Starting phenix.real_space_refine on Tue Mar 12 14:06:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3los_5137/03_2024/3los_5137.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3los_5137/03_2024/3los_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_5137/03_2024/3los_5137.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3los_5137/03_2024/3los_5137.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3los_5137/03_2024/3los_5137.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3los_5137/03_2024/3los_5137.pdb" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.014 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: 0.18s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 24.95, per 1000 atoms: 0.39 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: 21.86 Conformation dependent library (CDL) restraints added in 9.0 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: 4.25 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: 17.28 Time building geometry restraints manager: 23.76 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: 0.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 4.680 Check model and map are aligned: 0.720 Set scattering table: 0.450 Process input model: 128.770 Find NCS groups from input model: 3.410 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:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 141.620 ------------------------------------------------------------------------------- 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 % Allowed : 16.28 % Favored : 59.84 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 361 PHE 0.036 0.009 PHE B 433 TYR 0.037 0.009 TYR E 418 ARG 0.018 0.003 ARG M 416 *********************** 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 : 5.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ILE cc_start: 0.5223 (OUTLIER) cc_final: 0.4758 (mt) REVERT: A 72 HIS cc_start: 0.4439 (OUTLIER) cc_final: 0.4199 (t70) REVERT: A 88 GLU cc_start: 0.6114 (OUTLIER) cc_final: 0.4928 (tp30) REVERT: A 187 LYS cc_start: 0.5189 (ptmm) cc_final: 0.4680 (mttp) REVERT: A 241 ILE cc_start: 0.5361 (OUTLIER) cc_final: 0.5093 (mm) REVERT: A 243 GLU cc_start: 0.3741 (OUTLIER) cc_final: 0.3333 (pt0) REVERT: A 382 ARG cc_start: 0.4310 (OUTLIER) cc_final: 0.3911 (ptm160) REVERT: A 412 SER cc_start: 0.5402 (OUTLIER) cc_final: 0.4960 (p) REVERT: A 475 VAL cc_start: 0.7288 (t) cc_final: 0.7081 (p) REVERT: A 510 LEU cc_start: 0.7042 (OUTLIER) cc_final: 0.6784 (tm) REVERT: A 513 ASP cc_start: 0.5302 (m-30) cc_final: 0.4406 (p0) REVERT: A 527 MET cc_start: 0.3650 (OUTLIER) cc_final: 0.3096 (ttt) REVERT: A 530 MET cc_start: 0.4546 (OUTLIER) cc_final: 0.3281 (mmt) REVERT: B 25 ILE cc_start: 0.7691 (mm) cc_final: 0.7422 (mt) REVERT: B 45 ASP cc_start: 0.2207 (m-30) cc_final: 0.0908 (m-30) REVERT: B 64 ILE cc_start: 0.4980 (OUTLIER) cc_final: 0.4499 (mt) REVERT: B 88 GLU cc_start: 0.6536 (OUTLIER) cc_final: 0.5963 (tp30) REVERT: B 161 LYS cc_start: 0.2093 (OUTLIER) cc_final: 0.1496 (tptt) REVERT: B 187 LYS cc_start: 0.5239 (ptmm) cc_final: 0.4624 (mttt) REVERT: B 194 LYS cc_start: 0.3305 (OUTLIER) cc_final: 0.3054 (tttp) REVERT: B 210 LYS cc_start: 0.4247 (OUTLIER) cc_final: 0.3350 (tptt) REVERT: B 241 ILE cc_start: 0.4476 (OUTLIER) cc_final: 0.4181 (mm) REVERT: B 243 GLU cc_start: 0.3164 (OUTLIER) cc_final: 0.2253 (pt0) REVERT: B 249 GLU cc_start: 0.6193 (tp30) cc_final: 0.5357 (mm-30) REVERT: B 382 ARG cc_start: 0.4218 (OUTLIER) cc_final: 0.3798 (ptp-110) REVERT: B 413 MET cc_start: 0.5925 (pp-130) cc_final: 0.5704 (pp-130) REVERT: B 497 GLN cc_start: 0.6484 (mm110) cc_final: 0.6231 (tp40) REVERT: B 510 LEU cc_start: 0.7244 (OUTLIER) cc_final: 0.6799 (tm) REVERT: B 513 ASP cc_start: 0.4600 (m-30) cc_final: 0.4179 (p0) REVERT: B 519 GLU cc_start: 0.3693 (OUTLIER) cc_final: 0.2592 (tt0) REVERT: B 527 MET cc_start: 0.3018 (OUTLIER) cc_final: 0.1442 (mtt) REVERT: B 530 MET cc_start: 0.4102 (OUTLIER) cc_final: 0.2836 (mmt) REVERT: C 64 ILE cc_start: 0.5077 (OUTLIER) cc_final: 0.4667 (mt) REVERT: C 72 HIS cc_start: 0.4431 (OUTLIER) cc_final: 0.4202 (t70) REVERT: C 88 GLU cc_start: 0.6093 (OUTLIER) cc_final: 0.4903 (tp30) REVERT: C 187 LYS cc_start: 0.5186 (ptmm) cc_final: 0.4666 (mttp) REVERT: C 241 ILE cc_start: 0.5353 (OUTLIER) cc_final: 0.5103 (mm) REVERT: C 243 GLU cc_start: 0.3743 (OUTLIER) cc_final: 0.3317 (pt0) REVERT: C 382 ARG cc_start: 0.4317 (OUTLIER) cc_final: 0.3933 (ptm160) REVERT: C 412 SER cc_start: 0.5404 (OUTLIER) cc_final: 0.4954 (p) REVERT: C 475 VAL cc_start: 0.7284 (t) cc_final: 0.7084 (p) REVERT: C 510 LEU cc_start: 0.7110 (OUTLIER) cc_final: 0.6859 (tm) REVERT: C 513 ASP cc_start: 0.5290 (m-30) cc_final: 0.4422 (p0) REVERT: C 527 MET cc_start: 0.3720 (OUTLIER) cc_final: 0.3117 (ttt) REVERT: C 530 MET cc_start: 0.4530 (OUTLIER) cc_final: 0.3312 (mmt) REVERT: D 25 ILE cc_start: 0.7695 (mm) cc_final: 0.7426 (mt) REVERT: D 45 ASP cc_start: 0.2174 (m-30) cc_final: 0.0925 (m-30) REVERT: D 64 ILE cc_start: 0.4970 (OUTLIER) cc_final: 0.4497 (mt) REVERT: D 88 GLU cc_start: 0.6500 (OUTLIER) cc_final: 0.5877 (tp30) REVERT: D 93 THR cc_start: 0.4908 (OUTLIER) cc_final: 0.4696 (t) REVERT: D 161 LYS cc_start: 0.2081 (OUTLIER) cc_final: 0.1509 (tptt) REVERT: D 187 LYS cc_start: 0.5241 (ptmm) cc_final: 0.4608 (mttt) REVERT: D 194 LYS cc_start: 0.3331 (OUTLIER) cc_final: 0.3067 (tttp) REVERT: D 210 LYS cc_start: 0.4243 (OUTLIER) cc_final: 0.3331 (tptt) REVERT: D 241 ILE cc_start: 0.4477 (OUTLIER) cc_final: 0.4183 (mm) REVERT: D 243 GLU cc_start: 0.3157 (OUTLIER) cc_final: 0.2235 (pt0) REVERT: D 249 GLU cc_start: 0.6191 (tp30) cc_final: 0.5354 (mm-30) REVERT: D 382 ARG cc_start: 0.4234 (OUTLIER) cc_final: 0.3802 (ptp-110) REVERT: D 413 MET cc_start: 0.5941 (pp-130) cc_final: 0.5721 (pp-130) REVERT: D 510 LEU cc_start: 0.7260 (OUTLIER) cc_final: 0.6813 (tm) REVERT: D 513 ASP cc_start: 0.4602 (m-30) cc_final: 0.4146 (p0) REVERT: D 519 GLU cc_start: 0.3686 (OUTLIER) cc_final: 0.2578 (tt0) REVERT: D 527 MET cc_start: 0.3002 (OUTLIER) cc_final: 0.1432 (mtt) REVERT: D 530 MET cc_start: 0.4103 (OUTLIER) cc_final: 0.2838 (mmt) REVERT: E 64 ILE cc_start: 0.5091 (OUTLIER) cc_final: 0.4678 (mt) REVERT: E 72 HIS cc_start: 0.4437 (OUTLIER) cc_final: 0.4213 (t70) REVERT: E 88 GLU cc_start: 0.6100 (OUTLIER) cc_final: 0.4904 (tp30) REVERT: E 187 LYS cc_start: 0.5183 (ptmm) cc_final: 0.4672 (mttp) REVERT: E 241 ILE cc_start: 0.5374 (OUTLIER) cc_final: 0.5115 (mm) REVERT: E 243 GLU cc_start: 0.3748 (OUTLIER) cc_final: 0.3325 (pt0) REVERT: E 382 ARG cc_start: 0.4311 (OUTLIER) cc_final: 0.3916 (ptm160) REVERT: E 412 SER cc_start: 0.5400 (OUTLIER) cc_final: 0.4934 (p) REVERT: E 475 VAL cc_start: 0.7290 (t) cc_final: 0.7083 (p) REVERT: E 510 LEU cc_start: 0.7109 (OUTLIER) cc_final: 0.6859 (tm) REVERT: E 513 ASP cc_start: 0.5313 (m-30) cc_final: 0.4446 (p0) REVERT: E 527 MET cc_start: 0.3738 (OUTLIER) cc_final: 0.3121 (ttt) REVERT: E 530 MET cc_start: 0.4549 (OUTLIER) cc_final: 0.3328 (mmt) REVERT: F 25 ILE cc_start: 0.7705 (mm) cc_final: 0.7462 (mt) REVERT: F 45 ASP cc_start: 0.2173 (m-30) cc_final: 0.0936 (m-30) REVERT: F 64 ILE cc_start: 0.4978 (OUTLIER) cc_final: 0.4496 (mt) REVERT: F 88 GLU cc_start: 0.6502 (OUTLIER) cc_final: 0.5877 (tp30) REVERT: F 93 THR cc_start: 0.4910 (OUTLIER) cc_final: 0.4701 (t) REVERT: F 161 LYS cc_start: 0.2082 (OUTLIER) cc_final: 0.1508 (tptt) REVERT: F 187 LYS cc_start: 0.5243 (ptmm) cc_final: 0.4609 (mttt) REVERT: F 194 LYS cc_start: 0.3334 (OUTLIER) cc_final: 0.3068 (tttp) REVERT: F 210 LYS cc_start: 0.4251 (OUTLIER) cc_final: 0.3331 (tptt) REVERT: F 241 ILE cc_start: 0.4484 (OUTLIER) cc_final: 0.4190 (mm) REVERT: F 243 GLU cc_start: 0.3157 (OUTLIER) cc_final: 0.2236 (pt0) REVERT: F 249 GLU cc_start: 0.6187 (tp30) cc_final: 0.5351 (mm-30) REVERT: F 382 ARG cc_start: 0.4243 (OUTLIER) cc_final: 0.3810 (ptp-110) REVERT: F 413 MET cc_start: 0.5929 (pp-130) cc_final: 0.5716 (pp-130) REVERT: F 510 LEU cc_start: 0.7284 (OUTLIER) cc_final: 0.6838 (tm) REVERT: F 513 ASP cc_start: 0.4601 (m-30) cc_final: 0.4151 (p0) REVERT: F 519 GLU cc_start: 0.3676 (OUTLIER) cc_final: 0.2576 (tt0) REVERT: F 527 MET cc_start: 0.3012 (OUTLIER) cc_final: 0.1433 (mtt) REVERT: F 530 MET cc_start: 0.4115 (OUTLIER) cc_final: 0.2846 (mmt) REVERT: G 64 ILE cc_start: 0.5112 (OUTLIER) cc_final: 0.4694 (mt) REVERT: G 72 HIS cc_start: 0.4433 (OUTLIER) cc_final: 0.4203 (t70) REVERT: G 88 GLU cc_start: 0.6109 (OUTLIER) cc_final: 0.4911 (tp30) REVERT: G 187 LYS cc_start: 0.5183 (ptmm) cc_final: 0.4672 (mttp) REVERT: G 241 ILE cc_start: 0.5375 (OUTLIER) cc_final: 0.5125 (mm) REVERT: G 243 GLU cc_start: 0.3745 (OUTLIER) cc_final: 0.3326 (pt0) REVERT: G 382 ARG cc_start: 0.4315 (OUTLIER) cc_final: 0.3919 (ptm160) REVERT: G 412 SER cc_start: 0.5405 (OUTLIER) cc_final: 0.4953 (p) REVERT: G 475 VAL cc_start: 0.7281 (t) cc_final: 0.7077 (p) REVERT: G 510 LEU cc_start: 0.7108 (OUTLIER) cc_final: 0.6856 (tm) REVERT: G 513 ASP cc_start: 0.5298 (m-30) cc_final: 0.4437 (p0) REVERT: G 527 MET cc_start: 0.3749 (OUTLIER) cc_final: 0.3132 (ttt) REVERT: G 530 MET cc_start: 0.4572 (OUTLIER) cc_final: 0.3350 (mmt) REVERT: H 25 ILE cc_start: 0.7679 (mm) cc_final: 0.7439 (mt) REVERT: H 45 ASP cc_start: 0.2178 (m-30) cc_final: 0.0921 (m-30) REVERT: H 64 ILE cc_start: 0.4983 (OUTLIER) cc_final: 0.4493 (mt) REVERT: H 88 GLU cc_start: 0.6510 (OUTLIER) cc_final: 0.5892 (tp30) REVERT: H 93 THR cc_start: 0.4905 (OUTLIER) cc_final: 0.4692 (t) REVERT: H 161 LYS cc_start: 0.2091 (OUTLIER) cc_final: 0.1516 (tptt) REVERT: H 187 LYS cc_start: 0.5238 (ptmm) cc_final: 0.4589 (mttt) REVERT: H 194 LYS cc_start: 0.3312 (OUTLIER) cc_final: 0.3056 (tttp) REVERT: H 210 LYS cc_start: 0.4255 (OUTLIER) cc_final: 0.3335 (tptt) REVERT: H 241 ILE cc_start: 0.4478 (OUTLIER) cc_final: 0.4184 (mm) REVERT: H 243 GLU cc_start: 0.3160 (OUTLIER) cc_final: 0.2242 (pt0) REVERT: H 249 GLU cc_start: 0.6208 (tp30) cc_final: 0.5358 (mm-30) REVERT: H 382 ARG cc_start: 0.4242 (OUTLIER) cc_final: 0.3814 (ptp-110) REVERT: H 413 MET cc_start: 0.5919 (pp-130) cc_final: 0.5698 (pp-130) REVERT: H 510 LEU cc_start: 0.7263 (OUTLIER) cc_final: 0.6835 (tm) REVERT: H 513 ASP cc_start: 0.4576 (m-30) cc_final: 0.4117 (p0) REVERT: H 519 GLU cc_start: 0.3701 (OUTLIER) cc_final: 0.2621 (tt0) REVERT: H 527 MET cc_start: 0.3050 (OUTLIER) cc_final: 0.1456 (mtt) REVERT: H 530 MET cc_start: 0.4110 (OUTLIER) cc_final: 0.2855 (mmt) REVERT: I 25 ILE cc_start: 0.7703 (mm) cc_final: 0.7482 (mt) REVERT: I 45 ASP cc_start: 0.2190 (m-30) cc_final: 0.0944 (m-30) REVERT: I 64 ILE cc_start: 0.4976 (OUTLIER) cc_final: 0.4500 (mt) REVERT: I 88 GLU cc_start: 0.6507 (OUTLIER) cc_final: 0.5878 (tp30) REVERT: I 93 THR cc_start: 0.4906 (OUTLIER) cc_final: 0.4699 (t) REVERT: I 161 LYS cc_start: 0.2085 (OUTLIER) cc_final: 0.1506 (tptt) REVERT: I 187 LYS cc_start: 0.5242 (ptmm) cc_final: 0.4608 (mttt) REVERT: I 194 LYS cc_start: 0.3339 (OUTLIER) cc_final: 0.3072 (tttp) REVERT: I 210 LYS cc_start: 0.4227 (OUTLIER) cc_final: 0.3306 (tptt) REVERT: I 241 ILE cc_start: 0.4487 (OUTLIER) cc_final: 0.4186 (mm) REVERT: I 243 GLU cc_start: 0.3173 (OUTLIER) cc_final: 0.2252 (pt0) REVERT: I 249 GLU cc_start: 0.6171 (tp30) cc_final: 0.5355 (mm-30) REVERT: I 382 ARG cc_start: 0.4240 (OUTLIER) cc_final: 0.3811 (ptp-110) REVERT: I 413 MET cc_start: 0.5949 (pp-130) cc_final: 0.5733 (pp-130) REVERT: I 510 LEU cc_start: 0.7231 (OUTLIER) cc_final: 0.6788 (tm) REVERT: I 513 ASP cc_start: 0.4629 (m-30) cc_final: 0.4169 (p0) REVERT: I 519 GLU cc_start: 0.3684 (OUTLIER) cc_final: 0.2578 (tt0) REVERT: I 527 MET cc_start: 0.3017 (OUTLIER) cc_final: 0.1444 (mtt) REVERT: I 530 MET cc_start: 0.4107 (OUTLIER) cc_final: 0.2839 (mmt) REVERT: J 64 ILE cc_start: 0.5077 (OUTLIER) cc_final: 0.4675 (mt) REVERT: J 72 HIS cc_start: 0.4428 (OUTLIER) cc_final: 0.4204 (t70) REVERT: J 88 GLU cc_start: 0.6098 (OUTLIER) cc_final: 0.4902 (tp30) REVERT: J 187 LYS cc_start: 0.5194 (ptmm) cc_final: 0.4671 (mttp) REVERT: J 241 ILE cc_start: 0.5375 (OUTLIER) cc_final: 0.5114 (mm) REVERT: J 243 GLU cc_start: 0.3754 (OUTLIER) cc_final: 0.3331 (pt0) REVERT: J 382 ARG cc_start: 0.4310 (OUTLIER) cc_final: 0.3912 (ptm160) REVERT: J 412 SER cc_start: 0.5419 (OUTLIER) cc_final: 0.4944 (p) REVERT: J 475 VAL cc_start: 0.7287 (t) cc_final: 0.7078 (p) REVERT: J 510 LEU cc_start: 0.7105 (OUTLIER) cc_final: 0.6852 (tm) REVERT: J 513 ASP cc_start: 0.5311 (m-30) cc_final: 0.4436 (p0) REVERT: J 527 MET cc_start: 0.3751 (OUTLIER) cc_final: 0.3141 (ttt) REVERT: J 530 MET cc_start: 0.4548 (OUTLIER) cc_final: 0.3313 (mmt) REVERT: K 25 ILE cc_start: 0.7699 (mm) cc_final: 0.7458 (mt) REVERT: K 45 ASP cc_start: 0.2196 (m-30) cc_final: 0.0947 (m-30) REVERT: K 64 ILE cc_start: 0.4956 (OUTLIER) cc_final: 0.4488 (mt) REVERT: K 88 GLU cc_start: 0.6503 (OUTLIER) cc_final: 0.5873 (tp30) REVERT: K 93 THR cc_start: 0.4903 (OUTLIER) cc_final: 0.4683 (t) REVERT: K 161 LYS cc_start: 0.2082 (OUTLIER) cc_final: 0.1503 (tptt) REVERT: K 187 LYS cc_start: 0.5239 (ptmm) cc_final: 0.4595 (mttt) REVERT: K 194 LYS cc_start: 0.3335 (OUTLIER) cc_final: 0.3070 (tttp) REVERT: K 210 LYS cc_start: 0.4224 (OUTLIER) cc_final: 0.3311 (tptt) REVERT: K 241 ILE cc_start: 0.4483 (OUTLIER) cc_final: 0.4183 (mm) REVERT: K 243 GLU cc_start: 0.3170 (OUTLIER) cc_final: 0.2252 (pt0) REVERT: K 249 GLU cc_start: 0.6164 (tp30) cc_final: 0.5349 (mm-30) REVERT: K 382 ARG cc_start: 0.4236 (OUTLIER) cc_final: 0.3807 (ptp-110) REVERT: K 413 MET cc_start: 0.5946 (pp-130) cc_final: 0.5731 (pp-130) REVERT: K 510 LEU cc_start: 0.7262 (OUTLIER) cc_final: 0.6818 (tm) REVERT: K 513 ASP cc_start: 0.4602 (m-30) cc_final: 0.4149 (p0) REVERT: K 519 GLU cc_start: 0.3689 (OUTLIER) cc_final: 0.2584 (tt0) REVERT: K 527 MET cc_start: 0.3009 (OUTLIER) cc_final: 0.1446 (mtt) REVERT: K 530 MET cc_start: 0.4098 (OUTLIER) cc_final: 0.2835 (mmt) REVERT: L 64 ILE cc_start: 0.5073 (OUTLIER) cc_final: 0.4676 (mt) REVERT: L 72 HIS cc_start: 0.4435 (OUTLIER) cc_final: 0.4203 (t70) REVERT: L 88 GLU cc_start: 0.6095 (OUTLIER) cc_final: 0.4908 (tp30) REVERT: L 161 LYS cc_start: 0.3009 (OUTLIER) cc_final: 0.2809 (tptt) REVERT: L 187 LYS cc_start: 0.5187 (ptmm) cc_final: 0.4660 (mttp) REVERT: L 241 ILE cc_start: 0.5365 (OUTLIER) cc_final: 0.5106 (mm) REVERT: L 243 GLU cc_start: 0.3754 (OUTLIER) cc_final: 0.3328 (pt0) REVERT: L 382 ARG cc_start: 0.4307 (OUTLIER) cc_final: 0.3918 (ptm160) REVERT: L 412 SER cc_start: 0.5416 (OUTLIER) cc_final: 0.4949 (p) REVERT: L 475 VAL cc_start: 0.7289 (t) cc_final: 0.7081 (p) REVERT: L 510 LEU cc_start: 0.7106 (OUTLIER) cc_final: 0.6853 (tm) REVERT: L 513 ASP cc_start: 0.5294 (m-30) cc_final: 0.4419 (p0) REVERT: L 527 MET cc_start: 0.3732 (OUTLIER) cc_final: 0.3133 (ttt) REVERT: L 530 MET cc_start: 0.4520 (OUTLIER) cc_final: 0.3298 (mmt) REVERT: M 25 ILE cc_start: 0.7696 (mm) cc_final: 0.7455 (mt) REVERT: M 45 ASP cc_start: 0.2206 (m-30) cc_final: 0.0953 (m-30) REVERT: M 64 ILE cc_start: 0.4970 (OUTLIER) cc_final: 0.4492 (mt) REVERT: M 88 GLU cc_start: 0.6507 (OUTLIER) cc_final: 0.5882 (tp30) REVERT: M 93 THR cc_start: 0.4906 (OUTLIER) cc_final: 0.4680 (t) REVERT: M 161 LYS cc_start: 0.2071 (OUTLIER) cc_final: 0.1487 (tptt) REVERT: M 187 LYS cc_start: 0.5245 (ptmm) cc_final: 0.4600 (mttt) REVERT: M 194 LYS cc_start: 0.3317 (OUTLIER) cc_final: 0.3054 (tttp) REVERT: M 210 LYS cc_start: 0.4230 (OUTLIER) cc_final: 0.3320 (tptt) REVERT: M 241 ILE cc_start: 0.4477 (OUTLIER) cc_final: 0.4175 (mm) REVERT: M 243 GLU cc_start: 0.3164 (OUTLIER) cc_final: 0.2249 (pt0) REVERT: M 249 GLU cc_start: 0.6188 (tp30) cc_final: 0.5352 (mm-30) REVERT: M 382 ARG cc_start: 0.4233 (OUTLIER) cc_final: 0.3806 (ptp-110) REVERT: M 413 MET cc_start: 0.5936 (pp-130) cc_final: 0.5720 (pp-130) REVERT: M 510 LEU cc_start: 0.7249 (OUTLIER) cc_final: 0.6805 (tm) REVERT: M 513 ASP cc_start: 0.4610 (m-30) cc_final: 0.4153 (p0) REVERT: M 519 GLU cc_start: 0.3685 (OUTLIER) cc_final: 0.2580 (tt0) REVERT: M 527 MET cc_start: 0.3026 (OUTLIER) cc_final: 0.1451 (mtt) REVERT: M 530 MET cc_start: 0.4085 (OUTLIER) cc_final: 0.2830 (mmt) REVERT: N 64 ILE cc_start: 0.5088 (OUTLIER) cc_final: 0.4689 (mt) REVERT: N 72 HIS cc_start: 0.4453 (OUTLIER) cc_final: 0.4195 (t70) REVERT: N 88 GLU cc_start: 0.6100 (OUTLIER) cc_final: 0.4918 (tp30) REVERT: N 187 LYS cc_start: 0.5182 (ptmm) cc_final: 0.4662 (mttp) REVERT: N 241 ILE cc_start: 0.5357 (OUTLIER) cc_final: 0.5109 (mm) REVERT: N 243 GLU cc_start: 0.3758 (OUTLIER) cc_final: 0.3334 (pt0) REVERT: N 382 ARG cc_start: 0.4300 (OUTLIER) cc_final: 0.3918 (ptm160) REVERT: N 412 SER cc_start: 0.5406 (OUTLIER) cc_final: 0.4948 (p) REVERT: N 510 LEU cc_start: 0.7154 (OUTLIER) cc_final: 0.6892 (tm) REVERT: N 513 ASP cc_start: 0.5258 (m-30) cc_final: 0.4393 (p0) REVERT: N 527 MET cc_start: 0.3742 (OUTLIER) cc_final: 0.3130 (ttt) REVERT: N 530 MET cc_start: 0.4543 (OUTLIER) cc_final: 0.3306 (mmt) REVERT: O 25 ILE cc_start: 0.7699 (mm) cc_final: 0.7484 (mt) REVERT: O 45 ASP cc_start: 0.2204 (m-30) cc_final: 0.0936 (m-30) REVERT: O 64 ILE cc_start: 0.4979 (OUTLIER) cc_final: 0.4492 (mt) REVERT: O 88 GLU cc_start: 0.6513 (OUTLIER) cc_final: 0.5891 (tp30) REVERT: O 93 THR cc_start: 0.4901 (OUTLIER) cc_final: 0.4684 (t) REVERT: O 161 LYS cc_start: 0.2087 (OUTLIER) cc_final: 0.1515 (tptt) REVERT: O 187 LYS cc_start: 0.5241 (ptmm) cc_final: 0.4595 (mttt) REVERT: O 194 LYS cc_start: 0.3316 (OUTLIER) cc_final: 0.3057 (tttp) REVERT: O 210 LYS cc_start: 0.4244 (OUTLIER) cc_final: 0.3316 (tptt) REVERT: O 241 ILE cc_start: 0.4481 (OUTLIER) cc_final: 0.4178 (mm) REVERT: O 243 GLU cc_start: 0.3168 (OUTLIER) cc_final: 0.2247 (pt0) REVERT: O 249 GLU cc_start: 0.6191 (tp30) cc_final: 0.5353 (mm-30) REVERT: O 382 ARG cc_start: 0.4239 (OUTLIER) cc_final: 0.3819 (ptp-110) REVERT: O 413 MET cc_start: 0.5935 (pp-130) cc_final: 0.5715 (pp-130) REVERT: O 510 LEU cc_start: 0.7264 (OUTLIER) cc_final: 0.6820 (tm) REVERT: O 513 ASP cc_start: 0.4606 (m-30) cc_final: 0.4152 (p0) REVERT: O 519 GLU cc_start: 0.3696 (OUTLIER) cc_final: 0.2590 (tt0) REVERT: O 527 MET cc_start: 0.3051 (OUTLIER) cc_final: 0.1462 (mtt) REVERT: O 530 MET cc_start: 0.4083 (OUTLIER) cc_final: 0.2834 (mmt) REVERT: P 64 ILE cc_start: 0.5093 (OUTLIER) cc_final: 0.4683 (mt) REVERT: P 72 HIS cc_start: 0.4436 (OUTLIER) cc_final: 0.4196 (t70) REVERT: P 88 GLU cc_start: 0.6120 (OUTLIER) cc_final: 0.4930 (tp30) REVERT: P 187 LYS cc_start: 0.5187 (ptmm) cc_final: 0.4668 (mttp) REVERT: P 241 ILE cc_start: 0.5372 (OUTLIER) cc_final: 0.5121 (mm) REVERT: P 243 GLU cc_start: 0.3760 (OUTLIER) cc_final: 0.3334 (pt0) REVERT: P 382 ARG cc_start: 0.4310 (OUTLIER) cc_final: 0.3920 (ptm160) REVERT: P 412 SER cc_start: 0.5424 (OUTLIER) cc_final: 0.4964 (p) REVERT: P 510 LEU cc_start: 0.7102 (OUTLIER) cc_final: 0.6854 (tm) REVERT: P 513 ASP cc_start: 0.5296 (m-30) cc_final: 0.4429 (p0) REVERT: P 527 MET cc_start: 0.3758 (OUTLIER) cc_final: 0.3140 (ttt) REVERT: P 530 MET cc_start: 0.4558 (OUTLIER) cc_final: 0.3327 (mmt) outliers start: 1632 outliers final: 750 residues processed: 2865 average time/residue: 0.6582 time to fit residues: 3086.9462 Evaluate side-chains 2233 residues out of total 6832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 934 poor density : 1299 time to evaluate : 5.748 ------------------------------------------------------------------------------- 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: 4.9990 chunk 642 optimal weight: 2.9990 chunk 356 optimal weight: 7.9990 chunk 219 optimal weight: 3.9990 chunk 433 optimal weight: 6.9990 chunk 343 optimal weight: 7.9990 chunk 664 optimal weight: 10.0000 chunk 257 optimal weight: 0.8980 chunk 404 optimal weight: 0.9980 chunk 494 optimal weight: 0.8980 chunk 770 optimal weight: 9.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- 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 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** A 500 GLN B 4 GLN B 114 ASN ** B 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 324 ASN ** B 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 497 GLN 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 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 114 ASN ** D 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 324 ASN ** D 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 497 GLN E 4 GLN ** E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 114 ASN ** F 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 324 ASN ** F 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 497 GLN 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 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 324 ASN ** H 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 497 GLN I 4 GLN I 114 ASN ** I 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 296 HIS ** 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 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 114 ASN ** K 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 324 ASN ** K 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 497 GLN L 4 GLN ** L 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 324 ASN ** M 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 497 GLN N 4 GLN N 114 ASN ** N 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 296 HIS ** 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 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 324 ASN ** O 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 497 GLN P 4 GLN P 114 ASN ** 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: 55 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4728 moved from start: 0.5464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 64112 Z= 0.330 Angle : 1.413 14.167 86240 Z= 0.735 Chirality : 0.066 0.279 10448 Planarity : 0.008 0.130 11216 Dihedral : 9.550 35.253 8928 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 39.86 Ramachandran Plot: Outliers : 5.77 % Allowed : 21.57 % Favored : 72.67 % Rotamer: Outliers : 1.76 % Allowed : 10.17 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -5.77 (0.07), residues: 8480 helix: -2.46 (0.07), residues: 3232 sheet: None (None), residues: 0 loop : -5.11 (0.06), residues: 5248 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS M 463 PHE 0.014 0.003 PHE F 261 TYR 0.008 0.002 TYR A 418 ARG 0.006 0.001 ARG J 308 *********************** 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 2131 residues out of total 6832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 2011 time to evaluate : 5.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 MET cc_start: 0.4462 (mpp) cc_final: 0.3439 (mmt) REVERT: A 48 LEU cc_start: 0.4321 (OUTLIER) cc_final: 0.3843 (pp) REVERT: A 71 GLU cc_start: 0.5119 (mm-30) cc_final: 0.4421 (mm-30) REVERT: A 117 PRO cc_start: 0.7617 (Cg_endo) cc_final: 0.7341 (Cg_exo) REVERT: A 415 LEU cc_start: 0.6539 (mt) cc_final: 0.5862 (mm) REVERT: A 433 PHE cc_start: 0.2850 (t80) cc_final: 0.2528 (t80) REVERT: A 527 MET cc_start: 0.3806 (ttt) cc_final: 0.3453 (ttt) REVERT: B 12 MET cc_start: 0.4525 (mmt) cc_final: 0.3758 (mmt) REVERT: B 23 MET cc_start: 0.4225 (tpt) cc_final: 0.3880 (ttt) REVERT: B 48 LEU cc_start: 0.4339 (OUTLIER) cc_final: 0.3950 (pp) REVERT: B 71 GLU cc_start: 0.4822 (mm-30) cc_final: 0.4233 (mm-30) REVERT: B 297 TYR cc_start: 0.3916 (m-80) cc_final: 0.3497 (m-80) REVERT: B 482 ASP cc_start: 0.5112 (t0) cc_final: 0.4845 (t0) REVERT: B 527 MET cc_start: 0.3036 (ttt) cc_final: 0.2815 (ttt) REVERT: C 12 MET cc_start: 0.4456 (mmt) cc_final: 0.3592 (mmt) REVERT: C 48 LEU cc_start: 0.4232 (OUTLIER) cc_final: 0.3782 (pp) REVERT: C 71 GLU cc_start: 0.5169 (mm-30) cc_final: 0.4452 (mm-30) REVERT: C 117 PRO cc_start: 0.7618 (Cg_endo) cc_final: 0.7323 (Cg_exo) REVERT: C 164 GLU cc_start: 0.6065 (pp20) cc_final: 0.5835 (pp20) REVERT: C 269 LEU cc_start: 0.7302 (mm) cc_final: 0.6996 (tp) REVERT: C 415 LEU cc_start: 0.6542 (mt) cc_final: 0.5880 (mm) REVERT: C 433 PHE cc_start: 0.2821 (t80) cc_final: 0.2494 (t80) REVERT: C 475 VAL cc_start: 0.7164 (t) cc_final: 0.6943 (p) REVERT: C 527 MET cc_start: 0.3902 (ttt) cc_final: 0.3594 (ttt) REVERT: D 12 MET cc_start: 0.4550 (mmt) cc_final: 0.3751 (mmt) REVERT: D 23 MET cc_start: 0.4262 (tpt) cc_final: 0.3869 (ttt) REVERT: D 48 LEU cc_start: 0.4352 (OUTLIER) cc_final: 0.3896 (pp) REVERT: D 71 GLU cc_start: 0.4789 (mm-30) cc_final: 0.4220 (mm-30) REVERT: D 297 TYR cc_start: 0.3917 (m-80) cc_final: 0.3497 (m-80) REVERT: D 527 MET cc_start: 0.2984 (ttt) cc_final: 0.2762 (ttt) REVERT: E 12 MET cc_start: 0.4470 (mmt) cc_final: 0.3537 (mmt) REVERT: E 48 LEU cc_start: 0.4235 (OUTLIER) cc_final: 0.3769 (pp) REVERT: E 71 GLU cc_start: 0.5156 (mm-30) cc_final: 0.4437 (mm-30) REVERT: E 117 PRO cc_start: 0.7598 (Cg_endo) cc_final: 0.7326 (Cg_exo) REVERT: E 164 GLU cc_start: 0.6064 (pp20) cc_final: 0.5825 (pp20) REVERT: E 269 LEU cc_start: 0.7313 (mm) cc_final: 0.7004 (tp) REVERT: E 415 LEU cc_start: 0.6545 (mt) cc_final: 0.5869 (mm) REVERT: E 433 PHE cc_start: 0.2815 (t80) cc_final: 0.2496 (t80) REVERT: E 475 VAL cc_start: 0.7153 (t) cc_final: 0.6943 (p) REVERT: E 527 MET cc_start: 0.3912 (ttt) cc_final: 0.3596 (ttt) REVERT: F 12 MET cc_start: 0.4551 (mmt) cc_final: 0.3765 (mmt) REVERT: F 23 MET cc_start: 0.4297 (tpt) cc_final: 0.3909 (ttt) REVERT: F 48 LEU cc_start: 0.4346 (OUTLIER) cc_final: 0.3862 (pp) REVERT: F 71 GLU cc_start: 0.4783 (mm-30) cc_final: 0.4223 (mm-30) REVERT: F 297 TYR cc_start: 0.3903 (m-80) cc_final: 0.3470 (m-80) REVERT: F 527 MET cc_start: 0.2997 (ttt) cc_final: 0.2784 (ttt) REVERT: G 12 MET cc_start: 0.4459 (mmt) cc_final: 0.3538 (mmt) REVERT: G 23 MET cc_start: 0.4434 (tpt) cc_final: 0.4215 (ttt) REVERT: G 48 LEU cc_start: 0.4263 (OUTLIER) cc_final: 0.3779 (pp) REVERT: G 71 GLU cc_start: 0.5159 (mm-30) cc_final: 0.4436 (mm-30) REVERT: G 117 PRO cc_start: 0.7602 (Cg_endo) cc_final: 0.7331 (Cg_exo) REVERT: G 164 GLU cc_start: 0.6059 (pp20) cc_final: 0.5826 (pp20) REVERT: G 269 LEU cc_start: 0.7303 (mm) cc_final: 0.6985 (tp) REVERT: G 415 LEU cc_start: 0.6552 (mt) cc_final: 0.5877 (mm) REVERT: G 433 PHE cc_start: 0.2811 (t80) cc_final: 0.2498 (t80) REVERT: G 527 MET cc_start: 0.3923 (ttt) cc_final: 0.3583 (ttt) REVERT: H 23 MET cc_start: 0.4289 (tpt) cc_final: 0.3744 (ttt) REVERT: H 48 LEU cc_start: 0.4329 (OUTLIER) cc_final: 0.3841 (pp) REVERT: H 71 GLU cc_start: 0.4762 (mm-30) cc_final: 0.4182 (mm-30) REVERT: H 297 TYR cc_start: 0.3884 (m-80) cc_final: 0.3463 (m-80) REVERT: I 12 MET cc_start: 0.4616 (mmt) cc_final: 0.3764 (mmt) REVERT: I 23 MET cc_start: 0.4366 (tpt) cc_final: 0.3933 (ttt) REVERT: I 48 LEU cc_start: 0.4349 (OUTLIER) cc_final: 0.3872 (pp) REVERT: I 71 GLU cc_start: 0.4748 (mm-30) cc_final: 0.4198 (mm-30) REVERT: I 297 TYR cc_start: 0.3855 (m-80) cc_final: 0.3403 (m-80) REVERT: I 527 MET cc_start: 0.3035 (ttt) cc_final: 0.2815 (ttt) REVERT: J 12 MET cc_start: 0.4480 (mmt) cc_final: 0.3538 (mmt) REVERT: J 23 MET cc_start: 0.4420 (tpt) cc_final: 0.4216 (ttt) REVERT: J 48 LEU cc_start: 0.4280 (OUTLIER) cc_final: 0.3799 (pp) REVERT: J 71 GLU cc_start: 0.5120 (mm-30) cc_final: 0.4436 (mm-30) REVERT: J 117 PRO cc_start: 0.7607 (Cg_endo) cc_final: 0.7295 (Cg_exo) REVERT: J 164 GLU cc_start: 0.6065 (pp20) cc_final: 0.5828 (pp20) REVERT: J 269 LEU cc_start: 0.7300 (mm) cc_final: 0.7025 (tp) REVERT: J 415 LEU cc_start: 0.6534 (mt) cc_final: 0.5867 (mm) REVERT: J 433 PHE cc_start: 0.2824 (t80) cc_final: 0.2514 (t80) REVERT: J 527 MET cc_start: 0.3914 (ttt) cc_final: 0.3588 (ttt) REVERT: K 12 MET cc_start: 0.4611 (mmt) cc_final: 0.3762 (mmt) REVERT: K 23 MET cc_start: 0.4320 (tpt) cc_final: 0.3891 (ttt) REVERT: K 48 LEU cc_start: 0.4358 (OUTLIER) cc_final: 0.3914 (pp) REVERT: K 71 GLU cc_start: 0.4755 (mm-30) cc_final: 0.4199 (mm-30) REVERT: K 297 TYR cc_start: 0.3856 (m-80) cc_final: 0.3419 (m-80) REVERT: K 527 MET cc_start: 0.3032 (ttt) cc_final: 0.2792 (ttt) REVERT: L 12 MET cc_start: 0.4481 (mmt) cc_final: 0.3545 (mmt) REVERT: L 48 LEU cc_start: 0.4314 (OUTLIER) cc_final: 0.3826 (pp) REVERT: L 71 GLU cc_start: 0.5134 (mm-30) cc_final: 0.4498 (mm-30) REVERT: L 117 PRO cc_start: 0.7614 (Cg_endo) cc_final: 0.7297 (Cg_exo) REVERT: L 164 GLU cc_start: 0.6154 (pp20) cc_final: 0.5927 (pp20) REVERT: L 269 LEU cc_start: 0.7309 (mm) cc_final: 0.7033 (tp) REVERT: L 415 LEU cc_start: 0.6521 (mt) cc_final: 0.5858 (mm) REVERT: L 433 PHE cc_start: 0.2830 (t80) cc_final: 0.2521 (t80) REVERT: L 527 MET cc_start: 0.3917 (ttt) cc_final: 0.3598 (ttt) REVERT: M 12 MET cc_start: 0.4576 (mmt) cc_final: 0.3751 (mmt) REVERT: M 23 MET cc_start: 0.4301 (tpt) cc_final: 0.3945 (ttt) REVERT: M 48 LEU cc_start: 0.4321 (OUTLIER) cc_final: 0.3854 (pp) REVERT: M 71 GLU cc_start: 0.4774 (mm-30) cc_final: 0.4230 (mm-30) REVERT: M 297 TYR cc_start: 0.3850 (m-80) cc_final: 0.3409 (m-80) REVERT: M 527 MET cc_start: 0.2983 (ttt) cc_final: 0.2741 (ttt) REVERT: N 12 MET cc_start: 0.4454 (mmt) cc_final: 0.3432 (mmt) REVERT: N 23 MET cc_start: 0.4442 (tpt) cc_final: 0.4231 (ttt) REVERT: N 48 LEU cc_start: 0.4339 (OUTLIER) cc_final: 0.3841 (pp) REVERT: N 71 GLU cc_start: 0.5124 (mm-30) cc_final: 0.4453 (mm-30) REVERT: N 117 PRO cc_start: 0.7600 (Cg_endo) cc_final: 0.7277 (Cg_exo) REVERT: N 164 GLU cc_start: 0.6079 (pp20) cc_final: 0.5830 (pp20) REVERT: N 269 LEU cc_start: 0.7294 (mm) cc_final: 0.7016 (tp) REVERT: N 415 LEU cc_start: 0.6527 (mt) cc_final: 0.5854 (mm) REVERT: N 433 PHE cc_start: 0.2841 (t80) cc_final: 0.2557 (t80) REVERT: N 527 MET cc_start: 0.3900 (ttt) cc_final: 0.3623 (ttt) REVERT: O 23 MET cc_start: 0.4362 (tpt) cc_final: 0.3795 (ttt) REVERT: O 48 LEU cc_start: 0.4335 (OUTLIER) cc_final: 0.3857 (pp) REVERT: O 71 GLU cc_start: 0.4757 (mm-30) cc_final: 0.4169 (mm-30) REVERT: O 297 TYR cc_start: 0.3848 (m-80) cc_final: 0.3379 (m-80) REVERT: P 12 MET cc_start: 0.4462 (mmt) cc_final: 0.3523 (mmt) REVERT: P 23 MET cc_start: 0.4431 (tpt) cc_final: 0.4204 (ttt) REVERT: P 48 LEU cc_start: 0.4286 (OUTLIER) cc_final: 0.3787 (pp) REVERT: P 71 GLU cc_start: 0.5121 (mm-30) cc_final: 0.4425 (mm-30) REVERT: P 117 PRO cc_start: 0.7606 (Cg_endo) cc_final: 0.7313 (Cg_exo) REVERT: P 164 GLU cc_start: 0.6075 (pp20) cc_final: 0.5824 (pp20) REVERT: P 269 LEU cc_start: 0.7296 (mm) cc_final: 0.7003 (tp) REVERT: P 415 LEU cc_start: 0.6529 (mt) cc_final: 0.5858 (mm) REVERT: P 433 PHE cc_start: 0.2840 (t80) cc_final: 0.2594 (t80) REVERT: P 527 MET cc_start: 0.3912 (ttt) cc_final: 0.3588 (ttt) outliers start: 120 outliers final: 32 residues processed: 2051 average time/residue: 0.6363 time to fit residues: 2133.5166 Evaluate side-chains 1309 residues out of total 6832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 1261 time to evaluate : 5.567 ------------------------------------------------------------------------------- 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: 6.9990 chunk 238 optimal weight: 10.0000 chunk 640 optimal weight: 20.0000 chunk 524 optimal weight: 0.2980 chunk 212 optimal weight: 10.0000 chunk 771 optimal weight: 20.0000 chunk 833 optimal weight: 10.0000 chunk 687 optimal weight: 8.9990 chunk 765 optimal weight: 7.9990 chunk 263 optimal weight: 6.9990 chunk 618 optimal weight: 8.9990 overall best weight: 6.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 HIS ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 GLN ** B 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 ASN ** B 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 HIS ** C 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 222 GLN ** D 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 447 ASN ** D 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 116 HIS ** E 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 447 ASN ** F 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 116 HIS ** G 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 447 ASN ** H 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 222 GLN ** I 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 447 ASN ** I 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 116 HIS ** J 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 222 GLN ** K 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 447 ASN ** K 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 116 HIS ** L 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 222 GLN ** M 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 447 ASN ** M 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 116 HIS ** N 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 222 GLN ** O 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 447 ASN ** O 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 116 HIS ** P 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5076 moved from start: 0.6521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 64112 Z= 0.391 Angle : 1.381 17.954 86240 Z= 0.715 Chirality : 0.061 0.266 10448 Planarity : 0.010 0.175 11216 Dihedral : 9.792 34.689 8928 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 41.30 Ramachandran Plot: Outliers : 5.55 % Allowed : 22.08 % Favored : 72.37 % Rotamer: Outliers : 1.29 % Allowed : 12.34 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.44 % 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: -5.38 (0.07), residues: 8480 helix: -2.00 (0.08), residues: 3328 sheet: None (None), residues: 0 loop : -5.03 (0.06), residues: 5152 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.003 HIS D 463 PHE 0.015 0.003 PHE N 355 TYR 0.012 0.003 TYR B 418 ARG 0.013 0.001 ARG N 431 *********************** 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 1625 residues out of total 6832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 1537 time to evaluate : 5.640 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: A 66 ARG cc_start: 0.7398 (mmp-170) cc_final: 0.6868 (mmp80) REVERT: A 68 MET cc_start: 0.2999 (tpt) cc_final: 0.2338 (tpt) REVERT: A 77 MET cc_start: 0.5247 (mmt) cc_final: 0.4234 (tmm) REVERT: A 314 MET cc_start: 0.5476 (mpp) cc_final: 0.5063 (mpp) REVERT: A 319 LYS cc_start: 0.6175 (mmmt) cc_final: 0.5818 (tppt) REVERT: B 22 ARG cc_start: 0.5525 (mtp180) cc_final: 0.5206 (mtp180) REVERT: B 23 MET cc_start: 0.3709 (tpt) cc_final: 0.3258 (ttt) REVERT: B 527 MET cc_start: 0.3086 (ttt) cc_final: 0.1768 (mpp) REVERT: C 66 ARG cc_start: 0.7386 (mmp-170) cc_final: 0.6828 (mmp80) REVERT: C 68 MET cc_start: 0.3065 (tpt) cc_final: 0.2329 (tpt) REVERT: C 77 MET cc_start: 0.5236 (mmt) cc_final: 0.4372 (tmm) REVERT: C 156 THR cc_start: 0.5143 (p) cc_final: 0.4639 (m) REVERT: C 265 GLU cc_start: 0.4885 (tp30) cc_final: 0.4682 (tp30) REVERT: C 314 MET cc_start: 0.5408 (mpp) cc_final: 0.5124 (mpp) REVERT: C 319 LYS cc_start: 0.6165 (mmmt) cc_final: 0.5813 (tppt) REVERT: D 22 ARG cc_start: 0.5551 (mtp180) cc_final: 0.5336 (mtp180) REVERT: D 23 MET cc_start: 0.3894 (tpt) cc_final: 0.3549 (ttt) REVERT: D 508 MET cc_start: 0.5658 (mmp) cc_final: 0.5286 (tpp) REVERT: D 527 MET cc_start: 0.3094 (ttt) cc_final: 0.1870 (mpp) REVERT: E 66 ARG cc_start: 0.7392 (mmp-170) cc_final: 0.6830 (mmp80) REVERT: E 68 MET cc_start: 0.3064 (tpt) cc_final: 0.2325 (tpt) REVERT: E 77 MET cc_start: 0.5239 (mmt) cc_final: 0.4375 (tmm) REVERT: E 117 PRO cc_start: 0.8338 (Cg_endo) cc_final: 0.8129 (Cg_exo) REVERT: E 156 THR cc_start: 0.5195 (p) cc_final: 0.4693 (m) REVERT: E 314 MET cc_start: 0.5383 (mpp) cc_final: 0.5126 (mpp) REVERT: E 319 LYS cc_start: 0.6180 (mmmt) cc_final: 0.5822 (tppt) REVERT: F 22 ARG cc_start: 0.5524 (mtp180) cc_final: 0.5200 (mtp180) REVERT: F 23 MET cc_start: 0.3871 (tpt) cc_final: 0.3520 (ttt) REVERT: F 527 MET cc_start: 0.3110 (ttt) cc_final: 0.1891 (mpp) REVERT: G 23 MET cc_start: 0.4576 (tpt) cc_final: 0.4043 (ttt) REVERT: G 66 ARG cc_start: 0.7374 (mmp-170) cc_final: 0.6838 (mmp80) REVERT: G 68 MET cc_start: 0.3081 (tpt) cc_final: 0.2253 (tpt) REVERT: G 77 MET cc_start: 0.5249 (mmt) cc_final: 0.4382 (tmm) REVERT: G 117 PRO cc_start: 0.8360 (Cg_endo) cc_final: 0.8149 (Cg_exo) REVERT: G 156 THR cc_start: 0.5220 (p) cc_final: 0.4710 (m) REVERT: G 314 MET cc_start: 0.5407 (mpp) cc_final: 0.5154 (mpp) REVERT: G 319 LYS cc_start: 0.6173 (mmmt) cc_final: 0.5807 (tppt) REVERT: H 22 ARG cc_start: 0.5491 (mtp180) cc_final: 0.5116 (mtp180) REVERT: H 23 MET cc_start: 0.3802 (tpt) cc_final: 0.3445 (ttt) REVERT: H 508 MET cc_start: 0.5646 (mmp) cc_final: 0.5288 (tpp) REVERT: H 530 MET cc_start: 0.5107 (mmt) cc_final: 0.3180 (mtt) REVERT: I 22 ARG cc_start: 0.5540 (mtp180) cc_final: 0.5249 (mtp180) REVERT: I 23 MET cc_start: 0.3815 (tpt) cc_final: 0.3511 (ttt) REVERT: I 527 MET cc_start: 0.3101 (ttt) cc_final: 0.1880 (mpp) REVERT: J 23 MET cc_start: 0.4599 (tpt) cc_final: 0.3992 (ttt) REVERT: J 66 ARG cc_start: 0.7389 (mmp-170) cc_final: 0.6854 (mmp80) REVERT: J 68 MET cc_start: 0.3092 (tpt) cc_final: 0.2268 (tpt) REVERT: J 77 MET cc_start: 0.5244 (mmt) cc_final: 0.4354 (tmm) REVERT: J 156 THR cc_start: 0.5204 (p) cc_final: 0.4726 (m) REVERT: J 269 LEU cc_start: 0.6877 (mm) cc_final: 0.6660 (tp) REVERT: J 314 MET cc_start: 0.5386 (mpp) cc_final: 0.5118 (mpp) REVERT: J 319 LYS cc_start: 0.6171 (mmmt) cc_final: 0.5797 (tppt) REVERT: K 22 ARG cc_start: 0.5513 (mtp180) cc_final: 0.5223 (mtp180) REVERT: K 23 MET cc_start: 0.3835 (tpt) cc_final: 0.3515 (ttt) REVERT: K 527 MET cc_start: 0.3098 (ttt) cc_final: 0.1787 (mpp) REVERT: L 66 ARG cc_start: 0.7460 (mmp-170) cc_final: 0.6878 (mmp80) REVERT: L 68 MET cc_start: 0.3083 (tpt) cc_final: 0.2337 (tpt) REVERT: L 77 MET cc_start: 0.5252 (mmt) cc_final: 0.4367 (tmm) REVERT: L 156 THR cc_start: 0.5397 (p) cc_final: 0.4835 (m) REVERT: L 269 LEU cc_start: 0.6893 (mm) cc_final: 0.6673 (tp) REVERT: L 314 MET cc_start: 0.5368 (mpp) cc_final: 0.5108 (mpp) REVERT: L 319 LYS cc_start: 0.6160 (mmmt) cc_final: 0.5787 (tppt) REVERT: M 22 ARG cc_start: 0.5526 (mtp180) cc_final: 0.5172 (mtp180) REVERT: M 23 MET cc_start: 0.3862 (tpt) cc_final: 0.3510 (ttt) REVERT: M 527 MET cc_start: 0.3082 (ttt) cc_final: 0.1763 (mpp) REVERT: N 23 MET cc_start: 0.4601 (tpt) cc_final: 0.4055 (ttt) REVERT: N 66 ARG cc_start: 0.7368 (mmp-170) cc_final: 0.6863 (mmp80) REVERT: N 68 MET cc_start: 0.2951 (tpt) cc_final: 0.2267 (tpt) REVERT: N 77 MET cc_start: 0.5257 (mmt) cc_final: 0.4397 (tmm) REVERT: N 156 THR cc_start: 0.5190 (p) cc_final: 0.4687 (m) REVERT: N 269 LEU cc_start: 0.6887 (mm) cc_final: 0.6650 (tp) REVERT: N 314 MET cc_start: 0.5376 (mpp) cc_final: 0.5119 (mpp) REVERT: N 319 LYS cc_start: 0.6157 (mmmt) cc_final: 0.5770 (tppt) REVERT: O 22 ARG cc_start: 0.5537 (mtp180) cc_final: 0.5241 (mtp180) REVERT: O 23 MET cc_start: 0.3767 (tpt) cc_final: 0.3465 (ttt) REVERT: O 530 MET cc_start: 0.5070 (mmt) cc_final: 0.3151 (mtt) REVERT: P 23 MET cc_start: 0.4596 (tpt) cc_final: 0.4002 (ttt) REVERT: P 66 ARG cc_start: 0.7439 (mmp-170) cc_final: 0.6892 (mmp80) REVERT: P 68 MET cc_start: 0.3067 (tpt) cc_final: 0.2231 (tpt) REVERT: P 77 MET cc_start: 0.5258 (mmt) cc_final: 0.4379 (tmm) REVERT: P 156 THR cc_start: 0.5213 (p) cc_final: 0.4724 (m) REVERT: P 314 MET cc_start: 0.5385 (mpp) cc_final: 0.5125 (mpp) REVERT: P 319 LYS cc_start: 0.6168 (mmmt) cc_final: 0.5770 (tppt) outliers start: 88 outliers final: 40 residues processed: 1570 average time/residue: 0.6342 time to fit residues: 1641.0964 Evaluate side-chains 1162 residues out of total 6832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 1122 time to evaluate : 5.608 ------------------------------------------------------------------------------- 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: 2.9990 chunk 580 optimal weight: 5.9990 chunk 400 optimal weight: 2.9990 chunk 85 optimal weight: 20.0000 chunk 368 optimal weight: 5.9990 chunk 518 optimal weight: 8.9990 chunk 774 optimal weight: 20.0000 chunk 819 optimal weight: 7.9990 chunk 404 optimal weight: 4.9990 chunk 733 optimal weight: 9.9990 chunk 220 optimal weight: 0.8980 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 497 GLN ** 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 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 468 ASN ** 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 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 497 GLN ** 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 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 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 497 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 497 GLN ** L 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 497 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** M 497 GLN ** N 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 468 ASN ** 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 497 GLN ** P 287 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** ** P 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4954 moved from start: 0.7344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 64112 Z= 0.290 Angle : 1.218 14.346 86240 Z= 0.621 Chirality : 0.056 0.238 10448 Planarity : 0.008 0.152 11216 Dihedral : 9.218 32.065 8928 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 34.28 Ramachandran Plot: Outliers : 5.20 % Allowed : 20.40 % Favored : 74.40 % Rotamer: Outliers : 0.25 % Allowed : 9.62 % Favored : 90.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -5.14 (0.07), residues: 8480 helix: -1.80 (0.08), residues: 3472 sheet: None (None), residues: 0 loop : -4.96 (0.06), residues: 5008 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS K 463 PHE 0.019 0.002 PHE B 433 TYR 0.009 0.002 TYR D 15 ARG 0.013 0.001 ARG N 431 *********************** 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 1466 residues out of total 6832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 1449 time to evaluate : 5.585 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: A 1 MET cc_start: 0.4791 (ptt) cc_final: 0.4539 (ptp) REVERT: A 19 ASP cc_start: 0.1542 (t0) cc_final: 0.1018 (p0) REVERT: A 71 GLU cc_start: 0.5348 (mm-30) cc_final: 0.4126 (tt0) REVERT: A 77 MET cc_start: 0.5307 (mmt) cc_final: 0.4504 (tmm) REVERT: A 319 LYS cc_start: 0.6399 (mmmt) cc_final: 0.6007 (tppt) REVERT: A 425 ARG cc_start: 0.4863 (tmt170) cc_final: 0.4645 (ttt-90) REVERT: A 513 ASP cc_start: 0.4398 (m-30) cc_final: 0.4099 (p0) REVERT: B 22 ARG cc_start: 0.5307 (mtp180) cc_final: 0.4944 (mtp180) REVERT: B 269 LEU cc_start: 0.6179 (tp) cc_final: 0.5959 (tp) REVERT: B 527 MET cc_start: 0.2503 (ttt) cc_final: 0.1644 (tpp) REVERT: B 530 MET cc_start: 0.4513 (mmt) cc_final: 0.2593 (mtt) REVERT: C 68 MET cc_start: 0.2891 (tpt) cc_final: 0.2574 (tpt) REVERT: C 77 MET cc_start: 0.5416 (mmt) cc_final: 0.4499 (tmm) REVERT: C 156 THR cc_start: 0.5033 (p) cc_final: 0.4327 (m) REVERT: C 319 LYS cc_start: 0.6413 (mmmt) cc_final: 0.6091 (tppt) REVERT: C 513 ASP cc_start: 0.4623 (m-30) cc_final: 0.4082 (p0) REVERT: D 22 ARG cc_start: 0.5450 (mtp180) cc_final: 0.5228 (mmm-85) REVERT: D 153 ILE cc_start: 0.3791 (pt) cc_final: 0.3540 (pt) REVERT: D 170 LEU cc_start: 0.6210 (pp) cc_final: 0.5966 (pp) REVERT: D 527 MET cc_start: 0.2507 (ttt) cc_final: 0.1636 (tpp) REVERT: D 530 MET cc_start: 0.4561 (mmt) cc_final: 0.2622 (mtt) REVERT: E 68 MET cc_start: 0.2908 (tpt) cc_final: 0.2499 (tpt) REVERT: E 77 MET cc_start: 0.5420 (mmt) cc_final: 0.4538 (tmm) REVERT: E 156 THR cc_start: 0.5063 (p) cc_final: 0.4347 (m) REVERT: E 319 LYS cc_start: 0.6443 (mmmt) cc_final: 0.6085 (tppt) REVERT: E 425 ARG cc_start: 0.4835 (tmt170) cc_final: 0.4563 (ttt-90) REVERT: E 513 ASP cc_start: 0.4609 (m-30) cc_final: 0.4070 (p0) REVERT: F 71 GLU cc_start: 0.5254 (mm-30) cc_final: 0.5030 (mm-30) REVERT: F 269 LEU cc_start: 0.6133 (tp) cc_final: 0.5911 (tp) REVERT: F 527 MET cc_start: 0.2501 (ttt) cc_final: 0.1631 (tpp) REVERT: F 530 MET cc_start: 0.4541 (mmt) cc_final: 0.2632 (mtt) REVERT: G 23 MET cc_start: 0.4470 (tpt) cc_final: 0.4263 (ttt) REVERT: G 68 MET cc_start: 0.2916 (tpt) cc_final: 0.2502 (tpt) REVERT: G 77 MET cc_start: 0.5470 (mmt) cc_final: 0.4554 (tmm) REVERT: G 156 THR cc_start: 0.5078 (p) cc_final: 0.4348 (m) REVERT: G 319 LYS cc_start: 0.6431 (mmmt) cc_final: 0.6080 (tppt) REVERT: G 425 ARG cc_start: 0.4881 (tmt170) cc_final: 0.4580 (ttt-90) REVERT: G 513 ASP cc_start: 0.4470 (m-30) cc_final: 0.4038 (p0) REVERT: H 71 GLU cc_start: 0.5180 (mm-30) cc_final: 0.4957 (mm-30) REVERT: H 530 MET cc_start: 0.4019 (mmt) cc_final: 0.1895 (mtp) REVERT: I 71 GLU cc_start: 0.5297 (mm-30) cc_final: 0.5083 (mm-30) REVERT: I 527 MET cc_start: 0.2503 (ttt) cc_final: 0.1634 (tpp) REVERT: I 530 MET cc_start: 0.4601 (mmt) cc_final: 0.2644 (mtt) REVERT: J 1 MET cc_start: 0.2743 (ptt) cc_final: 0.2462 (ptp) REVERT: J 23 MET cc_start: 0.4432 (tpt) cc_final: 0.4192 (ttt) REVERT: J 68 MET cc_start: 0.2963 (tpt) cc_final: 0.2485 (tpt) REVERT: J 77 MET cc_start: 0.5424 (mmt) cc_final: 0.4511 (tmm) REVERT: J 156 THR cc_start: 0.5074 (p) cc_final: 0.4363 (m) REVERT: J 269 LEU cc_start: 0.6766 (mm) cc_final: 0.6566 (tp) REVERT: J 319 LYS cc_start: 0.6416 (mmmt) cc_final: 0.6081 (tppt) REVERT: J 425 ARG cc_start: 0.4844 (tmt170) cc_final: 0.4519 (ttt-90) REVERT: J 513 ASP cc_start: 0.4425 (m-30) cc_final: 0.4040 (p0) REVERT: K 527 MET cc_start: 0.2813 (ttt) cc_final: 0.1833 (tpp) REVERT: K 530 MET cc_start: 0.4558 (mmt) cc_final: 0.2606 (mtt) REVERT: L 1 MET cc_start: 0.2826 (ptt) cc_final: 0.2350 (ptp) REVERT: L 68 MET cc_start: 0.2919 (tpt) cc_final: 0.2531 (tpt) REVERT: L 77 MET cc_start: 0.5424 (mmt) cc_final: 0.4519 (tmm) REVERT: L 156 THR cc_start: 0.4953 (p) cc_final: 0.4277 (m) REVERT: L 319 LYS cc_start: 0.6400 (mmmt) cc_final: 0.6091 (tppt) REVERT: L 425 ARG cc_start: 0.4836 (tmt170) cc_final: 0.4525 (ttt-90) REVERT: L 513 ASP cc_start: 0.4551 (m-30) cc_final: 0.4015 (p0) REVERT: M 527 MET cc_start: 0.2487 (ttt) cc_final: 0.1645 (tpp) REVERT: M 530 MET cc_start: 0.4570 (mmt) cc_final: 0.2586 (mtt) REVERT: N 1 MET cc_start: 0.2448 (ptt) cc_final: 0.0055 (ptp) REVERT: N 71 GLU cc_start: 0.5399 (mm-30) cc_final: 0.4222 (tt0) REVERT: N 77 MET cc_start: 0.5447 (mmt) cc_final: 0.4548 (tmm) REVERT: N 156 THR cc_start: 0.5076 (p) cc_final: 0.4334 (m) REVERT: N 269 LEU cc_start: 0.6746 (mm) cc_final: 0.6545 (tp) REVERT: N 319 LYS cc_start: 0.6386 (mmmt) cc_final: 0.6081 (tppt) REVERT: N 425 ARG cc_start: 0.4620 (tmt170) cc_final: 0.4373 (ttt-90) REVERT: N 442 ARG cc_start: 0.6633 (ttt180) cc_final: 0.6330 (ttt180) REVERT: N 513 ASP cc_start: 0.4400 (m-30) cc_final: 0.4012 (p0) REVERT: O 71 GLU cc_start: 0.5246 (mm-30) cc_final: 0.5027 (mm-30) REVERT: O 530 MET cc_start: 0.3961 (mmt) cc_final: 0.1694 (mtp) REVERT: P 1 MET cc_start: 0.3041 (ptt) cc_final: 0.2779 (ptm) REVERT: P 23 MET cc_start: 0.4435 (tpt) cc_final: 0.4209 (ttt) REVERT: P 68 MET cc_start: 0.2916 (tpt) cc_final: 0.2510 (tpt) REVERT: P 77 MET cc_start: 0.5453 (mmt) cc_final: 0.4512 (tmm) REVERT: P 156 THR cc_start: 0.5070 (p) cc_final: 0.4331 (m) REVERT: P 319 LYS cc_start: 0.6392 (mmmt) cc_final: 0.6066 (tppt) REVERT: P 425 ARG cc_start: 0.4814 (tmt170) cc_final: 0.4510 (ttt-90) REVERT: P 513 ASP cc_start: 0.4416 (m-30) cc_final: 0.4049 (p0) outliers start: 17 outliers final: 0 residues processed: 1466 average time/residue: 0.6163 time to fit residues: 1488.6299 Evaluate side-chains 1073 residues out of total 6832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1073 time to evaluate : 5.566 ------------------------------------------------------------------------------- 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: 9.9990 chunk 465 optimal weight: 5.9990 chunk 11 optimal weight: 7.9990 chunk 610 optimal weight: 6.9990 chunk 338 optimal weight: 3.9990 chunk 699 optimal weight: 1.9990 chunk 566 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 418 optimal weight: 2.9990 chunk 735 optimal weight: 9.9990 chunk 206 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 HIS ** 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 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 HIS ** C 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 497 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 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 296 HIS ** E 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 296 HIS ** G 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 497 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 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 497 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 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 296 HIS ** P 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4890 moved from start: 0.8020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 64112 Z= 0.256 Angle : 1.164 18.113 86240 Z= 0.583 Chirality : 0.055 0.241 10448 Planarity : 0.008 0.170 11216 Dihedral : 8.789 32.629 8928 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 30.31 Ramachandran Plot: Outliers : 5.00 % Allowed : 20.83 % Favored : 74.17 % Rotamer: Outliers : 0.01 % Allowed : 6.62 % Favored : 93.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 7.95 % 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: -4.79 (0.08), residues: 8480 helix: -1.46 (0.09), residues: 3312 sheet: None (None), residues: 0 loop : -4.71 (0.06), residues: 5168 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS A 463 PHE 0.020 0.002 PHE D 433 TYR 0.007 0.002 TYR E 15 ARG 0.005 0.001 ARG G 431 *********************** 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 1378 residues out of total 6832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1377 time to evaluate : 5.783 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: A 77 MET cc_start: 0.5111 (mmt) cc_final: 0.4655 (tmm) REVERT: A 156 THR cc_start: 0.5508 (p) cc_final: 0.5106 (m) REVERT: A 513 ASP cc_start: 0.4274 (OUTLIER) cc_final: 0.3752 (p0) REVERT: B 156 THR cc_start: 0.4968 (p) cc_final: 0.4588 (m) REVERT: B 527 MET cc_start: 0.2059 (ttt) cc_final: 0.1331 (tpp) REVERT: B 530 MET cc_start: 0.4586 (mmt) cc_final: 0.2492 (mtt) REVERT: C 68 MET cc_start: 0.3282 (tpt) cc_final: 0.2927 (tpt) REVERT: C 77 MET cc_start: 0.5358 (mmt) cc_final: 0.4782 (tmm) REVERT: C 156 THR cc_start: 0.5430 (p) cc_final: 0.5056 (m) REVERT: C 319 LYS cc_start: 0.6510 (mmmt) cc_final: 0.5670 (mmmm) REVERT: D 363 LYS cc_start: 0.3684 (mmmt) cc_final: 0.2741 (pttm) REVERT: D 451 ASP cc_start: 0.5562 (t0) cc_final: 0.5335 (t0) REVERT: D 527 MET cc_start: 0.2039 (ttt) cc_final: 0.1305 (tpp) REVERT: D 530 MET cc_start: 0.4546 (mmt) cc_final: 0.2487 (mtt) REVERT: E 68 MET cc_start: 0.3250 (tpt) cc_final: 0.2940 (tpt) REVERT: E 77 MET cc_start: 0.5362 (mmt) cc_final: 0.4772 (tmm) REVERT: E 156 THR cc_start: 0.5479 (p) cc_final: 0.5131 (m) REVERT: E 319 LYS cc_start: 0.6536 (mmmt) cc_final: 0.5682 (mmmm) REVERT: E 368 LEU cc_start: 0.4340 (pp) cc_final: 0.4124 (pp) REVERT: F 98 VAL cc_start: 0.8439 (t) cc_final: 0.8170 (t) REVERT: F 451 ASP cc_start: 0.5594 (t0) cc_final: 0.5344 (t0) REVERT: F 527 MET cc_start: 0.2034 (ttt) cc_final: 0.1275 (tpp) REVERT: F 530 MET cc_start: 0.4549 (mmt) cc_final: 0.2482 (mtt) REVERT: G 23 MET cc_start: 0.4450 (tpt) cc_final: 0.4040 (ttt) REVERT: G 68 MET cc_start: 0.3251 (tpt) cc_final: 0.2893 (tpt) REVERT: G 77 MET cc_start: 0.5480 (mmt) cc_final: 0.4839 (tmm) REVERT: G 156 THR cc_start: 0.5540 (p) cc_final: 0.5162 (m) REVERT: G 319 LYS cc_start: 0.6532 (mmmt) cc_final: 0.5686 (mmmm) REVERT: H 10 GLU cc_start: 0.5181 (tp30) cc_final: 0.4716 (tp30) REVERT: H 98 VAL cc_start: 0.8466 (t) cc_final: 0.8193 (t) REVERT: H 451 ASP cc_start: 0.5599 (t0) cc_final: 0.5371 (t0) REVERT: H 527 MET cc_start: 0.2641 (ttt) cc_final: 0.1956 (ttt) REVERT: H 530 MET cc_start: 0.4575 (mmt) cc_final: 0.1885 (mtm) REVERT: I 98 VAL cc_start: 0.8459 (t) cc_final: 0.8139 (t) REVERT: I 527 MET cc_start: 0.2038 (ttt) cc_final: 0.1355 (tpp) REVERT: I 530 MET cc_start: 0.4604 (mmt) cc_final: 0.2500 (mtt) REVERT: J 22 ARG cc_start: 0.5467 (ppt170) cc_final: 0.5244 (ppt170) REVERT: J 23 MET cc_start: 0.4408 (tpt) cc_final: 0.4076 (ttt) REVERT: J 68 MET cc_start: 0.3232 (tpt) cc_final: 0.2794 (tpt) REVERT: J 77 MET cc_start: 0.5398 (mmt) cc_final: 0.4737 (tmm) REVERT: J 156 THR cc_start: 0.5528 (p) cc_final: 0.5153 (m) REVERT: J 319 LYS cc_start: 0.6508 (mmmt) cc_final: 0.5699 (mmmm) REVERT: J 368 LEU cc_start: 0.4319 (pp) cc_final: 0.4075 (pp) REVERT: J 513 ASP cc_start: 0.4170 (m-30) cc_final: 0.3644 (p0) REVERT: K 98 VAL cc_start: 0.8444 (t) cc_final: 0.8121 (t) REVERT: K 451 ASP cc_start: 0.5570 (t0) cc_final: 0.5353 (t0) REVERT: K 527 MET cc_start: 0.2027 (ttt) cc_final: 0.1314 (tpp) REVERT: K 530 MET cc_start: 0.4566 (mmt) cc_final: 0.2581 (mtt) REVERT: L 22 ARG cc_start: 0.5272 (ppt170) cc_final: 0.5070 (ppt170) REVERT: L 68 MET cc_start: 0.3246 (tpt) cc_final: 0.2849 (tpt) REVERT: L 77 MET cc_start: 0.5318 (mmt) cc_final: 0.4700 (tmm) REVERT: L 156 THR cc_start: 0.5195 (p) cc_final: 0.4900 (m) REVERT: L 319 LYS cc_start: 0.6514 (mmmt) cc_final: 0.5684 (mmmm) REVERT: L 368 LEU cc_start: 0.4306 (pp) cc_final: 0.4067 (pp) REVERT: L 513 ASP cc_start: 0.4302 (m-30) cc_final: 0.3656 (p0) REVERT: M 98 VAL cc_start: 0.8436 (t) cc_final: 0.8179 (t) REVERT: M 527 MET cc_start: 0.2032 (ttt) cc_final: 0.1287 (tpp) REVERT: M 530 MET cc_start: 0.4565 (mmt) cc_final: 0.2570 (mtt) REVERT: N 77 MET cc_start: 0.5386 (mmt) cc_final: 0.4767 (tmm) REVERT: N 156 THR cc_start: 0.5534 (p) cc_final: 0.5113 (m) REVERT: N 319 LYS cc_start: 0.6491 (mmmt) cc_final: 0.5665 (mmmm) REVERT: N 368 LEU cc_start: 0.4285 (pp) cc_final: 0.4076 (pp) REVERT: N 513 ASP cc_start: 0.4226 (m-30) cc_final: 0.3484 (p0) REVERT: O 10 GLU cc_start: 0.4957 (tp30) cc_final: 0.4542 (tp30) REVERT: O 98 VAL cc_start: 0.8637 (t) cc_final: 0.8227 (t) REVERT: O 527 MET cc_start: 0.2624 (ttt) cc_final: 0.1936 (ttt) REVERT: O 530 MET cc_start: 0.4621 (mmt) cc_final: 0.1794 (mtm) REVERT: P 1 MET cc_start: 0.2097 (ptt) cc_final: 0.1293 (ptp) REVERT: P 22 ARG cc_start: 0.5491 (ppt170) cc_final: 0.5190 (ppt170) REVERT: P 23 MET cc_start: 0.4436 (tpt) cc_final: 0.4081 (ttt) REVERT: P 68 MET cc_start: 0.3275 (tpt) cc_final: 0.2849 (tpt) REVERT: P 77 MET cc_start: 0.5457 (mmt) cc_final: 0.4793 (tmm) REVERT: P 156 THR cc_start: 0.5541 (p) cc_final: 0.5160 (m) REVERT: P 319 LYS cc_start: 0.6496 (mmmt) cc_final: 0.5660 (mmmm) REVERT: P 368 LEU cc_start: 0.4300 (pp) cc_final: 0.4075 (pp) REVERT: P 513 ASP cc_start: 0.4115 (m-30) cc_final: 0.3547 (p0) outliers start: 1 outliers final: 0 residues processed: 1377 average time/residue: 0.6105 time to fit residues: 1397.6965 Evaluate side-chains 1082 residues out of total 6832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1081 time to evaluate : 5.613 ------------------------------------------------------------------------------- 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: 5.9990 chunk 738 optimal weight: 0.9990 chunk 162 optimal weight: 10.0000 chunk 481 optimal weight: 5.9990 chunk 202 optimal weight: 1.9990 chunk 820 optimal weight: 0.9980 chunk 681 optimal weight: 7.9990 chunk 379 optimal weight: 10.0000 chunk 68 optimal weight: 3.9990 chunk 271 optimal weight: 5.9990 chunk 430 optimal weight: 9.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 497 GLN ** 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 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 HIS ** C 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 497 GLN ** D 296 HIS ** 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 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 296 HIS ** E 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 497 GLN F 296 HIS ** F 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 296 HIS ** G 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 497 GLN ** H 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 427 GLN ** H 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 497 GLN ** K 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 497 GLN ** M 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 497 GLN O 427 GLN ** O 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 287 GLN ** 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: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4888 moved from start: 0.8345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 64112 Z= 0.257 Angle : 1.117 15.328 86240 Z= 0.564 Chirality : 0.053 0.237 10448 Planarity : 0.008 0.149 11216 Dihedral : 8.619 31.504 8928 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 30.04 Ramachandran Plot: Outliers : 4.42 % Allowed : 21.13 % Favored : 74.45 % Rotamer: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % 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: -4.69 (0.08), residues: 8480 helix: -1.47 (0.08), residues: 3440 sheet: None (None), residues: 0 loop : -4.64 (0.07), residues: 5040 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.002 HIS P 296 PHE 0.020 0.002 PHE N 433 TYR 0.009 0.002 TYR A 297 ARG 0.008 0.001 ARG M 22 *********************** 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 1377 residues out of total 6832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1377 time to evaluate : 5.768 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: A 77 MET cc_start: 0.5076 (mmt) cc_final: 0.4458 (tmm) REVERT: A 156 THR cc_start: 0.5975 (p) cc_final: 0.5513 (m) REVERT: A 236 ASN cc_start: 0.6543 (m110) cc_final: 0.6313 (m110) REVERT: A 267 LYS cc_start: 0.7896 (tmtt) cc_final: 0.7642 (tmtt) REVERT: B 16 MET cc_start: 0.4244 (ttm) cc_final: 0.4040 (ttm) REVERT: B 527 MET cc_start: 0.2315 (ttt) cc_final: 0.1473 (tpp) REVERT: B 530 MET cc_start: 0.4878 (mmt) cc_final: 0.2693 (mtt) REVERT: C 68 MET cc_start: 0.3026 (tpt) cc_final: 0.2582 (tpt) REVERT: C 77 MET cc_start: 0.5036 (mmt) cc_final: 0.4447 (tmm) REVERT: C 156 THR cc_start: 0.5959 (p) cc_final: 0.5553 (m) REVERT: C 314 MET cc_start: 0.4941 (mpp) cc_final: 0.4402 (mpp) REVERT: D 363 LYS cc_start: 0.4108 (mmmt) cc_final: 0.2988 (mtmm) REVERT: D 394 THR cc_start: 0.6031 (p) cc_final: 0.5723 (m) REVERT: D 527 MET cc_start: 0.2313 (ttt) cc_final: 0.1448 (tpp) REVERT: D 530 MET cc_start: 0.4828 (mmt) cc_final: 0.2742 (mtt) REVERT: E 1 MET cc_start: 0.0066 (ptm) cc_final: -0.0206 (ptm) REVERT: E 68 MET cc_start: 0.3030 (tpt) cc_final: 0.2816 (tpt) REVERT: E 77 MET cc_start: 0.5040 (mmt) cc_final: 0.4452 (tmm) REVERT: E 156 THR cc_start: 0.5997 (p) cc_final: 0.5568 (m) REVERT: E 314 MET cc_start: 0.4937 (mpp) cc_final: 0.4197 (mpp) REVERT: E 394 THR cc_start: 0.6550 (p) cc_final: 0.6044 (m) REVERT: F 153 ILE cc_start: 0.3615 (pt) cc_final: 0.3390 (pt) REVERT: F 363 LYS cc_start: 0.4093 (tppt) cc_final: 0.3390 (mtmm) REVERT: F 527 MET cc_start: 0.2244 (ttt) cc_final: 0.1409 (tpp) REVERT: F 530 MET cc_start: 0.4778 (mmt) cc_final: 0.2729 (mtt) REVERT: G 68 MET cc_start: 0.3258 (tpt) cc_final: 0.2761 (tpt) REVERT: G 77 MET cc_start: 0.5110 (mmt) cc_final: 0.4464 (tmm) REVERT: G 156 THR cc_start: 0.6088 (p) cc_final: 0.5526 (m) REVERT: G 314 MET cc_start: 0.4943 (mpp) cc_final: 0.4216 (mpp) REVERT: G 394 THR cc_start: 0.6605 (p) cc_final: 0.6118 (m) REVERT: H 10 GLU cc_start: 0.5340 (tp30) cc_final: 0.4545 (tp30) REVERT: H 363 LYS cc_start: 0.4036 (tppt) cc_final: 0.3349 (mtmm) REVERT: H 527 MET cc_start: 0.2593 (ttt) cc_final: 0.2092 (ttt) REVERT: H 530 MET cc_start: 0.4816 (mmt) cc_final: 0.2053 (mtm) REVERT: I 153 ILE cc_start: 0.3877 (pt) cc_final: 0.3652 (pt) REVERT: I 363 LYS cc_start: 0.4063 (tppt) cc_final: 0.3364 (mtmm) REVERT: I 513 ASP cc_start: 0.4397 (m-30) cc_final: 0.4160 (m-30) REVERT: I 527 MET cc_start: 0.2347 (ttt) cc_final: 0.1449 (tpp) REVERT: I 530 MET cc_start: 0.4862 (mmt) cc_final: 0.2757 (mtt) REVERT: J 23 MET cc_start: 0.4383 (tpt) cc_final: 0.4006 (ttt) REVERT: J 68 MET cc_start: 0.3200 (tpt) cc_final: 0.2977 (tpt) REVERT: J 77 MET cc_start: 0.5026 (mmt) cc_final: 0.4376 (tmm) REVERT: J 156 THR cc_start: 0.6055 (p) cc_final: 0.5563 (m) REVERT: J 314 MET cc_start: 0.4906 (mpp) cc_final: 0.4360 (mpp) REVERT: J 394 THR cc_start: 0.6568 (p) cc_final: 0.6074 (m) REVERT: K 153 ILE cc_start: 0.3869 (pt) cc_final: 0.3626 (pt) REVERT: K 170 LEU cc_start: 0.5913 (pp) cc_final: 0.5634 (pp) REVERT: K 363 LYS cc_start: 0.4119 (tppt) cc_final: 0.3371 (mtmm) REVERT: K 527 MET cc_start: 0.2352 (ttt) cc_final: 0.1499 (tpp) REVERT: K 530 MET cc_start: 0.4532 (mmt) cc_final: 0.2615 (mtt) REVERT: L 68 MET cc_start: 0.3135 (tpt) cc_final: 0.2724 (tpt) REVERT: L 77 MET cc_start: 0.5011 (mmt) cc_final: 0.4395 (tmm) REVERT: L 156 THR cc_start: 0.5629 (p) cc_final: 0.5177 (m) REVERT: L 236 ASN cc_start: 0.6491 (m110) cc_final: 0.6289 (m110) REVERT: L 314 MET cc_start: 0.4931 (mpp) cc_final: 0.4382 (mpp) REVERT: L 394 THR cc_start: 0.6689 (p) cc_final: 0.6149 (m) REVERT: M 153 ILE cc_start: 0.3659 (pt) cc_final: 0.3433 (pt) REVERT: M 363 LYS cc_start: 0.4083 (tppt) cc_final: 0.3357 (mtmm) REVERT: M 527 MET cc_start: 0.2389 (ttt) cc_final: 0.1564 (tpp) REVERT: M 530 MET cc_start: 0.4537 (mmt) cc_final: 0.2636 (mtt) REVERT: N 77 MET cc_start: 0.4993 (mmt) cc_final: 0.4458 (tmm) REVERT: N 156 THR cc_start: 0.6088 (p) cc_final: 0.5563 (m) REVERT: N 314 MET cc_start: 0.4917 (mpp) cc_final: 0.4360 (mpp) REVERT: N 394 THR cc_start: 0.6622 (p) cc_final: 0.6104 (m) REVERT: O 10 GLU cc_start: 0.5305 (tp30) cc_final: 0.4518 (tp30) REVERT: O 153 ILE cc_start: 0.3881 (pt) cc_final: 0.3607 (pt) REVERT: O 170 LEU cc_start: 0.5885 (pp) cc_final: 0.5598 (pp) REVERT: O 363 LYS cc_start: 0.4061 (tppt) cc_final: 0.3346 (mtmm) REVERT: O 527 MET cc_start: 0.2591 (ttt) cc_final: 0.2040 (ttt) REVERT: O 530 MET cc_start: 0.4738 (mmt) cc_final: 0.2157 (mtm) REVERT: P 23 MET cc_start: 0.4295 (tpt) cc_final: 0.3866 (ttt) REVERT: P 68 MET cc_start: 0.2978 (tpt) cc_final: 0.2674 (tpt) REVERT: P 77 MET cc_start: 0.5055 (mmt) cc_final: 0.4442 (tmm) REVERT: P 156 THR cc_start: 0.6108 (p) cc_final: 0.5539 (m) REVERT: P 314 MET cc_start: 0.4931 (mpp) cc_final: 0.4319 (mpp) REVERT: P 394 THR cc_start: 0.6542 (p) cc_final: 0.6084 (m) outliers start: 0 outliers final: 0 residues processed: 1377 average time/residue: 0.6111 time to fit residues: 1396.5263 Evaluate side-chains 1085 residues out of total 6832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1085 time to evaluate : 5.645 ------------------------------------------------------------------------------- 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: 4.9990 chunk 92 optimal weight: 30.0000 chunk 467 optimal weight: 6.9990 chunk 599 optimal weight: 9.9990 chunk 464 optimal weight: 1.9990 chunk 690 optimal weight: 9.9990 chunk 458 optimal weight: 3.9990 chunk 817 optimal weight: 8.9990 chunk 511 optimal weight: 7.9990 chunk 498 optimal weight: 10.0000 chunk 377 optimal weight: 7.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 ASN ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 HIS ** 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 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 468 ASN C 497 GLN ** D 296 HIS ** 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 E 497 GLN ** F 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 468 ASN G 497 GLN ** H 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 427 GLN ** H 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 296 HIS ** I 468 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 J 497 GLN K 296 HIS ** K 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 468 ASN L 497 GLN M 296 HIS ** M 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 468 ASN N 497 GLN O 296 HIS O 427 GLN ** O 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 468 ASN P 497 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5033 moved from start: 0.8601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 64112 Z= 0.321 Angle : 1.201 16.160 86240 Z= 0.605 Chirality : 0.057 0.296 10448 Planarity : 0.008 0.161 11216 Dihedral : 8.933 39.084 8928 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 33.92 Ramachandran Plot: Outliers : 4.43 % Allowed : 23.03 % Favored : 72.54 % Rotamer: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 9.09 % Twisted General : 0.20 % 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: -4.63 (0.08), residues: 8480 helix: -1.36 (0.09), residues: 3232 sheet: None (None), residues: 0 loop : -4.55 (0.07), residues: 5248 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS P 463 PHE 0.013 0.002 PHE L 355 TYR 0.016 0.003 TYR A 15 ARG 0.013 0.001 ARG N 431 *********************** 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 1287 residues out of total 6832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1287 time to evaluate : 5.639 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: A 77 MET cc_start: 0.5117 (mmt) cc_final: 0.4174 (tmm) REVERT: A 79 ILE cc_start: 0.7537 (mt) cc_final: 0.7310 (mt) REVERT: A 156 THR cc_start: 0.6063 (p) cc_final: 0.5693 (m) REVERT: A 314 MET cc_start: 0.5560 (mpp) cc_final: 0.3877 (mpp) REVERT: A 451 ASP cc_start: 0.4643 (t0) cc_final: 0.4393 (t0) REVERT: B 68 MET cc_start: 0.3517 (tpt) cc_final: 0.3254 (tpt) REVERT: B 527 MET cc_start: 0.2386 (ttt) cc_final: 0.1424 (tpp) REVERT: B 530 MET cc_start: 0.4856 (mmt) cc_final: 0.2967 (mtt) REVERT: C 16 MET cc_start: 0.6608 (tpp) cc_final: 0.6301 (tpp) REVERT: C 68 MET cc_start: 0.4153 (tpt) cc_final: 0.3672 (tpt) REVERT: C 77 MET cc_start: 0.5052 (mmt) cc_final: 0.4235 (tmm) REVERT: C 84 THR cc_start: 0.4179 (p) cc_final: 0.3801 (t) REVERT: C 156 THR cc_start: 0.6117 (p) cc_final: 0.5653 (m) REVERT: C 314 MET cc_start: 0.5725 (mpp) cc_final: 0.5120 (mpp) REVERT: C 442 ARG cc_start: 0.5948 (ptm160) cc_final: 0.5241 (ttp-170) REVERT: D 68 MET cc_start: 0.2869 (tpt) cc_final: 0.2524 (tpt) REVERT: D 394 THR cc_start: 0.6089 (p) cc_final: 0.5675 (m) REVERT: D 527 MET cc_start: 0.2388 (ttt) cc_final: 0.1467 (tpp) REVERT: D 530 MET cc_start: 0.4958 (mmt) cc_final: 0.2962 (mtt) REVERT: E 1 MET cc_start: 0.0314 (ptm) cc_final: -0.0087 (ptm) REVERT: E 68 MET cc_start: 0.3365 (tpt) cc_final: 0.2848 (tpt) REVERT: E 77 MET cc_start: 0.5054 (mmt) cc_final: 0.4147 (tmm) REVERT: E 156 THR cc_start: 0.6117 (p) cc_final: 0.5708 (m) REVERT: E 267 LYS cc_start: 0.7164 (tptt) cc_final: 0.6866 (tptp) REVERT: E 314 MET cc_start: 0.5717 (mpp) cc_final: 0.5088 (mpp) REVERT: E 442 ARG cc_start: 0.5898 (ptm160) cc_final: 0.5225 (ttp-170) REVERT: E 513 ASP cc_start: 0.4139 (m-30) cc_final: 0.3788 (p0) REVERT: F 68 MET cc_start: 0.3519 (tpt) cc_final: 0.3252 (tpt) REVERT: F 527 MET cc_start: 0.2362 (ttt) cc_final: 0.1418 (tpp) REVERT: F 530 MET cc_start: 0.4924 (mmt) cc_final: 0.3032 (mtt) REVERT: G 68 MET cc_start: 0.3999 (tpt) cc_final: 0.3391 (tpt) REVERT: G 77 MET cc_start: 0.5090 (mmt) cc_final: 0.4205 (tmm) REVERT: G 156 THR cc_start: 0.6138 (p) cc_final: 0.5698 (m) REVERT: G 267 LYS cc_start: 0.7161 (tptt) cc_final: 0.6916 (tptp) REVERT: G 314 MET cc_start: 0.5693 (mpp) cc_final: 0.5056 (mpp) REVERT: G 442 ARG cc_start: 0.5962 (ptm160) cc_final: 0.5288 (ttp-170) REVERT: G 513 ASP cc_start: 0.4325 (m-30) cc_final: 0.3947 (p0) REVERT: H 10 GLU cc_start: 0.5593 (tp30) cc_final: 0.5028 (tp30) REVERT: H 68 MET cc_start: 0.3115 (tpt) cc_final: 0.2819 (tpt) REVERT: H 530 MET cc_start: 0.4944 (mmt) cc_final: 0.2416 (mtm) REVERT: I 68 MET cc_start: 0.3575 (tpt) cc_final: 0.3326 (tpt) REVERT: I 267 LYS cc_start: 0.6837 (tptt) cc_final: 0.6445 (tptm) REVERT: I 527 MET cc_start: 0.2449 (ttt) cc_final: 0.1460 (tpp) REVERT: I 530 MET cc_start: 0.5096 (mmt) cc_final: 0.3074 (mtt) REVERT: J 23 MET cc_start: 0.4322 (tpt) cc_final: 0.4110 (ttt) REVERT: J 68 MET cc_start: 0.3598 (tpt) cc_final: 0.3342 (tpt) REVERT: J 71 GLU cc_start: 0.4873 (mm-30) cc_final: 0.4638 (mm-30) REVERT: J 77 MET cc_start: 0.5002 (mmt) cc_final: 0.4131 (tmm) REVERT: J 156 THR cc_start: 0.6101 (p) cc_final: 0.5692 (m) REVERT: J 236 ASN cc_start: 0.6717 (m110) cc_final: 0.6464 (m-40) REVERT: J 314 MET cc_start: 0.5714 (mpp) cc_final: 0.5049 (mpp) REVERT: J 442 ARG cc_start: 0.6001 (ptm160) cc_final: 0.5282 (ttp-170) REVERT: K 1 MET cc_start: 0.2428 (ptm) cc_final: 0.1294 (ptm) REVERT: K 267 LYS cc_start: 0.6995 (tptt) cc_final: 0.6676 (tptm) REVERT: K 527 MET cc_start: 0.2431 (ttt) cc_final: 0.1456 (tpp) REVERT: K 530 MET cc_start: 0.4826 (mmt) cc_final: 0.2734 (mtp) REVERT: L 16 MET cc_start: 0.5556 (tmm) cc_final: 0.5128 (tpt) REVERT: L 68 MET cc_start: 0.4051 (tpt) cc_final: 0.3482 (tpt) REVERT: L 77 MET cc_start: 0.5038 (mmt) cc_final: 0.4170 (tmm) REVERT: L 156 THR cc_start: 0.6039 (p) cc_final: 0.5589 (m) REVERT: L 236 ASN cc_start: 0.6811 (m110) cc_final: 0.6592 (m-40) REVERT: L 314 MET cc_start: 0.5729 (mpp) cc_final: 0.5067 (mpp) REVERT: L 442 ARG cc_start: 0.6023 (ptm160) cc_final: 0.5282 (ttp-170) REVERT: M 68 MET cc_start: 0.3329 (tpt) cc_final: 0.3085 (tpt) REVERT: M 267 LYS cc_start: 0.7005 (tptt) cc_final: 0.6663 (tptm) REVERT: M 527 MET cc_start: 0.2406 (ttt) cc_final: 0.1498 (tpp) REVERT: M 530 MET cc_start: 0.4794 (mmt) cc_final: 0.2779 (mtp) REVERT: N 71 GLU cc_start: 0.4701 (mm-30) cc_final: 0.4490 (mm-30) REVERT: N 77 MET cc_start: 0.4891 (mmt) cc_final: 0.4147 (tmm) REVERT: N 156 THR cc_start: 0.6121 (p) cc_final: 0.5672 (m) REVERT: N 236 ASN cc_start: 0.6689 (m110) cc_final: 0.6438 (m-40) REVERT: N 314 MET cc_start: 0.5739 (mpp) cc_final: 0.5060 (mpp) REVERT: N 442 ARG cc_start: 0.5873 (ptt180) cc_final: 0.5563 (ttt180) REVERT: O 10 GLU cc_start: 0.5718 (tp30) cc_final: 0.5114 (tp30) REVERT: O 68 MET cc_start: 0.3102 (tpt) cc_final: 0.2895 (tpt) REVERT: O 267 LYS cc_start: 0.7001 (tptt) cc_final: 0.6680 (tptm) REVERT: O 530 MET cc_start: 0.4833 (mmt) cc_final: 0.2237 (mtm) REVERT: P 23 MET cc_start: 0.4478 (tpt) cc_final: 0.4244 (ttt) REVERT: P 68 MET cc_start: 0.3317 (tpt) cc_final: 0.2846 (tpt) REVERT: P 77 MET cc_start: 0.5096 (mmt) cc_final: 0.4239 (tmm) REVERT: P 156 THR cc_start: 0.6140 (p) cc_final: 0.5707 (m) REVERT: P 314 MET cc_start: 0.5704 (mpp) cc_final: 0.5079 (mpp) REVERT: P 442 ARG cc_start: 0.5997 (ptm160) cc_final: 0.5295 (ttp-170) outliers start: 0 outliers final: 0 residues processed: 1287 average time/residue: 0.6638 time to fit residues: 1418.7410 Evaluate side-chains 984 residues out of total 6832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 984 time to evaluate : 5.693 ------------------------------------------------------------------------------- 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: 0.4980 chunk 326 optimal weight: 5.9990 chunk 488 optimal weight: 7.9990 chunk 246 optimal weight: 4.9990 chunk 160 optimal weight: 4.9990 chunk 158 optimal weight: 0.9990 chunk 519 optimal weight: 10.0000 chunk 556 optimal weight: 5.9990 chunk 404 optimal weight: 20.0000 chunk 76 optimal weight: 4.9990 chunk 642 optimal weight: 5.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** B 497 GLN ** 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 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 296 HIS ** F 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 296 HIS ** I 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 296 HIS ** K 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 296 HIS ** M 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 296 HIS ** O 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4943 moved from start: 0.8964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 64112 Z= 0.276 Angle : 1.146 16.225 86240 Z= 0.572 Chirality : 0.055 0.276 10448 Planarity : 0.007 0.142 11216 Dihedral : 8.650 32.100 8928 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 31.46 Ramachandran Plot: Outliers : 4.27 % Allowed : 21.44 % Favored : 74.29 % Rotamer: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 8.52 % 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: -4.65 (0.08), residues: 8480 helix: -1.38 (0.09), residues: 3440 sheet: None (None), residues: 0 loop : -4.67 (0.07), residues: 5040 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.002 HIS F 296 PHE 0.010 0.002 PHE O 285 TYR 0.011 0.002 TYR F 297 ARG 0.014 0.001 ARG G 382 *********************** 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 1240 residues out of total 6832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1240 time to evaluate : 5.716 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: A 33 GLU cc_start: 0.5920 (pp20) cc_final: 0.5717 (pp20) REVERT: A 44 MET cc_start: 0.3220 (pmm) cc_final: 0.2364 (pmm) REVERT: A 77 MET cc_start: 0.4932 (mmt) cc_final: 0.4250 (tmm) REVERT: A 156 THR cc_start: 0.5885 (p) cc_final: 0.5593 (m) REVERT: A 314 MET cc_start: 0.5768 (mpp) cc_final: 0.4169 (mpp) REVERT: A 394 THR cc_start: 0.6007 (p) cc_final: 0.5741 (m) REVERT: A 527 MET cc_start: 0.3614 (ttt) cc_final: 0.2840 (tpp) REVERT: A 530 MET cc_start: 0.5371 (mmt) cc_final: 0.3794 (mtt) REVERT: B 1 MET cc_start: 0.1906 (ppp) cc_final: 0.1507 (ppp) REVERT: B 46 LYS cc_start: 0.5097 (mmmt) cc_final: 0.4741 (tptp) REVERT: B 507 GLU cc_start: 0.6425 (mm-30) cc_final: 0.5751 (mm-30) REVERT: B 527 MET cc_start: 0.2678 (ttt) cc_final: 0.1547 (tpp) REVERT: B 530 MET cc_start: 0.5064 (mmt) cc_final: 0.2746 (mtp) REVERT: C 68 MET cc_start: 0.3648 (tpt) cc_final: 0.3195 (tpt) REVERT: C 77 MET cc_start: 0.4874 (mmt) cc_final: 0.4413 (tmm) REVERT: C 156 THR cc_start: 0.5835 (p) cc_final: 0.5539 (m) REVERT: C 267 LYS cc_start: 0.7083 (tptp) cc_final: 0.6693 (tptt) REVERT: C 268 MET cc_start: 0.6276 (ttt) cc_final: 0.6069 (ttm) REVERT: C 314 MET cc_start: 0.5550 (mpp) cc_final: 0.5049 (mpp) REVERT: C 442 ARG cc_start: 0.5763 (ptm160) cc_final: 0.5293 (ttp-170) REVERT: C 530 MET cc_start: 0.5716 (mmt) cc_final: 0.3786 (mtt) REVERT: D 394 THR cc_start: 0.6026 (p) cc_final: 0.5660 (m) REVERT: D 507 GLU cc_start: 0.6516 (mm-30) cc_final: 0.5773 (mm-30) REVERT: D 527 MET cc_start: 0.2513 (ttt) cc_final: 0.1185 (tpp) REVERT: D 530 MET cc_start: 0.5123 (mmt) cc_final: 0.2828 (mtp) REVERT: E 44 MET cc_start: 0.3322 (pmm) cc_final: 0.2157 (pmm) REVERT: E 68 MET cc_start: 0.3547 (tpt) cc_final: 0.3105 (tpt) REVERT: E 77 MET cc_start: 0.4884 (mmt) cc_final: 0.4308 (tmm) REVERT: E 156 THR cc_start: 0.5821 (p) cc_final: 0.5582 (m) REVERT: E 249 GLU cc_start: 0.4831 (mt-10) cc_final: 0.4261 (mt-10) REVERT: E 267 LYS cc_start: 0.6953 (tptt) cc_final: 0.6481 (tptp) REVERT: E 314 MET cc_start: 0.5513 (mpp) cc_final: 0.5022 (mpp) REVERT: E 442 ARG cc_start: 0.5740 (ptm160) cc_final: 0.5280 (ttp-170) REVERT: E 530 MET cc_start: 0.5567 (mmt) cc_final: 0.3591 (mtt) REVERT: F 47 MET cc_start: 0.5060 (tpp) cc_final: 0.4632 (tpt) REVERT: F 513 ASP cc_start: 0.4331 (m-30) cc_final: 0.4006 (m-30) REVERT: F 527 MET cc_start: 0.2487 (ttt) cc_final: 0.1179 (tpp) REVERT: F 530 MET cc_start: 0.5132 (mmt) cc_final: 0.2889 (mtp) REVERT: G 44 MET cc_start: 0.3154 (pmm) cc_final: 0.2190 (pmm) REVERT: G 68 MET cc_start: 0.3637 (tpt) cc_final: 0.3146 (tpt) REVERT: G 77 MET cc_start: 0.4897 (mmt) cc_final: 0.4446 (tmm) REVERT: G 106 LYS cc_start: 0.6916 (tptp) cc_final: 0.6080 (tppt) REVERT: G 156 THR cc_start: 0.5821 (p) cc_final: 0.5565 (m) REVERT: G 267 LYS cc_start: 0.6944 (tptt) cc_final: 0.6512 (tptp) REVERT: G 314 MET cc_start: 0.5509 (mpp) cc_final: 0.4991 (mpp) REVERT: G 442 ARG cc_start: 0.5917 (ptm160) cc_final: 0.5444 (ttp-170) REVERT: G 530 MET cc_start: 0.5255 (mmt) cc_final: 0.3476 (mtt) REVERT: H 47 MET cc_start: 0.5108 (tpp) cc_final: 0.4656 (tpt) REVERT: H 108 GLU cc_start: 0.3143 (tt0) cc_final: 0.2867 (tt0) REVERT: H 451 ASP cc_start: 0.6006 (t0) cc_final: 0.5796 (t0) REVERT: H 527 MET cc_start: 0.2822 (ttt) cc_final: 0.2233 (tpp) REVERT: H 530 MET cc_start: 0.4944 (mmt) cc_final: 0.3400 (mtm) REVERT: I 108 GLU cc_start: 0.3120 (tt0) cc_final: 0.2808 (tt0) REVERT: I 527 MET cc_start: 0.2585 (ttt) cc_final: 0.1452 (tpp) REVERT: I 530 MET cc_start: 0.5253 (mmt) cc_final: 0.2832 (mtp) REVERT: J 23 MET cc_start: 0.4547 (tpt) cc_final: 0.4023 (ttt) REVERT: J 44 MET cc_start: 0.3170 (pmm) cc_final: 0.2286 (pmm) REVERT: J 68 MET cc_start: 0.3322 (tpt) cc_final: 0.2971 (tpt) REVERT: J 77 MET cc_start: 0.4958 (mmt) cc_final: 0.4388 (tmm) REVERT: J 106 LYS cc_start: 0.7042 (tptp) cc_final: 0.6289 (tppt) REVERT: J 156 THR cc_start: 0.5780 (p) cc_final: 0.5563 (m) REVERT: J 267 LYS cc_start: 0.7410 (tptp) cc_final: 0.7179 (tptt) REVERT: J 314 MET cc_start: 0.5491 (mpp) cc_final: 0.4940 (mpp) REVERT: J 442 ARG cc_start: 0.5868 (ptm160) cc_final: 0.5406 (ttp-170) REVERT: J 530 MET cc_start: 0.5552 (mmt) cc_final: 0.3551 (mtt) REVERT: K 1 MET cc_start: 0.2995 (ptm) cc_final: 0.1589 (ptm) REVERT: K 108 GLU cc_start: 0.3100 (tt0) cc_final: 0.2787 (tt0) REVERT: K 513 ASP cc_start: 0.4382 (m-30) cc_final: 0.4073 (m-30) REVERT: K 514 ASP cc_start: 0.2715 (p0) cc_final: 0.2321 (m-30) REVERT: K 527 MET cc_start: 0.2459 (ttt) cc_final: 0.1421 (tpp) REVERT: K 530 MET cc_start: 0.5085 (mmt) cc_final: 0.3017 (mtp) REVERT: L 16 MET cc_start: 0.5258 (tmm) cc_final: 0.4941 (tpt) REVERT: L 33 GLU cc_start: 0.6098 (pp20) cc_final: 0.5878 (pp20) REVERT: L 44 MET cc_start: 0.3271 (pmm) cc_final: 0.2400 (pmm) REVERT: L 68 MET cc_start: 0.3621 (tpt) cc_final: 0.3140 (tpt) REVERT: L 77 MET cc_start: 0.4783 (mmt) cc_final: 0.4268 (tmm) REVERT: L 156 THR cc_start: 0.5785 (p) cc_final: 0.5475 (m) REVERT: L 314 MET cc_start: 0.5495 (mpp) cc_final: 0.4958 (mpp) REVERT: L 442 ARG cc_start: 0.5947 (ptm160) cc_final: 0.5434 (ttp-170) REVERT: L 530 MET cc_start: 0.5265 (mmt) cc_final: 0.3594 (mtt) REVERT: M 507 GLU cc_start: 0.6444 (mm-30) cc_final: 0.5664 (mm-30) REVERT: M 513 ASP cc_start: 0.4277 (m-30) cc_final: 0.4028 (m-30) REVERT: M 527 MET cc_start: 0.2510 (ttt) cc_final: 0.1467 (tpp) REVERT: M 530 MET cc_start: 0.5108 (mmt) cc_final: 0.2932 (mtt) REVERT: N 44 MET cc_start: 0.3199 (pmm) cc_final: 0.2207 (pmm) REVERT: N 77 MET cc_start: 0.4868 (mmt) cc_final: 0.4406 (tmm) REVERT: N 156 THR cc_start: 0.5874 (p) cc_final: 0.5592 (m) REVERT: N 267 LYS cc_start: 0.7391 (tptp) cc_final: 0.7173 (tptt) REVERT: N 314 MET cc_start: 0.5514 (mpp) cc_final: 0.4968 (mpp) REVERT: N 530 MET cc_start: 0.5300 (mmt) cc_final: 0.3608 (mtt) REVERT: O 527 MET cc_start: 0.2782 (ttt) cc_final: 0.2219 (tpp) REVERT: O 530 MET cc_start: 0.5275 (mmt) cc_final: 0.2456 (mtm) REVERT: P 23 MET cc_start: 0.4437 (tpt) cc_final: 0.4048 (ttt) REVERT: P 44 MET cc_start: 0.3162 (pmm) cc_final: 0.2110 (pmm) REVERT: P 68 MET cc_start: 0.3511 (tpt) cc_final: 0.3080 (tpt) REVERT: P 77 MET cc_start: 0.4882 (mmt) cc_final: 0.4386 (tmm) REVERT: P 106 LYS cc_start: 0.6874 (tptp) cc_final: 0.6085 (tppt) REVERT: P 156 THR cc_start: 0.5831 (p) cc_final: 0.5561 (m) REVERT: P 314 MET cc_start: 0.5494 (mpp) cc_final: 0.5002 (mpp) REVERT: P 442 ARG cc_start: 0.5976 (ptm160) cc_final: 0.5441 (ttp-170) REVERT: P 530 MET cc_start: 0.5550 (mmt) cc_final: 0.3562 (mtt) outliers start: 0 outliers final: 0 residues processed: 1240 average time/residue: 0.6408 time to fit residues: 1299.5790 Evaluate side-chains 1006 residues out of total 6832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1006 time to evaluate : 5.573 ------------------------------------------------------------------------------- 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: 0.0470 chunk 783 optimal weight: 5.9990 chunk 714 optimal weight: 0.9980 chunk 761 optimal weight: 5.9990 chunk 782 optimal weight: 0.3980 chunk 458 optimal weight: 9.9990 chunk 331 optimal weight: 1.9990 chunk 598 optimal weight: 5.9990 chunk 233 optimal weight: 20.0000 chunk 688 optimal weight: 6.9990 chunk 720 optimal weight: 7.9990 overall best weight: 1.8882 ------------------------------------------------------------------------------- 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 ** 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 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 287 GLN ** D 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 497 GLN ** E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 287 GLN ** F 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 287 GLN ** H 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 287 GLN ** I 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 287 GLN ** K 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 287 GLN ** M 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 287 GLN ** O 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4866 moved from start: 0.9293 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= 0.241 Angle : 1.110 16.478 86240 Z= 0.552 Chirality : 0.054 0.264 10448 Planarity : 0.007 0.132 11216 Dihedral : 8.362 31.901 8928 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 29.67 Ramachandran Plot: Outliers : 4.12 % Allowed : 20.54 % Favored : 75.34 % Rotamer: Outliers : 0.01 % Allowed : 2.21 % Favored : 97.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 8.52 % 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: -4.55 (0.08), residues: 8480 helix: -1.25 (0.09), residues: 3472 sheet: None (None), residues: 0 loop : -4.67 (0.07), residues: 5008 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS N 463 PHE 0.008 0.001 PHE B 355 TYR 0.008 0.001 TYR E 15 ARG 0.012 0.001 ARG G 382 *********************** 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 1273 residues out of total 6832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1272 time to evaluate : 5.975 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: A 33 GLU cc_start: 0.6258 (pp20) cc_final: 0.6054 (pp20) REVERT: A 77 MET cc_start: 0.4848 (mmt) cc_final: 0.4557 (tmm) REVERT: A 156 THR cc_start: 0.5691 (p) cc_final: 0.5374 (m) REVERT: A 314 MET cc_start: 0.5496 (mpp) cc_final: 0.3919 (mpp) REVERT: A 527 MET cc_start: 0.3054 (ttt) cc_final: 0.2607 (tpp) REVERT: A 530 MET cc_start: 0.5415 (mmt) cc_final: 0.3775 (mtm) REVERT: B 527 MET cc_start: 0.2413 (ttt) cc_final: 0.1309 (tpp) REVERT: B 530 MET cc_start: 0.5104 (mmt) cc_final: 0.2923 (mtp) REVERT: C 10 GLU cc_start: 0.5154 (tp30) cc_final: 0.3581 (tp30) REVERT: C 68 MET cc_start: 0.3432 (tpt) cc_final: 0.2854 (tpt) REVERT: C 77 MET cc_start: 0.4944 (mmt) cc_final: 0.4571 (tmm) REVERT: C 106 LYS cc_start: 0.6840 (tptp) cc_final: 0.6232 (tppt) REVERT: C 156 THR cc_start: 0.5712 (p) cc_final: 0.5380 (m) REVERT: C 314 MET cc_start: 0.5722 (mpp) cc_final: 0.5349 (mpp) REVERT: C 442 ARG cc_start: 0.5940 (ptm160) cc_final: 0.5304 (ttp-170) REVERT: C 530 MET cc_start: 0.5102 (mmt) cc_final: 0.3439 (mtm) REVERT: D 71 GLU cc_start: 0.4764 (mm-30) cc_final: 0.4554 (mm-30) REVERT: D 527 MET cc_start: 0.2380 (ttt) cc_final: 0.1336 (tpp) REVERT: D 530 MET cc_start: 0.5184 (mmt) cc_final: 0.2984 (mtm) REVERT: E 10 GLU cc_start: 0.4924 (tp30) cc_final: 0.4664 (tp30) REVERT: E 68 MET cc_start: 0.3640 (tpt) cc_final: 0.3140 (tpt) REVERT: E 106 LYS cc_start: 0.6880 (tptp) cc_final: 0.6238 (tppt) REVERT: E 156 THR cc_start: 0.5593 (p) cc_final: 0.5273 (m) REVERT: E 249 GLU cc_start: 0.4937 (mt-10) cc_final: 0.4715 (mt-10) REVERT: E 250 ILE cc_start: 0.5085 (tt) cc_final: 0.4467 (tt) REVERT: E 314 MET cc_start: 0.5703 (mpp) cc_final: 0.5435 (mpp) REVERT: E 442 ARG cc_start: 0.5887 (ptm160) cc_final: 0.5270 (ttp-170) REVERT: E 530 MET cc_start: 0.5208 (mmt) cc_final: 0.3297 (mtm) REVERT: F 530 MET cc_start: 0.5161 (mmt) cc_final: 0.2996 (mtm) REVERT: G 44 MET cc_start: 0.2767 (pmm) cc_final: 0.1927 (pmm) REVERT: G 68 MET cc_start: 0.3579 (tpt) cc_final: 0.2824 (tpt) REVERT: G 77 MET cc_start: 0.5188 (mmt) cc_final: 0.4651 (tmm) REVERT: G 106 LYS cc_start: 0.7097 (tptp) cc_final: 0.6209 (tppt) REVERT: G 156 THR cc_start: 0.5717 (p) cc_final: 0.5374 (m) REVERT: G 314 MET cc_start: 0.5713 (mpp) cc_final: 0.5370 (mpp) REVERT: G 442 ARG cc_start: 0.6044 (ptm160) cc_final: 0.5519 (ttp-170) REVERT: G 530 MET cc_start: 0.5050 (mmt) cc_final: 0.3264 (mtm) REVERT: H 527 MET cc_start: 0.2452 (ttt) cc_final: 0.2065 (tpp) REVERT: H 530 MET cc_start: 0.4622 (mmt) cc_final: 0.2693 (mtm) REVERT: I 530 MET cc_start: 0.5209 (mmt) cc_final: 0.3054 (mtm) REVERT: J 1 MET cc_start: 0.2205 (ptm) cc_final: 0.1877 (ptm) REVERT: J 23 MET cc_start: 0.4492 (tpt) cc_final: 0.4052 (ttt) REVERT: J 44 MET cc_start: 0.2777 (pmm) cc_final: 0.1852 (pmm) REVERT: J 68 MET cc_start: 0.2859 (tpt) cc_final: 0.2366 (tpt) REVERT: J 77 MET cc_start: 0.4992 (mmt) cc_final: 0.4524 (tmm) REVERT: J 156 THR cc_start: 0.5532 (p) cc_final: 0.5167 (m) REVERT: J 267 LYS cc_start: 0.7375 (tptp) cc_final: 0.7092 (tptt) REVERT: J 314 MET cc_start: 0.5579 (mpp) cc_final: 0.5287 (mpp) REVERT: J 442 ARG cc_start: 0.5890 (ptm160) cc_final: 0.5309 (ttp-170) REVERT: J 530 MET cc_start: 0.5185 (mmt) cc_final: 0.3315 (mtm) REVERT: K 267 LYS cc_start: 0.7185 (tptt) cc_final: 0.6650 (tptm) REVERT: K 527 MET cc_start: 0.2844 (ttt) cc_final: 0.1833 (tpp) REVERT: K 530 MET cc_start: 0.5173 (mmt) cc_final: 0.2836 (mtp) REVERT: L 16 MET cc_start: 0.5281 (tmm) cc_final: 0.4918 (tpt) REVERT: L 33 GLU cc_start: 0.6102 (pp20) cc_final: 0.5764 (pp20) REVERT: L 44 MET cc_start: 0.3038 (pmm) cc_final: 0.2287 (ptp) REVERT: L 68 MET cc_start: 0.3562 (tpt) cc_final: 0.2967 (tpt) REVERT: L 77 MET cc_start: 0.4845 (mmt) cc_final: 0.4537 (tmm) REVERT: L 156 THR cc_start: 0.5701 (p) cc_final: 0.5386 (m) REVERT: L 314 MET cc_start: 0.5596 (mpp) cc_final: 0.5311 (mpp) REVERT: L 442 ARG cc_start: 0.6225 (ptm160) cc_final: 0.5719 (ttp-170) REVERT: L 530 MET cc_start: 0.5244 (mmt) cc_final: 0.3414 (mtm) REVERT: M 1 MET cc_start: 0.2019 (ptm) cc_final: 0.0898 (ptm) REVERT: M 267 LYS cc_start: 0.7262 (tptt) cc_final: 0.6762 (tptm) REVERT: M 530 MET cc_start: 0.5215 (mmt) cc_final: 0.2828 (mtp) REVERT: N 1 MET cc_start: 0.2565 (ptm) cc_final: 0.2204 (ptm) REVERT: N 77 MET cc_start: 0.4872 (mmt) cc_final: 0.4491 (tmm) REVERT: N 156 THR cc_start: 0.5608 (p) cc_final: 0.5227 (m) REVERT: N 267 LYS cc_start: 0.7345 (tptp) cc_final: 0.7093 (tptt) REVERT: N 314 MET cc_start: 0.5624 (mpp) cc_final: 0.5310 (mpp) REVERT: N 433 PHE cc_start: 0.3054 (t80) cc_final: 0.2589 (t80) REVERT: N 530 MET cc_start: 0.5302 (mmt) cc_final: 0.3528 (mtm) REVERT: O 267 LYS cc_start: 0.7179 (tptt) cc_final: 0.6642 (tptm) REVERT: O 527 MET cc_start: 0.2623 (ttt) cc_final: 0.2092 (tpp) REVERT: O 530 MET cc_start: 0.5297 (mmt) cc_final: 0.2902 (mtm) REVERT: P 23 MET cc_start: 0.4207 (tpt) cc_final: 0.3884 (ttt) REVERT: P 44 MET cc_start: 0.2712 (pmm) cc_final: 0.1840 (pmm) REVERT: P 68 MET cc_start: 0.3535 (tpt) cc_final: 0.3082 (tpt) REVERT: P 106 LYS cc_start: 0.7059 (tptp) cc_final: 0.6216 (tppt) REVERT: P 156 THR cc_start: 0.5588 (p) cc_final: 0.5170 (m) REVERT: P 314 MET cc_start: 0.5693 (mpp) cc_final: 0.5343 (mpp) REVERT: P 442 ARG cc_start: 0.6052 (ptm160) cc_final: 0.5455 (ttp-170) REVERT: P 530 MET cc_start: 0.5194 (mmt) cc_final: 0.3330 (mtm) outliers start: 1 outliers final: 0 residues processed: 1273 average time/residue: 0.6160 time to fit residues: 1299.8205 Evaluate side-chains 1013 residues out of total 6832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1013 time to evaluate : 5.632 ------------------------------------------------------------------------------- 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: 5.9990 chunk 500 optimal weight: 8.9990 chunk 805 optimal weight: 0.6980 chunk 491 optimal weight: 0.9990 chunk 382 optimal weight: 9.9990 chunk 559 optimal weight: 10.0000 chunk 844 optimal weight: 0.8980 chunk 777 optimal weight: 7.9990 chunk 672 optimal weight: 7.9990 chunk 69 optimal weight: 6.9990 chunk 519 optimal weight: 6.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- 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 ** B 375 HIS ** 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 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 287 GLN ** D 375 HIS ** 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 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 295 GLN ** G 497 GLN ** 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 497 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 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 375 HIS ** 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 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 497 GLN ** 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 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4925 moved from start: 0.9459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 64112 Z= 0.271 Angle : 1.134 17.616 86240 Z= 0.563 Chirality : 0.055 0.275 10448 Planarity : 0.007 0.130 11216 Dihedral : 8.355 31.954 8928 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 31.78 Ramachandran Plot: Outliers : 4.01 % Allowed : 21.06 % Favored : 74.93 % Rotamer: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 9.09 % Twisted General : 0.04 % 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: -4.50 (0.08), residues: 8480 helix: -1.21 (0.09), residues: 3456 sheet: None (None), residues: 0 loop : -4.63 (0.07), residues: 5024 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS I 296 PHE 0.011 0.002 PHE L 355 TYR 0.010 0.002 TYR E 15 ARG 0.012 0.001 ARG G 382 ********************** 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 1226 residues out of total 6832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1226 time to evaluate : 5.646 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: A 33 GLU cc_start: 0.6405 (pp20) cc_final: 0.6064 (pp20) REVERT: A 44 MET cc_start: 0.2786 (pmm) cc_final: 0.2054 (pmm) REVERT: A 77 MET cc_start: 0.4670 (mmt) cc_final: 0.4268 (tmm) REVERT: A 156 THR cc_start: 0.5650 (p) cc_final: 0.5413 (m) REVERT: A 267 LYS cc_start: 0.6806 (tptt) cc_final: 0.6203 (tptp) REVERT: A 287 GLN cc_start: 0.7306 (mm-40) cc_final: 0.7047 (mm-40) REVERT: A 314 MET cc_start: 0.5754 (mpp) cc_final: 0.4491 (mpp) REVERT: A 527 MET cc_start: 0.2957 (ttt) cc_final: 0.2591 (tpp) REVERT: A 530 MET cc_start: 0.4924 (mmt) cc_final: 0.3365 (mtm) REVERT: B 1 MET cc_start: 0.2571 (ppp) cc_final: 0.2325 (ppp) REVERT: B 46 LYS cc_start: 0.4880 (mmmt) cc_final: 0.4549 (mmmt) REVERT: B 530 MET cc_start: 0.5051 (mmt) cc_final: 0.3196 (mtm) REVERT: C 30 ILE cc_start: 0.6616 (tp) cc_final: 0.6384 (tp) REVERT: C 33 GLU cc_start: 0.6247 (pp20) cc_final: 0.5988 (pp20) REVERT: C 68 MET cc_start: 0.3420 (tpt) cc_final: 0.3176 (tpt) REVERT: C 77 MET cc_start: 0.4953 (mmt) cc_final: 0.4373 (tmm) REVERT: C 84 THR cc_start: 0.3866 (p) cc_final: 0.3580 (t) REVERT: C 156 THR cc_start: 0.5692 (p) cc_final: 0.5386 (m) REVERT: C 267 LYS cc_start: 0.7490 (tptt) cc_final: 0.6521 (tptt) REVERT: C 314 MET cc_start: 0.5912 (mpp) cc_final: 0.5519 (mpp) REVERT: C 442 ARG cc_start: 0.5984 (ptm160) cc_final: 0.5357 (ttp-170) REVERT: C 493 ARG cc_start: 0.5152 (mmm160) cc_final: 0.4817 (tmt170) REVERT: C 530 MET cc_start: 0.5034 (mmt) cc_final: 0.3382 (mtm) REVERT: D 530 MET cc_start: 0.5116 (mmt) cc_final: 0.3328 (mtm) REVERT: E 10 GLU cc_start: 0.5497 (tp30) cc_final: 0.5175 (tp30) REVERT: E 44 MET cc_start: 0.3037 (pmm) cc_final: 0.2408 (pmm) REVERT: E 68 MET cc_start: 0.3406 (tpt) cc_final: 0.3159 (tpt) REVERT: E 84 THR cc_start: 0.4053 (p) cc_final: 0.3654 (t) REVERT: E 156 THR cc_start: 0.5678 (p) cc_final: 0.5423 (m) REVERT: E 223 MET cc_start: 0.3629 (ptp) cc_final: 0.3416 (ptt) REVERT: E 249 GLU cc_start: 0.5085 (mt-10) cc_final: 0.4849 (mt-10) REVERT: E 314 MET cc_start: 0.6003 (mpp) cc_final: 0.5520 (mpp) REVERT: E 368 LEU cc_start: 0.4751 (pp) cc_final: 0.4461 (pp) REVERT: E 442 ARG cc_start: 0.5838 (ptm160) cc_final: 0.5204 (ttp-170) REVERT: E 530 MET cc_start: 0.5068 (mmt) cc_final: 0.3188 (mtm) REVERT: F 530 MET cc_start: 0.5119 (mmt) cc_final: 0.3316 (mtm) REVERT: G 44 MET cc_start: 0.2699 (pmm) cc_final: 0.2117 (pmm) REVERT: G 68 MET cc_start: 0.3742 (tpt) cc_final: 0.3046 (tpt) REVERT: G 77 MET cc_start: 0.4929 (mmt) cc_final: 0.4529 (tmm) REVERT: G 108 GLU cc_start: 0.2962 (tp30) cc_final: 0.2750 (tp30) REVERT: G 156 THR cc_start: 0.5623 (p) cc_final: 0.5407 (m) REVERT: G 314 MET cc_start: 0.5975 (mpp) cc_final: 0.5478 (mpp) REVERT: G 368 LEU cc_start: 0.4746 (pp) cc_final: 0.4532 (pp) REVERT: G 442 ARG cc_start: 0.5934 (ptm160) cc_final: 0.5409 (ttp-110) REVERT: G 530 MET cc_start: 0.4911 (mmt) cc_final: 0.3307 (mtm) REVERT: H 16 MET cc_start: 0.5488 (tmm) cc_final: 0.5161 (tpt) REVERT: H 68 MET cc_start: 0.2564 (mmm) cc_final: 0.2151 (mmm) REVERT: H 78 LEU cc_start: 0.6062 (pp) cc_final: 0.5760 (pp) REVERT: H 527 MET cc_start: 0.2601 (ttt) cc_final: 0.2367 (tpp) REVERT: H 530 MET cc_start: 0.4620 (mmt) cc_final: 0.2773 (mtm) REVERT: I 78 LEU cc_start: 0.5997 (pp) cc_final: 0.5768 (pp) REVERT: I 527 MET cc_start: 0.3457 (ttt) cc_final: 0.2495 (tpp) REVERT: I 530 MET cc_start: 0.5121 (mmt) cc_final: 0.3227 (mtm) REVERT: J 10 GLU cc_start: 0.5253 (tp30) cc_final: 0.4281 (tt0) REVERT: J 23 MET cc_start: 0.4286 (tpt) cc_final: 0.3856 (ttt) REVERT: J 44 MET cc_start: 0.2596 (pmm) cc_final: 0.1755 (pmm) REVERT: J 68 MET cc_start: 0.3491 (tpt) cc_final: 0.2906 (tpt) REVERT: J 77 MET cc_start: 0.4922 (mmt) cc_final: 0.4391 (tmm) REVERT: J 84 THR cc_start: 0.3834 (p) cc_final: 0.3490 (t) REVERT: J 156 THR cc_start: 0.5721 (p) cc_final: 0.5456 (m) REVERT: J 267 LYS cc_start: 0.7295 (tptp) cc_final: 0.6858 (tptt) REVERT: J 314 MET cc_start: 0.5918 (mpp) cc_final: 0.5510 (mpp) REVERT: J 442 ARG cc_start: 0.5900 (ptm160) cc_final: 0.5273 (ttp-110) REVERT: J 530 MET cc_start: 0.5093 (mmt) cc_final: 0.3383 (mtm) REVERT: K 78 LEU cc_start: 0.6104 (pp) cc_final: 0.5863 (pp) REVERT: K 267 LYS cc_start: 0.7065 (tptt) cc_final: 0.6752 (tptm) REVERT: K 514 ASP cc_start: 0.2351 (p0) cc_final: 0.2082 (m-30) REVERT: K 527 MET cc_start: 0.2509 (ttt) cc_final: 0.1591 (tpp) REVERT: K 530 MET cc_start: 0.5071 (mmt) cc_final: 0.2676 (mtp) REVERT: L 16 MET cc_start: 0.5678 (tmm) cc_final: 0.5307 (tpt) REVERT: L 30 ILE cc_start: 0.7164 (tp) cc_final: 0.6925 (tp) REVERT: L 33 GLU cc_start: 0.6468 (pp20) cc_final: 0.6154 (pp20) REVERT: L 44 MET cc_start: 0.2700 (pmm) cc_final: 0.2187 (ptp) REVERT: L 46 LYS cc_start: 0.4937 (mmmt) cc_final: 0.4707 (mmmt) REVERT: L 68 MET cc_start: 0.3777 (tpt) cc_final: 0.3020 (tpt) REVERT: L 77 MET cc_start: 0.4999 (mmt) cc_final: 0.4477 (tmm) REVERT: L 84 THR cc_start: 0.3843 (p) cc_final: 0.3542 (t) REVERT: L 156 THR cc_start: 0.5559 (p) cc_final: 0.5248 (m) REVERT: L 314 MET cc_start: 0.5912 (mpp) cc_final: 0.5544 (mpp) REVERT: L 368 LEU cc_start: 0.4707 (pp) cc_final: 0.4453 (pp) REVERT: L 442 ARG cc_start: 0.6034 (ptm160) cc_final: 0.5482 (ttp-170) REVERT: L 530 MET cc_start: 0.5148 (mmt) cc_final: 0.3402 (mtm) REVERT: M 1 MET cc_start: 0.2493 (ptm) cc_final: 0.1576 (ptm) REVERT: M 267 LYS cc_start: 0.7193 (tptt) cc_final: 0.6639 (tptm) REVERT: M 527 MET cc_start: 0.3313 (ttt) cc_final: 0.2487 (tpp) REVERT: M 530 MET cc_start: 0.5089 (mmt) cc_final: 0.2920 (mtp) REVERT: N 1 MET cc_start: 0.1544 (ptm) cc_final: 0.1262 (ptm) REVERT: N 38 THR cc_start: 0.5291 (p) cc_final: 0.5077 (p) REVERT: N 44 MET cc_start: 0.2625 (pmm) cc_final: 0.2128 (pmm) REVERT: N 77 MET cc_start: 0.4854 (mmt) cc_final: 0.4368 (tmm) REVERT: N 156 THR cc_start: 0.5779 (p) cc_final: 0.5466 (m) REVERT: N 267 LYS cc_start: 0.7231 (tptp) cc_final: 0.6878 (tptt) REVERT: N 314 MET cc_start: 0.5920 (mpp) cc_final: 0.5538 (mpp) REVERT: N 530 MET cc_start: 0.5199 (mmt) cc_final: 0.3453 (mtm) REVERT: O 68 MET cc_start: 0.2608 (mmm) cc_final: 0.2339 (mmm) REVERT: O 267 LYS cc_start: 0.7165 (tptt) cc_final: 0.6846 (tptm) REVERT: O 527 MET cc_start: 0.2788 (ttt) cc_final: 0.2207 (tpp) REVERT: O 530 MET cc_start: 0.5138 (mmt) cc_final: 0.2786 (mtm) REVERT: P 44 MET cc_start: 0.2576 (pmm) cc_final: 0.1656 (pmm) REVERT: P 68 MET cc_start: 0.3318 (tpt) cc_final: 0.3027 (tpt) REVERT: P 84 THR cc_start: 0.4030 (p) cc_final: 0.3505 (t) REVERT: P 156 THR cc_start: 0.5757 (p) cc_final: 0.5470 (m) REVERT: P 267 LYS cc_start: 0.7558 (tptt) cc_final: 0.7047 (tptt) REVERT: P 314 MET cc_start: 0.5924 (mpp) cc_final: 0.5556 (mpp) REVERT: P 368 LEU cc_start: 0.4719 (pp) cc_final: 0.4505 (pp) REVERT: P 442 ARG cc_start: 0.5966 (ptm160) cc_final: 0.5347 (ttp-110) REVERT: P 530 MET cc_start: 0.5091 (mmt) cc_final: 0.3380 (mtm) outliers start: 0 outliers final: 0 residues processed: 1226 average time/residue: 0.6242 time to fit residues: 1259.7387 Evaluate side-chains 984 residues out of total 6832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 984 time to evaluate : 5.583 ------------------------------------------------------------------------------- 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: 9.9990 chunk 716 optimal weight: 5.9990 chunk 206 optimal weight: 20.0000 chunk 620 optimal weight: 10.0000 chunk 99 optimal weight: 2.9990 chunk 186 optimal weight: 0.1980 chunk 673 optimal weight: 20.0000 chunk 281 optimal weight: 9.9990 chunk 691 optimal weight: 6.9990 chunk 85 optimal weight: 10.0000 overall best weight: 4.6388 ------------------------------------------------------------------------------- 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 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 375 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 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 375 HIS ** 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 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 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 375 HIS ** 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 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 296 HIS ** L 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 375 HIS ** 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 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4630 r_free = 0.4630 target = 0.186614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.170317 restraints weight = 165951.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.172853 restraints weight = 118514.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.174930 restraints weight = 90174.479| |-----------------------------------------------------------------------------| r_work (final): 0.4512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5708 moved from start: 0.9512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 64112 Z= 0.311 Angle : 1.180 24.008 86240 Z= 0.586 Chirality : 0.056 0.269 10448 Planarity : 0.008 0.190 11216 Dihedral : 8.579 37.310 8928 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 33.19 Ramachandran Plot: Outliers : 3.93 % Allowed : 21.92 % Favored : 74.15 % Rotamer: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % 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: -4.38 (0.08), residues: 8480 helix: -1.08 (0.09), residues: 3328 sheet: None (None), residues: 0 loop : -4.50 (0.07), residues: 5152 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS F 296 PHE 0.014 0.002 PHE A 355 TYR 0.013 0.002 TYR I 418 ARG 0.011 0.001 ARG G 382 =============================================================================== Job complete usr+sys time: 20851.82 seconds wall clock time: 364 minutes 23.11 seconds (21863.11 seconds total)