), residues: 3280 sheet: None (None), residues: 0 loop : -4.56 (0.07), residues: 5200 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16960 Ramachandran restraints generated. 8480 Oldfield, 0 Emsley, 8480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16960 Ramachandran restraints generated. 8480 Oldfield, 0 Emsley, 8480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1398 residues out of total 6832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1398 time to evaluate : 5.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 1398 average time/residue: 0.6362 time to fit residues: 1473.5310 Evaluate side-chains 1062 residues out of total 6832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1062 time to evaluate : 5.602 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.7017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 848 random chunks: chunk 505 optimal weight: 30.0000 chunk 326 optimal weight: 7.9990 chunk 488 optimal weight: 1.9990 chunk 246 optimal weight: 7.9990 chunk 160 optimal weight: 8.9990 chunk 158 optimal weight: 0.0470 chunk 519 optimal weight: 20.0000 chunk 556 optimal weight: 2.9990 chunk 404 optimal weight: 10.0000 chunk 76 optimal weight: 4.9990 chunk 642 optimal weight: 0.7980 overall best weight: 2.1684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 468 ASN ** B 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 468 ASN ** D 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 468 ASN ** F 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 468 ASN ** H 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 468 ASN ** K 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 468 ASN ** M 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 468 ASN ** O 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 468 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4896 moved from start: 0.9157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 64112 Z= 0.235 Angle : 1.081 15.804 86240 Z= 0.543 Chirality : 0.052 0.272 10448 Planarity : 0.008 0.158 11216 Dihedral : 8.466 34.916 8928 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 28.01 Ramachandran Plot: Outliers : 4.29 % Allowed : 20.79 % Favored : 74.92 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 9.09 % Twisted General : 0.10 % 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: -4.34 (0.08), residues: 8480 helix: -0.98 (0.09), residues: 3376 sheet: None (None), residues: 0 loop : -4.57 (0.07), residues: 5104 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16960 Ramachandran restraints generated. 8480 Oldfield, 0 Emsley, 8480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16960 Ramachandran restraints generated. 8480 Oldfield, 0 Emsley, 8480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1323 residues out of total 6832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1323 time to evaluate : 5.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 1323 average time/residue: 0.6297 time to fit residues: 1375.6099 Evaluate side-chains 1048 residues out of total 6832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1048 time to evaluate : 5.586 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.7311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 848 random chunks: chunk 743 optimal weight: 4.9990 chunk 783 optimal weight: 9.9990 chunk 714 optimal weight: 9.9990 chunk 761 optimal weight: 5.9990 chunk 782 optimal weight: 5.9990 chunk 458 optimal weight: 9.9990 chunk 331 optimal weight: 0.7980 chunk 598 optimal weight: 8.9990 chunk 233 optimal weight: 6.9990 chunk 688 optimal weight: 0.9990 chunk 720 optimal weight: 9.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 GLN ** B 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 497 GLN ** D 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 116 HIS ** E 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 116 HIS G 497 GLN ** H 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 497 GLN ** K 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 497 GLN ** M 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 497 GLN ** O 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 497 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4982 moved from start: 0.9275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.060 64112 Z= 0.266 Angle : 1.101 21.375 86240 Z= 0.559 Chirality : 0.055 0.285 10448 Planarity : 0.008 0.181 11216 Dihedral : 8.577 35.834 8928 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 30.57 Ramachandran Plot: Outliers : 4.13 % Allowed : 22.46 % Favored : 73.41 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 9.09 % Twisted General : 0.11 % 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: -4.33 (0.08), residues: 8480 helix: -0.91 (0.09), residues: 3328 sheet: None (None), residues: 0 loop : -4.59 (0.07), residues: 5152 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16960 Ramachandran restraints generated. 8480 Oldfield, 0 Emsley, 8480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16960 Ramachandran restraints generated. 8480 Oldfield, 0 Emsley, 8480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1263 residues out of total 6832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1263 time to evaluate : 5.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 1263 average time/residue: 0.6435 time to fit residues: 1336.0064 Evaluate side-chains 1022 residues out of total 6832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1022 time to evaluate : 5.552 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.6710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 848 random chunks: chunk 758 optimal weight: 9.9990 chunk 500 optimal weight: 7.9990 chunk 805 optimal weight: 0.0270 chunk 491 optimal weight: 8.9990 chunk 382 optimal weight: 0.0980 chunk 559 optimal weight: 0.9990 chunk 844 optimal weight: 0.6980 chunk 777 optimal weight: 1.9990 chunk 672 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 chunk 519 optimal weight: 1.9990 overall best weight: 0.7642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 497 GLN ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 236 ASN C 295 GLN ** C 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 295 GLN ** E 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 295 GLN ** H 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 295 GLN ** K 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 295 GLN ** M 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 295 GLN ** O 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 295 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4776 moved from start: 0.9766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 64112 Z= 0.219 Angle : 1.051 16.972 86240 Z= 0.526 Chirality : 0.051 0.247 10448 Planarity : 0.007 0.163 11216 Dihedral : 8.092 37.216 8928 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 25.78 Ramachandran Plot: Outliers : 4.12 % Allowed : 19.00 % Favored : 76.89 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 9.09 % Twisted General : 0.13 % 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: -4.23 (0.08), residues: 8480 helix: -0.74 (0.09), residues: 3344 sheet: None (None), residues: 0 loop : -4.60 (0.07), residues: 5136 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16960 Ramachandran restraints generated. 8480 Oldfield, 0 Emsley, 8480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16960 Ramachandran restraints generated. 8480 Oldfield, 0 Emsley, 8480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1368 residues out of total 6832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1368 time to evaluate : 5.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 1368 average time/residue: 0.6170 time to fit residues: 1412.7633 Evaluate side-chains 1032 residues out of total 6832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1032 time to evaluate : 5.510 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.6260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 848 random chunks: chunk 412 optimal weight: 6.9990 chunk 534 optimal weight: 5.9990 chunk 716 optimal weight: 4.9990 chunk 206 optimal weight: 20.0000 chunk 620 optimal weight: 0.7980 chunk 99 optimal weight: 7.9990 chunk 186 optimal weight: 7.9990 chunk 673 optimal weight: 0.8980 chunk 281 optimal weight: 6.9990 chunk 691 optimal weight: 2.9990 chunk 85 optimal weight: 0.0670 overall best weight: 1.9522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 116 HIS ** E 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 116 HIS ** H 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 497 GLN ** O 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 497 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4699 r_free = 0.4699 target = 0.190598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.176398 restraints weight = 176054.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4568 r_free = 0.4568 target = 0.178588 restraints weight = 129344.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4587 r_free = 0.4587 target = 0.180299 restraints weight = 100721.420| |-----------------------------------------------------------------------------| r_work (final): 0.4588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5529 moved from start: 0.9908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 64112 Z= 0.231 Angle : 1.047 20.209 86240 Z= 0.528 Chirality : 0.052 0.230 10448 Planarity : 0.007 0.176 11216 Dihedral : 8.047 37.862 8928 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 27.07 Ramachandran Plot: Outliers : 4.10 % Allowed : 20.19 % Favored : 75.71 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 9.09 % Twisted General : 0.05 % 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: -4.25 (0.08), residues: 8480 helix: -0.81 (0.09), residues: 3392 sheet: None (None), residues: 0 loop : -4.60 (0.07), residues: 5088 =============================================================================== Job complete usr+sys time: 21870.02 seconds wall clock time: 381 minutes 21.52 seconds (22881.52 seconds total)