Starting phenix.real_space_refine on Mon Mar 11 18:15:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rfe_24439/03_2024/7rfe_24439_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rfe_24439/03_2024/7rfe_24439.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rfe_24439/03_2024/7rfe_24439.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rfe_24439/03_2024/7rfe_24439.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rfe_24439/03_2024/7rfe_24439_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rfe_24439/03_2024/7rfe_24439_trim_updated.pdb" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.009 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: 6 Type Number sf(0) Gaussians P 80 5.49 5 S 192 5.16 5 C 18368 2.51 5 N 5072 2.21 5 O 5808 1.98 5 H 29200 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 15": "OE1" <-> "OE2" Residue "A ASP 16": "OD1" <-> "OD2" Residue "A PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 28": "OD1" <-> "OD2" Residue "A GLU 48": "OE1" <-> "OE2" Residue "A ASP 50": "OD1" <-> "OD2" Residue "A ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 75": "OE1" <-> "OE2" Residue "A PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 103": "OE1" <-> "OE2" Residue "A ARG 105": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 117": "OD1" <-> "OD2" Residue "A ASP 129": "OD1" <-> "OD2" Residue "A ARG 136": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 146": "OE1" <-> "OE2" Residue "A ARG 182": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 184": "OE1" <-> "OE2" Residue "A GLU 217": "OE1" <-> "OE2" Residue "A TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 239": "OD1" <-> "OD2" Residue "A ARG 253": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 255": "OD1" <-> "OD2" Residue "A ASP 256": "OD1" <-> "OD2" Residue "A TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 319": "OD1" <-> "OD2" Residue "A GLU 335": "OE1" <-> "OE2" Residue "A ARG 355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 399": "OE1" <-> "OE2" Residue "A PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 404": "OD1" <-> "OD2" Residue "A ARG 407": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 449": "OD1" <-> "OD2" Residue "A ARG 474": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 509": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 510": "OE1" <-> "OE2" Residue "A ARG 512": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 514": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 28": "OD1" <-> "OD2" Residue "B ASP 47": "OD1" <-> "OD2" Residue "B GLU 48": "OE1" <-> "OE2" Residue "B ASP 50": "OD1" <-> "OD2" Residue "B ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 75": "OE1" <-> "OE2" Residue "B PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 103": "OE1" <-> "OE2" Residue "B ARG 105": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 117": "OD1" <-> "OD2" Residue "B ARG 136": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 146": "OE1" <-> "OE2" Residue "B ARG 182": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 184": "OE1" <-> "OE2" Residue "B GLU 217": "OE1" <-> "OE2" Residue "B TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 239": "OD1" <-> "OD2" Residue "B ARG 253": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 255": "OD1" <-> "OD2" Residue "B ASP 256": "OD1" <-> "OD2" Residue "B TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 319": "OD1" <-> "OD2" Residue "B GLU 335": "OE1" <-> "OE2" Residue "B ARG 355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 399": "OE1" <-> "OE2" Residue "B PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 407": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 449": "OD1" <-> "OD2" Residue "B ARG 474": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 509": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 510": "OE1" <-> "OE2" Residue "B ARG 512": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 514": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 15": "OE1" <-> "OE2" Residue "C ASP 16": "OD1" <-> "OD2" Residue "C PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 28": "OD1" <-> "OD2" Residue "C ASP 47": "OD1" <-> "OD2" Residue "C GLU 48": "OE1" <-> "OE2" Residue "C ASP 50": "OD1" <-> "OD2" Residue "C ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 75": "OE1" <-> "OE2" Residue "C PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 103": "OE1" <-> "OE2" Residue "C ARG 105": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 129": "OD1" <-> "OD2" Residue "C ARG 136": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 146": "OE1" <-> "OE2" Residue "C ARG 182": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 184": "OE1" <-> "OE2" Residue "C ASP 226": "OD1" <-> "OD2" Residue "C TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 239": "OD1" <-> "OD2" Residue "C ARG 253": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ASP 255": "OD1" <-> "OD2" Residue "C ASP 256": "OD1" <-> "OD2" Residue "C ASP 261": "OD1" <-> "OD2" Residue "C ASP 269": "OD1" <-> "OD2" Residue "C TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 319": "OD1" <-> "OD2" Residue "C GLU 335": "OE1" <-> "OE2" Residue "C ARG 355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 399": "OE1" <-> "OE2" Residue "C PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 404": "OD1" <-> "OD2" Residue "C ARG 407": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 470": "OD1" <-> "OD2" Residue "C ARG 474": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 509": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 510": "OE1" <-> "OE2" Residue "C ARG 512": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 514": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 15": "OE1" <-> "OE2" Residue "D ASP 16": "OD1" <-> "OD2" Residue "D PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 28": "OD1" <-> "OD2" Residue "D ASP 47": "OD1" <-> "OD2" Residue "D ASP 50": "OD1" <-> "OD2" Residue "D ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 75": "OE1" <-> "OE2" Residue "D PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 103": "OE1" <-> "OE2" Residue "D ARG 105": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 117": "OD1" <-> "OD2" Residue "D ASP 129": "OD1" <-> "OD2" Residue "D GLU 132": "OE1" <-> "OE2" Residue "D ARG 136": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 146": "OE1" <-> "OE2" Residue "D ARG 182": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 184": "OE1" <-> "OE2" Residue "D GLU 196": "OE1" <-> "OE2" Residue "D ASP 216": "OD1" <-> "OD2" Residue "D GLU 217": "OE1" <-> "OE2" Residue "D TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 239": "OD1" <-> "OD2" Residue "D ARG 253": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ASP 255": "OD1" <-> "OD2" Residue "D ASP 256": "OD1" <-> "OD2" Residue "D TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 319": "OD1" <-> "OD2" Residue "D GLU 335": "OE1" <-> "OE2" Residue "D ARG 355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 399": "OE1" <-> "OE2" Residue "D PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 404": "OD1" <-> "OD2" Residue "D ARG 407": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 449": "OD1" <-> "OD2" Residue "D ASP 470": "OD1" <-> "OD2" Residue "D ARG 474": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 509": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 510": "OE1" <-> "OE2" Residue "D ARG 512": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 514": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 15": "OE1" <-> "OE2" Residue "E ASP 16": "OD1" <-> "OD2" Residue "E PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 28": "OD1" <-> "OD2" Residue "E ASP 50": "OD1" <-> "OD2" Residue "E ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 75": "OE1" <-> "OE2" Residue "E ASP 77": "OD1" <-> "OD2" Residue "E PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 103": "OE1" <-> "OE2" Residue "E ARG 105": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 136": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 182": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 184": "OE1" <-> "OE2" Residue "E ASP 214": "OD1" <-> "OD2" Residue "E GLU 217": "OE1" <-> "OE2" Residue "E TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 239": "OD1" <-> "OD2" Residue "E ARG 253": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ASP 255": "OD1" <-> "OD2" Residue "E ASP 256": "OD1" <-> "OD2" Residue "E ASP 261": "OD1" <-> "OD2" Residue "E TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 319": "OD1" <-> "OD2" Residue "E GLU 335": "OE1" <-> "OE2" Residue "E ARG 355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 399": "OE1" <-> "OE2" Residue "E PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 404": "OD1" <-> "OD2" Residue "E ARG 407": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 449": "OD1" <-> "OD2" Residue "E ASP 470": "OD1" <-> "OD2" Residue "E ARG 474": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 509": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 510": "OE1" <-> "OE2" Residue "E ARG 512": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E TYR 514": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 15": "OE1" <-> "OE2" Residue "F ASP 16": "OD1" <-> "OD2" Residue "F PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 28": "OD1" <-> "OD2" Residue "F ASP 47": "OD1" <-> "OD2" Residue "F GLU 48": "OE1" <-> "OE2" Residue "F ASP 50": "OD1" <-> "OD2" Residue "F ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F GLU 75": "OE1" <-> "OE2" Residue "F PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 103": "OE1" <-> "OE2" Residue "F ARG 105": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 136": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 146": "OE1" <-> "OE2" Residue "F ARG 182": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F GLU 184": "OE1" <-> "OE2" Residue "F GLU 196": "OE1" <-> "OE2" Residue "F ASP 214": "OD1" <-> "OD2" Residue "F GLU 217": "OE1" <-> "OE2" Residue "F TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 239": "OD1" <-> "OD2" Residue "F ARG 253": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ASP 255": "OD1" <-> "OD2" Residue "F ASP 256": "OD1" <-> "OD2" Residue "F ASP 269": "OD1" <-> "OD2" Residue "F TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 319": "OD1" <-> "OD2" Residue "F GLU 335": "OE1" <-> "OE2" Residue "F ARG 355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 399": "OE1" <-> "OE2" Residue "F PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 407": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 449": "OD1" <-> "OD2" Residue "F ARG 474": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 509": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 510": "OE1" <-> "OE2" Residue "F ARG 512": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 16": "OD1" <-> "OD2" Residue "G PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 28": "OD1" <-> "OD2" Residue "G ASP 47": "OD1" <-> "OD2" Residue "G GLU 48": "OE1" <-> "OE2" Residue "G ASP 50": "OD1" <-> "OD2" Residue "G ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G GLU 75": "OE1" <-> "OE2" Residue "G ASP 77": "OD1" <-> "OD2" Residue "G PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 103": "OE1" <-> "OE2" Residue "G ARG 105": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 117": "OD1" <-> "OD2" Residue "G ASP 129": "OD1" <-> "OD2" Residue "G GLU 132": "OE1" <-> "OE2" Residue "G ARG 136": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 146": "OE1" <-> "OE2" Residue "G ARG 182": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G GLU 184": "OE1" <-> "OE2" Residue "G GLU 217": "OE1" <-> "OE2" Residue "G TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 239": "OD1" <-> "OD2" Residue "G ARG 253": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ASP 255": "OD1" <-> "OD2" Residue "G ASP 256": "OD1" <-> "OD2" Residue "G TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 319": "OD1" <-> "OD2" Residue "G GLU 335": "OE1" <-> "OE2" Residue "G ARG 355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 399": "OE1" <-> "OE2" Residue "G PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ARG 407": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 449": "OD1" <-> "OD2" Residue "G ARG 474": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 509": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 510": "OE1" <-> "OE2" Residue "G ARG 512": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 15": "OE1" <-> "OE2" Residue "H ASP 16": "OD1" <-> "OD2" Residue "H PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 28": "OD1" <-> "OD2" Residue "H ASP 47": "OD1" <-> "OD2" Residue "H ASP 50": "OD1" <-> "OD2" Residue "H ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H GLU 75": "OE1" <-> "OE2" Residue "H ASP 77": "OD1" <-> "OD2" Residue "H PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 103": "OE1" <-> "OE2" Residue "H ARG 105": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 117": "OD1" <-> "OD2" Residue "H ASP 129": "OD1" <-> "OD2" Residue "H GLU 132": "OE1" <-> "OE2" Residue "H ARG 136": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ARG 182": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ASP 216": "OD1" <-> "OD2" Residue "H GLU 217": "OE1" <-> "OE2" Residue "H TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 239": "OD1" <-> "OD2" Residue "H ARG 253": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ASP 255": "OD1" <-> "OD2" Residue "H ASP 256": "OD1" <-> "OD2" Residue "H TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 319": "OD1" <-> "OD2" Residue "H GLU 335": "OE1" <-> "OE2" Residue "H ARG 355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 399": "OE1" <-> "OE2" Residue "H PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 404": "OD1" <-> "OD2" Residue "H ARG 407": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 470": "OD1" <-> "OD2" Residue "H ARG 474": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 509": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 510": "OE1" <-> "OE2" Residue "H ARG 512": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H TYR 514": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 58720 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 7222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 7222 Classifications: {'peptide': 475} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 17, 'TRANS': 457} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 7222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 7222 Classifications: {'peptide': 475} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 17, 'TRANS': 457} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 7222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 7222 Classifications: {'peptide': 475} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 17, 'TRANS': 457} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 7222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 7222 Classifications: {'peptide': 475} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 17, 'TRANS': 457} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 7222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 7222 Classifications: {'peptide': 475} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 17, 'TRANS': 457} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 7222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 7222 Classifications: {'peptide': 475} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 17, 'TRANS': 457} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 7222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 7222 Classifications: {'peptide': 475} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 17, 'TRANS': 457} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 7222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 7222 Classifications: {'peptide': 475} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 17, 'TRANS': 457} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 118 Unusual residues: {'ATP': 1, 'GTP': 2} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "B" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 118 Unusual residues: {'ATP': 1, 'GTP': 2} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "C" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 118 Unusual residues: {'ATP': 1, 'GTP': 2} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "D" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 118 Unusual residues: {'ATP': 1, 'GTP': 2} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "E" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 118 Unusual residues: {'ATP': 1, 'GTP': 2} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "F" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 118 Unusual residues: {'ATP': 1, 'GTP': 2} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "G" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 118 Unusual residues: {'ATP': 1, 'GTP': 2} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "H" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 118 Unusual residues: {'ATP': 1, 'GTP': 2} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Time building chain proxies: 18.77, per 1000 atoms: 0.32 Number of scatterers: 58720 At special positions: 0 Unit cell: (169.05, 169.05, 128.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 192 16.00 P 80 15.00 O 5808 8.00 N 5072 7.00 C 18368 6.00 H 29200 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 42.88 Conformation dependent library (CDL) restraints added in 4.4 seconds 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6816 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 139 helices and 52 sheets defined 34.8% alpha, 11.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.02 Creating SS restraints... Processing helix chain 'A' and resid 20 through 25 Processing helix chain 'A' and resid 32 through 34 No H-bonds generated for 'chain 'A' and resid 32 through 34' Processing helix chain 'A' and resid 46 through 48 No H-bonds generated for 'chain 'A' and resid 46 through 48' Processing helix chain 'A' and resid 76 through 84 Processing helix chain 'A' and resid 97 through 110 Processing helix chain 'A' and resid 127 through 137 Processing helix chain 'A' and resid 160 through 162 No H-bonds generated for 'chain 'A' and resid 160 through 162' Processing helix chain 'A' and resid 194 through 204 Processing helix chain 'A' and resid 224 through 232 Processing helix chain 'A' and resid 255 through 265 removed outlier: 3.528A pdb=" N ARG A 259 " --> pdb=" O ASP A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 293 Processing helix chain 'A' and resid 307 through 316 removed outlier: 3.639A pdb=" N ASN A 312 " --> pdb=" O ALA A 308 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU A 313 " --> pdb=" O GLN A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 336 No H-bonds generated for 'chain 'A' and resid 333 through 336' Processing helix chain 'A' and resid 343 through 357 removed outlier: 4.427A pdb=" N ARG A 356 " --> pdb=" O GLU A 352 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N PHE A 357 " --> pdb=" O TYR A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 378 Processing helix chain 'A' and resid 453 through 471 Proline residue: A 458 - end of helix Processing helix chain 'A' and resid 476 through 485 Processing helix chain 'A' and resid 495 through 501 Processing helix chain 'B' and resid 20 through 25 Processing helix chain 'B' and resid 32 through 34 No H-bonds generated for 'chain 'B' and resid 32 through 34' Processing helix chain 'B' and resid 46 through 48 No H-bonds generated for 'chain 'B' and resid 46 through 48' Processing helix chain 'B' and resid 76 through 84 Processing helix chain 'B' and resid 97 through 110 Processing helix chain 'B' and resid 127 through 137 Processing helix chain 'B' and resid 194 through 204 Processing helix chain 'B' and resid 224 through 232 Processing helix chain 'B' and resid 255 through 265 removed outlier: 3.569A pdb=" N ARG B 259 " --> pdb=" O ASP B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 293 Processing helix chain 'B' and resid 307 through 316 removed outlier: 3.607A pdb=" N ASN B 312 " --> pdb=" O ALA B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 336 No H-bonds generated for 'chain 'B' and resid 333 through 336' Processing helix chain 'B' and resid 343 through 357 removed outlier: 4.441A pdb=" N ARG B 356 " --> pdb=" O GLU B 352 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N PHE B 357 " --> pdb=" O TYR B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 378 Processing helix chain 'B' and resid 453 through 471 Proline residue: B 458 - end of helix Processing helix chain 'B' and resid 476 through 485 Processing helix chain 'B' and resid 495 through 501 Processing helix chain 'C' and resid 20 through 25 Processing helix chain 'C' and resid 32 through 34 No H-bonds generated for 'chain 'C' and resid 32 through 34' Processing helix chain 'C' and resid 46 through 48 No H-bonds generated for 'chain 'C' and resid 46 through 48' Processing helix chain 'C' and resid 76 through 84 Processing helix chain 'C' and resid 97 through 110 Processing helix chain 'C' and resid 127 through 137 Processing helix chain 'C' and resid 160 through 162 No H-bonds generated for 'chain 'C' and resid 160 through 162' Processing helix chain 'C' and resid 194 through 204 Processing helix chain 'C' and resid 224 through 232 Processing helix chain 'C' and resid 255 through 265 removed outlier: 3.516A pdb=" N ARG C 259 " --> pdb=" O ASP C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 293 Processing helix chain 'C' and resid 307 through 316 removed outlier: 3.678A pdb=" N ASN C 312 " --> pdb=" O ALA C 308 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU C 313 " --> pdb=" O GLN C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 336 No H-bonds generated for 'chain 'C' and resid 333 through 336' Processing helix chain 'C' and resid 343 through 357 removed outlier: 4.463A pdb=" N ARG C 356 " --> pdb=" O GLU C 352 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N PHE C 357 " --> pdb=" O TYR C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 378 Processing helix chain 'C' and resid 453 through 471 Proline residue: C 458 - end of helix Processing helix chain 'C' and resid 476 through 485 Processing helix chain 'C' and resid 495 through 501 Processing helix chain 'D' and resid 20 through 25 Processing helix chain 'D' and resid 32 through 34 No H-bonds generated for 'chain 'D' and resid 32 through 34' Processing helix chain 'D' and resid 46 through 48 No H-bonds generated for 'chain 'D' and resid 46 through 48' Processing helix chain 'D' and resid 76 through 84 Processing helix chain 'D' and resid 97 through 110 Processing helix chain 'D' and resid 127 through 137 Processing helix chain 'D' and resid 160 through 162 No H-bonds generated for 'chain 'D' and resid 160 through 162' Processing helix chain 'D' and resid 194 through 204 Processing helix chain 'D' and resid 224 through 232 Processing helix chain 'D' and resid 255 through 265 removed outlier: 3.581A pdb=" N ARG D 259 " --> pdb=" O ASP D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 293 Processing helix chain 'D' and resid 307 through 316 removed outlier: 3.653A pdb=" N ASN D 312 " --> pdb=" O ALA D 308 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU D 313 " --> pdb=" O GLN D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 336 No H-bonds generated for 'chain 'D' and resid 333 through 336' Processing helix chain 'D' and resid 343 through 357 removed outlier: 4.442A pdb=" N ARG D 356 " --> pdb=" O GLU D 352 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N PHE D 357 " --> pdb=" O TYR D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 378 Processing helix chain 'D' and resid 453 through 471 Proline residue: D 458 - end of helix Processing helix chain 'D' and resid 476 through 485 Processing helix chain 'D' and resid 495 through 501 Processing helix chain 'E' and resid 20 through 25 Processing helix chain 'E' and resid 32 through 34 No H-bonds generated for 'chain 'E' and resid 32 through 34' Processing helix chain 'E' and resid 46 through 48 No H-bonds generated for 'chain 'E' and resid 46 through 48' Processing helix chain 'E' and resid 76 through 84 Processing helix chain 'E' and resid 97 through 110 Processing helix chain 'E' and resid 127 through 137 Processing helix chain 'E' and resid 194 through 204 Processing helix chain 'E' and resid 224 through 232 Processing helix chain 'E' and resid 255 through 265 removed outlier: 3.640A pdb=" N ARG E 259 " --> pdb=" O ASP E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 293 Processing helix chain 'E' and resid 307 through 316 removed outlier: 3.675A pdb=" N ASN E 312 " --> pdb=" O ALA E 308 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU E 313 " --> pdb=" O GLN E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 333 through 336 No H-bonds generated for 'chain 'E' and resid 333 through 336' Processing helix chain 'E' and resid 343 through 357 removed outlier: 4.429A pdb=" N ARG E 356 " --> pdb=" O GLU E 352 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N PHE E 357 " --> pdb=" O TYR E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 370 through 378 Processing helix chain 'E' and resid 453 through 471 Proline residue: E 458 - end of helix Processing helix chain 'E' and resid 476 through 485 Processing helix chain 'E' and resid 495 through 501 Processing helix chain 'F' and resid 20 through 25 Processing helix chain 'F' and resid 32 through 34 No H-bonds generated for 'chain 'F' and resid 32 through 34' Processing helix chain 'F' and resid 46 through 48 No H-bonds generated for 'chain 'F' and resid 46 through 48' Processing helix chain 'F' and resid 76 through 84 Processing helix chain 'F' and resid 97 through 110 Processing helix chain 'F' and resid 127 through 137 Processing helix chain 'F' and resid 194 through 204 Processing helix chain 'F' and resid 224 through 232 Processing helix chain 'F' and resid 255 through 265 removed outlier: 3.528A pdb=" N ARG F 259 " --> pdb=" O ASP F 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 293 Processing helix chain 'F' and resid 307 through 316 removed outlier: 3.654A pdb=" N ASN F 312 " --> pdb=" O ALA F 308 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU F 313 " --> pdb=" O GLN F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 336 No H-bonds generated for 'chain 'F' and resid 333 through 336' Processing helix chain 'F' and resid 343 through 357 removed outlier: 4.414A pdb=" N ARG F 356 " --> pdb=" O GLU F 352 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N PHE F 357 " --> pdb=" O TYR F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 370 through 378 Processing helix chain 'F' and resid 453 through 471 Proline residue: F 458 - end of helix Processing helix chain 'F' and resid 476 through 485 Processing helix chain 'F' and resid 495 through 501 Processing helix chain 'G' and resid 20 through 25 Processing helix chain 'G' and resid 32 through 34 No H-bonds generated for 'chain 'G' and resid 32 through 34' Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'G' and resid 76 through 84 Processing helix chain 'G' and resid 97 through 110 Processing helix chain 'G' and resid 127 through 137 Processing helix chain 'G' and resid 194 through 204 Processing helix chain 'G' and resid 224 through 232 Processing helix chain 'G' and resid 255 through 265 removed outlier: 3.568A pdb=" N ARG G 259 " --> pdb=" O ASP G 255 " (cutoff:3.500A) Processing helix chain 'G' and resid 281 through 293 Processing helix chain 'G' and resid 307 through 316 removed outlier: 3.662A pdb=" N ASN G 312 " --> pdb=" O ALA G 308 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU G 313 " --> pdb=" O GLN G 309 " (cutoff:3.500A) Processing helix chain 'G' and resid 333 through 336 No H-bonds generated for 'chain 'G' and resid 333 through 336' Processing helix chain 'G' and resid 343 through 357 removed outlier: 4.399A pdb=" N ARG G 356 " --> pdb=" O GLU G 352 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N PHE G 357 " --> pdb=" O TYR G 353 " (cutoff:3.500A) Processing helix chain 'G' and resid 370 through 378 Processing helix chain 'G' and resid 453 through 471 Proline residue: G 458 - end of helix Processing helix chain 'G' and resid 476 through 485 Processing helix chain 'G' and resid 495 through 501 Processing helix chain 'H' and resid 20 through 25 Processing helix chain 'H' and resid 32 through 34 No H-bonds generated for 'chain 'H' and resid 32 through 34' Processing helix chain 'H' and resid 46 through 48 No H-bonds generated for 'chain 'H' and resid 46 through 48' Processing helix chain 'H' and resid 76 through 84 Processing helix chain 'H' and resid 97 through 110 Processing helix chain 'H' and resid 127 through 137 Processing helix chain 'H' and resid 194 through 204 Processing helix chain 'H' and resid 224 through 232 Processing helix chain 'H' and resid 255 through 265 Processing helix chain 'H' and resid 281 through 293 Processing helix chain 'H' and resid 307 through 316 removed outlier: 3.635A pdb=" N ASN H 312 " --> pdb=" O ALA H 308 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU H 313 " --> pdb=" O GLN H 309 " (cutoff:3.500A) Processing helix chain 'H' and resid 333 through 336 No H-bonds generated for 'chain 'H' and resid 333 through 336' Processing helix chain 'H' and resid 343 through 357 removed outlier: 4.440A pdb=" N ARG H 356 " --> pdb=" O GLU H 352 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N PHE H 357 " --> pdb=" O TYR H 353 " (cutoff:3.500A) Processing helix chain 'H' and resid 370 through 378 Processing helix chain 'H' and resid 453 through 471 Proline residue: H 458 - end of helix Processing helix chain 'H' and resid 476 through 485 Processing helix chain 'H' and resid 495 through 501 Processing sheet with id= A, first strand: chain 'A' and resid 35 through 37 Processing sheet with id= B, first strand: chain 'A' and resid 65 through 67 removed outlier: 6.409A pdb=" N VAL A 384 " --> pdb=" O ILE A 66 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASN A 303 " --> pdb=" O ARG A 322 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLY A 302 " --> pdb=" O LEU A 273 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 187 through 189 removed outlier: 8.219A pdb=" N ALA A 188 " --> pdb=" O LYS A 208 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 400 through 402 Processing sheet with id= E, first strand: chain 'A' and resid 142 through 145 Processing sheet with id= F, first strand: chain 'B' and resid 35 through 37 Processing sheet with id= G, first strand: chain 'B' and resid 65 through 67 removed outlier: 6.405A pdb=" N VAL B 384 " --> pdb=" O ILE B 66 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 187 through 189 removed outlier: 8.310A pdb=" N ALA B 188 " --> pdb=" O LYS B 208 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 247 through 250 removed outlier: 6.651A pdb=" N VAL B 270 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N VAL B 250 " --> pdb=" O VAL B 270 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N VAL B 272 " --> pdb=" O VAL B 250 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N GLN B 298 " --> pdb=" O ILE B 271 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N LEU B 273 " --> pdb=" O GLN B 298 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N ILE B 300 " --> pdb=" O LEU B 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'B' and resid 400 through 403 Processing sheet with id= K, first strand: chain 'B' and resid 142 through 145 Processing sheet with id= L, first strand: chain 'C' and resid 35 through 37 Processing sheet with id= M, first strand: chain 'C' and resid 65 through 67 removed outlier: 6.408A pdb=" N VAL C 384 " --> pdb=" O ILE C 66 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 187 through 189 removed outlier: 8.221A pdb=" N ALA C 188 " --> pdb=" O LYS C 208 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 247 through 250 removed outlier: 6.643A pdb=" N VAL C 270 " --> pdb=" O ALA C 248 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N VAL C 250 " --> pdb=" O VAL C 270 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N VAL C 272 " --> pdb=" O VAL C 250 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N GLN C 298 " --> pdb=" O ILE C 271 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N LEU C 273 " --> pdb=" O GLN C 298 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N ILE C 300 " --> pdb=" O LEU C 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'C' and resid 400 through 402 Processing sheet with id= Q, first strand: chain 'C' and resid 142 through 145 Processing sheet with id= R, first strand: chain 'D' and resid 35 through 37 Processing sheet with id= S, first strand: chain 'D' and resid 65 through 67 removed outlier: 6.381A pdb=" N VAL D 384 " --> pdb=" O ILE D 66 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 187 through 189 removed outlier: 8.261A pdb=" N ALA D 188 " --> pdb=" O LYS D 208 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 247 through 250 removed outlier: 6.638A pdb=" N VAL D 270 " --> pdb=" O ALA D 248 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N VAL D 250 " --> pdb=" O VAL D 270 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N VAL D 272 " --> pdb=" O VAL D 250 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N GLN D 298 " --> pdb=" O ILE D 271 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N LEU D 273 " --> pdb=" O GLN D 298 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N ILE D 300 " --> pdb=" O LEU D 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'D' and resid 400 through 402 Processing sheet with id= W, first strand: chain 'D' and resid 53 through 56 removed outlier: 6.604A pdb=" N ILE D 59 " --> pdb=" O LEU D 55 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 142 through 145 Processing sheet with id= Y, first strand: chain 'E' and resid 35 through 37 Processing sheet with id= Z, first strand: chain 'E' and resid 65 through 67 removed outlier: 6.418A pdb=" N VAL E 384 " --> pdb=" O ILE E 66 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'E' and resid 187 through 189 removed outlier: 8.183A pdb=" N ALA E 188 " --> pdb=" O LYS E 208 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'E' and resid 247 through 250 removed outlier: 6.632A pdb=" N VAL E 270 " --> pdb=" O ALA E 248 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N VAL E 250 " --> pdb=" O VAL E 270 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N VAL E 272 " --> pdb=" O VAL E 250 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N GLN E 298 " --> pdb=" O ILE E 271 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N LEU E 273 " --> pdb=" O GLN E 298 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N ILE E 300 " --> pdb=" O LEU E 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'E' and resid 400 through 402 Processing sheet with id= AD, first strand: chain 'E' and resid 53 through 56 removed outlier: 6.611A pdb=" N ILE E 59 " --> pdb=" O LEU E 55 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'E' and resid 142 through 145 Processing sheet with id= AF, first strand: chain 'F' and resid 35 through 37 Processing sheet with id= AG, first strand: chain 'F' and resid 65 through 67 removed outlier: 6.394A pdb=" N VAL F 384 " --> pdb=" O ILE F 66 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'F' and resid 187 through 189 removed outlier: 8.291A pdb=" N ALA F 188 " --> pdb=" O LYS F 208 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA F 220 " --> pdb=" O ILE F 211 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'F' and resid 247 through 250 removed outlier: 6.657A pdb=" N VAL F 270 " --> pdb=" O ALA F 248 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N VAL F 250 " --> pdb=" O VAL F 270 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N VAL F 272 " --> pdb=" O VAL F 250 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N GLN F 298 " --> pdb=" O ILE F 271 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N LEU F 273 " --> pdb=" O GLN F 298 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ILE F 300 " --> pdb=" O LEU F 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= AI Processing sheet with id= AJ, first strand: chain 'F' and resid 400 through 402 Processing sheet with id= AK, first strand: chain 'F' and resid 53 through 56 removed outlier: 6.631A pdb=" N ILE F 59 " --> pdb=" O LEU F 55 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'F' and resid 142 through 145 Processing sheet with id= AM, first strand: chain 'G' and resid 35 through 37 Processing sheet with id= AN, first strand: chain 'G' and resid 65 through 67 removed outlier: 6.384A pdb=" N VAL G 384 " --> pdb=" O ILE G 66 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'G' and resid 187 through 189 removed outlier: 8.207A pdb=" N ALA G 188 " --> pdb=" O LYS G 208 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'G' and resid 247 through 250 removed outlier: 6.646A pdb=" N VAL G 270 " --> pdb=" O ALA G 248 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N VAL G 250 " --> pdb=" O VAL G 270 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N VAL G 272 " --> pdb=" O VAL G 250 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N GLN G 298 " --> pdb=" O ILE G 271 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N LEU G 273 " --> pdb=" O GLN G 298 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ILE G 300 " --> pdb=" O LEU G 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= AP Processing sheet with id= AQ, first strand: chain 'G' and resid 400 through 402 Processing sheet with id= AR, first strand: chain 'G' and resid 53 through 56 removed outlier: 6.615A pdb=" N ILE G 59 " --> pdb=" O LEU G 55 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'G' and resid 142 through 145 Processing sheet with id= AT, first strand: chain 'H' and resid 35 through 37 Processing sheet with id= AU, first strand: chain 'H' and resid 65 through 67 removed outlier: 6.382A pdb=" N VAL H 384 " --> pdb=" O ILE H 66 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'H' and resid 187 through 189 removed outlier: 8.238A pdb=" N ALA H 188 " --> pdb=" O LYS H 208 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'H' and resid 247 through 250 removed outlier: 6.605A pdb=" N VAL H 270 " --> pdb=" O ALA H 248 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N VAL H 250 " --> pdb=" O VAL H 270 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N VAL H 272 " --> pdb=" O VAL H 250 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N GLN H 298 " --> pdb=" O ILE H 271 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N LEU H 273 " --> pdb=" O GLN H 298 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N ILE H 300 " --> pdb=" O LEU H 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= AW Processing sheet with id= AX, first strand: chain 'H' and resid 400 through 402 Processing sheet with id= AY, first strand: chain 'H' and resid 53 through 56 removed outlier: 6.620A pdb=" N ILE H 59 " --> pdb=" O LEU H 55 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'H' and resid 142 through 145 931 hydrogen bonds defined for protein. 2700 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: 20.29 Time building geometry restraints manager: 44.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.13: 29144 1.13 - 1.30: 5204 1.30 - 1.48: 11245 1.48 - 1.66: 13287 1.66 - 1.83: 328 Bond restraints: 59208 Sorted by residual: bond pdb=" N GLY C 501 " pdb=" H GLY C 501 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N GLN G 292 " pdb=" H GLN G 292 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N ASP A 71 " pdb=" H ASP A 71 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N THR C 180 " pdb=" H THR C 180 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" N HIS C 466 " pdb=" H HIS C 466 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 ... (remaining 59203 not shown) Histogram of bond angle deviations from ideal: 93.09 - 100.92: 183 100.92 - 108.75: 28429 108.75 - 116.59: 47288 116.59 - 124.42: 29020 124.42 - 132.25: 2216 Bond angle restraints: 107136 Sorted by residual: angle pdb=" PB ATP E 603 " pdb=" O3B ATP E 603 " pdb=" PG ATP E 603 " ideal model delta sigma weight residual 139.87 122.50 17.37 1.00e+00 1.00e+00 3.02e+02 angle pdb=" PB ATP H 603 " pdb=" O3B ATP H 603 " pdb=" PG ATP H 603 " ideal model delta sigma weight residual 139.87 123.58 16.29 1.00e+00 1.00e+00 2.65e+02 angle pdb=" PB ATP A 603 " pdb=" O3B ATP A 603 " pdb=" PG ATP A 603 " ideal model delta sigma weight residual 139.87 123.66 16.21 1.00e+00 1.00e+00 2.63e+02 angle pdb=" PB ATP B 603 " pdb=" O3B ATP B 603 " pdb=" PG ATP B 603 " ideal model delta sigma weight residual 139.87 123.70 16.17 1.00e+00 1.00e+00 2.61e+02 angle pdb=" PB ATP G 603 " pdb=" O3B ATP G 603 " pdb=" PG ATP G 603 " ideal model delta sigma weight residual 139.87 123.77 16.10 1.00e+00 1.00e+00 2.59e+02 ... (remaining 107131 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.73: 26100 35.73 - 71.46: 1464 71.46 - 107.19: 86 107.19 - 142.92: 42 142.92 - 178.65: 20 Dihedral angle restraints: 27712 sinusoidal: 15720 harmonic: 11992 Sorted by residual: dihedral pdb=" C8 GTP G 601 " pdb=" C1' GTP G 601 " pdb=" N9 GTP G 601 " pdb=" O4' GTP G 601 " ideal model delta sinusoidal sigma weight residual 104.59 -74.05 178.65 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C8 GTP A 601 " pdb=" C1' GTP A 601 " pdb=" N9 GTP A 601 " pdb=" O4' GTP A 601 " ideal model delta sinusoidal sigma weight residual 104.59 -73.16 177.76 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C8 GTP F 601 " pdb=" C1' GTP F 601 " pdb=" N9 GTP F 601 " pdb=" O4' GTP F 601 " ideal model delta sinusoidal sigma weight residual 104.59 -79.24 -176.16 1 2.00e+01 2.50e-03 4.79e+01 ... (remaining 27709 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 3283 0.100 - 0.200: 1215 0.200 - 0.300: 174 0.300 - 0.400: 16 0.400 - 0.501: 8 Chirality restraints: 4696 Sorted by residual: chirality pdb=" CA TYR D 514 " pdb=" N TYR D 514 " pdb=" C TYR D 514 " pdb=" CB TYR D 514 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.26e+00 chirality pdb=" CA TYR A 514 " pdb=" N TYR A 514 " pdb=" C TYR A 514 " pdb=" CB TYR A 514 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.76e+00 chirality pdb=" CA TYR F 514 " pdb=" N TYR F 514 " pdb=" C TYR F 514 " pdb=" CB TYR F 514 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.48 2.00e-01 2.50e+01 5.65e+00 ... (remaining 4693 not shown) Planarity restraints: 8704 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG F 412 " 0.569 9.50e-02 1.11e+02 2.25e-01 3.61e+02 pdb=" NE ARG F 412 " 0.079 2.00e-02 2.50e+03 pdb=" CZ ARG F 412 " 0.060 2.00e-02 2.50e+03 pdb=" NH1 ARG F 412 " 0.124 2.00e-02 2.50e+03 pdb=" NH2 ARG F 412 " -0.041 2.00e-02 2.50e+03 pdb="HH11 ARG F 412 " -0.280 2.00e-02 2.50e+03 pdb="HH12 ARG F 412 " 0.136 2.00e-02 2.50e+03 pdb="HH21 ARG F 412 " -0.071 2.00e-02 2.50e+03 pdb="HH22 ARG F 412 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 412 " 0.535 9.50e-02 1.11e+02 2.13e-01 3.36e+02 pdb=" NE ARG C 412 " 0.077 2.00e-02 2.50e+03 pdb=" CZ ARG C 412 " 0.056 2.00e-02 2.50e+03 pdb=" NH1 ARG C 412 " 0.122 2.00e-02 2.50e+03 pdb=" NH2 ARG C 412 " -0.072 2.00e-02 2.50e+03 pdb="HH11 ARG C 412 " -0.268 2.00e-02 2.50e+03 pdb="HH12 ARG C 412 " 0.134 2.00e-02 2.50e+03 pdb="HH21 ARG C 412 " -0.049 2.00e-02 2.50e+03 pdb="HH22 ARG C 412 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 412 " -0.578 9.50e-02 1.11e+02 2.24e-01 3.35e+02 pdb=" NE ARG B 412 " -0.079 2.00e-02 2.50e+03 pdb=" CZ ARG B 412 " -0.047 2.00e-02 2.50e+03 pdb=" NH1 ARG B 412 " -0.110 2.00e-02 2.50e+03 pdb=" NH2 ARG B 412 " 0.055 2.00e-02 2.50e+03 pdb="HH11 ARG B 412 " 0.266 2.00e-02 2.50e+03 pdb="HH12 ARG B 412 " -0.146 2.00e-02 2.50e+03 pdb="HH21 ARG B 412 " 0.052 2.00e-02 2.50e+03 pdb="HH22 ARG B 412 " 0.035 2.00e-02 2.50e+03 ... (remaining 8701 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.16: 3897 2.16 - 2.77: 105402 2.77 - 3.38: 184205 3.38 - 3.99: 252940 3.99 - 4.60: 366032 Nonbonded interactions: 912476 Sorted by model distance: nonbonded pdb=" HH TYR D 411 " pdb=" O3P IMP D 604 " model vdw 1.544 1.850 nonbonded pdb=" HH TYR H 411 " pdb=" O1P IMP H 604 " model vdw 1.548 1.850 nonbonded pdb=" HH TYR C 411 " pdb=" O3P IMP C 604 " model vdw 1.552 1.850 nonbonded pdb=" HH TYR B 411 " pdb=" O3P IMP B 604 " model vdw 1.556 1.850 nonbonded pdb=" HH TYR G 411 " pdb=" O1P IMP G 604 " model vdw 1.558 1.850 ... (remaining 912471 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.710 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: 0.660 Extract box with map and model: 9.700 Check model and map are aligned: 0.700 Set scattering table: 0.440 Process input model: 150.490 Find NCS groups from input model: 2.230 Set up NCS constraints: 0.280 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: 0.010 Load rotamer database and sin/cos tables:10.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 176.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 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 : 0.013 0.086 30008 Z= 0.858 Angle : 2.068 17.366 40728 Z= 1.329 Chirality : 0.099 0.501 4696 Planarity : 0.019 0.211 5064 Dihedral : 20.132 178.647 11328 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 1.13 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.54 % Favored : 96.24 % Rotamer: Outliers : 2.87 % Allowed : 5.39 % Favored : 91.74 % Cbeta Deviations : 0.38 % Peptide Plane: Cis-proline : 0.00 % 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: -0.73 (0.12), residues: 3752 helix: -0.66 (0.11), residues: 1416 sheet: -0.75 (0.29), residues: 280 loop : -0.17 (0.13), residues: 2056 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.017 0.005 HIS D 93 PHE 0.087 0.016 PHE B 24 TYR 0.138 0.027 TYR H 514 ARG 0.016 0.002 ARG D 407 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Evaluate side-chains 581 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 493 time to evaluate : 3.387 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 78 MET cc_start: 0.9204 (tpp) cc_final: 0.8935 (tpp) REVERT: A 82 MET cc_start: 0.9067 (mmm) cc_final: 0.8591 (mmm) REVERT: A 146 GLU cc_start: 0.5326 (tp30) cc_final: 0.5118 (tp30) REVERT: A 150 MET cc_start: 0.6996 (tpt) cc_final: 0.6600 (tpp) REVERT: A 205 LYS cc_start: 0.7782 (mttp) cc_final: 0.6709 (mmtt) REVERT: A 286 MET cc_start: 0.8477 (tpp) cc_final: 0.8225 (tpt) REVERT: A 508 SER cc_start: 0.7664 (t) cc_final: 0.7337 (p) REVERT: A 509 TYR cc_start: 0.6498 (OUTLIER) cc_final: 0.4923 (t80) REVERT: B 78 MET cc_start: 0.9197 (tpp) cc_final: 0.8943 (tpp) REVERT: B 82 MET cc_start: 0.9035 (mmm) cc_final: 0.8586 (mmm) REVERT: B 150 MET cc_start: 0.7089 (tpt) cc_final: 0.6533 (tmm) REVERT: B 161 ARG cc_start: 0.7104 (mtt180) cc_final: 0.6806 (mtt-85) REVERT: B 179 MET cc_start: 0.6670 (mtm) cc_final: 0.6456 (mtm) REVERT: B 205 LYS cc_start: 0.7768 (mttp) cc_final: 0.6752 (mmtt) REVERT: B 277 GLN cc_start: 0.9324 (OUTLIER) cc_final: 0.9008 (tm-30) REVERT: B 286 MET cc_start: 0.8459 (tpp) cc_final: 0.7615 (tpt) REVERT: B 455 LYS cc_start: 0.7970 (mmtt) cc_final: 0.7431 (mtmt) REVERT: B 509 TYR cc_start: 0.6137 (OUTLIER) cc_final: 0.4208 (t80) REVERT: B 512 ARG cc_start: 0.6879 (ttt180) cc_final: 0.4680 (mmt-90) REVERT: C 78 MET cc_start: 0.9222 (tpp) cc_final: 0.8978 (tpp) REVERT: C 82 MET cc_start: 0.9056 (mmm) cc_final: 0.8666 (mmm) REVERT: C 146 GLU cc_start: 0.5343 (tp30) cc_final: 0.5108 (tp30) REVERT: C 150 MET cc_start: 0.6934 (tpt) cc_final: 0.6173 (mmm) REVERT: C 179 MET cc_start: 0.6839 (mtm) cc_final: 0.6621 (mtm) REVERT: C 195 LYS cc_start: 0.7646 (ttmt) cc_final: 0.7443 (ttmt) REVERT: C 205 LYS cc_start: 0.7852 (mttp) cc_final: 0.6906 (mmtt) REVERT: C 277 GLN cc_start: 0.9323 (OUTLIER) cc_final: 0.8946 (tm-30) REVERT: C 286 MET cc_start: 0.8422 (tpt) cc_final: 0.8218 (tpt) REVERT: C 482 MET cc_start: 0.9019 (mtp) cc_final: 0.8796 (mtp) REVERT: C 508 SER cc_start: 0.7654 (t) cc_final: 0.7437 (p) REVERT: C 509 TYR cc_start: 0.6243 (OUTLIER) cc_final: 0.4403 (t80) REVERT: D 82 MET cc_start: 0.9084 (mmm) cc_final: 0.8647 (mmm) REVERT: D 150 MET cc_start: 0.6928 (tpt) cc_final: 0.6631 (tpp) REVERT: D 205 LYS cc_start: 0.7548 (mttp) cc_final: 0.6522 (mmtt) REVERT: D 277 GLN cc_start: 0.9298 (OUTLIER) cc_final: 0.9008 (tm-30) REVERT: D 286 MET cc_start: 0.8536 (tpt) cc_final: 0.7538 (tpt) REVERT: D 441 GLN cc_start: 0.7517 (mt0) cc_final: 0.7293 (mm-40) REVERT: D 482 MET cc_start: 0.9015 (mtp) cc_final: 0.8787 (mtp) REVERT: D 508 SER cc_start: 0.7542 (t) cc_final: 0.7189 (p) REVERT: D 509 TYR cc_start: 0.6486 (OUTLIER) cc_final: 0.4948 (t80) REVERT: E 78 MET cc_start: 0.9190 (tpp) cc_final: 0.8906 (tpp) REVERT: E 82 MET cc_start: 0.9070 (mmm) cc_final: 0.8601 (mmm) REVERT: E 146 GLU cc_start: 0.5573 (tp30) cc_final: 0.5343 (tp30) REVERT: E 149 THR cc_start: 0.7500 (m) cc_final: 0.7182 (m) REVERT: E 150 MET cc_start: 0.6984 (tpt) cc_final: 0.6615 (tpp) REVERT: E 205 LYS cc_start: 0.7575 (mttp) cc_final: 0.6585 (mmtt) REVERT: E 286 MET cc_start: 0.8446 (tpp) cc_final: 0.7603 (tpt) REVERT: E 482 MET cc_start: 0.8986 (mtp) cc_final: 0.8782 (mtp) REVERT: E 508 SER cc_start: 0.7584 (t) cc_final: 0.7261 (p) REVERT: E 509 TYR cc_start: 0.6410 (OUTLIER) cc_final: 0.4635 (t80) REVERT: E 512 ARG cc_start: 0.6632 (ttt180) cc_final: 0.3928 (mmm160) REVERT: F 82 MET cc_start: 0.9098 (mmm) cc_final: 0.8717 (mmm) REVERT: F 146 GLU cc_start: 0.5243 (tp30) cc_final: 0.4955 (tp30) REVERT: F 150 MET cc_start: 0.7108 (tpt) cc_final: 0.6053 (mmm) REVERT: F 205 LYS cc_start: 0.7769 (mttp) cc_final: 0.6683 (mmtt) REVERT: F 228 LYS cc_start: 0.8139 (ttpt) cc_final: 0.7585 (tttt) REVERT: F 277 GLN cc_start: 0.9306 (OUTLIER) cc_final: 0.8951 (tm-30) REVERT: F 286 MET cc_start: 0.8504 (tpt) cc_final: 0.8229 (tpt) REVERT: F 356 ARG cc_start: 0.7452 (mtt180) cc_final: 0.7222 (mtp180) REVERT: G 78 MET cc_start: 0.9174 (tpp) cc_final: 0.8942 (tpp) REVERT: G 82 MET cc_start: 0.9044 (mmm) cc_final: 0.8501 (mmm) REVERT: G 150 MET cc_start: 0.6906 (tpt) cc_final: 0.6564 (tpp) REVERT: G 179 MET cc_start: 0.6954 (mtm) cc_final: 0.6687 (mtm) REVERT: G 195 LYS cc_start: 0.7684 (ttmt) cc_final: 0.7450 (ttmt) REVERT: G 205 LYS cc_start: 0.7790 (mttp) cc_final: 0.6717 (mmtt) REVERT: G 277 GLN cc_start: 0.9381 (OUTLIER) cc_final: 0.9084 (tm-30) REVERT: G 286 MET cc_start: 0.8450 (tpp) cc_final: 0.8240 (tpt) REVERT: G 455 LYS cc_start: 0.7894 (mmtt) cc_final: 0.7345 (mtmt) REVERT: G 482 MET cc_start: 0.9018 (mtp) cc_final: 0.8805 (mtp) REVERT: G 509 TYR cc_start: 0.7779 (p90) cc_final: 0.7577 (p90) REVERT: H 82 MET cc_start: 0.9082 (mmm) cc_final: 0.8550 (mmm) REVERT: H 150 MET cc_start: 0.7011 (tpt) cc_final: 0.6680 (tpp) REVERT: H 179 MET cc_start: 0.6668 (mtm) cc_final: 0.6386 (mtm) REVERT: H 205 LYS cc_start: 0.7746 (mttp) cc_final: 0.6685 (mmtt) REVERT: H 277 GLN cc_start: 0.9308 (OUTLIER) cc_final: 0.9001 (tm-30) REVERT: H 286 MET cc_start: 0.8450 (tpp) cc_final: 0.8206 (tpt) REVERT: H 509 TYR cc_start: 0.6584 (OUTLIER) cc_final: 0.5050 (t80) outliers start: 88 outliers final: 24 residues processed: 553 average time/residue: 2.4512 time to fit residues: 1608.4421 Evaluate side-chains 400 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 364 time to evaluate : 3.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 509 TYR Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain B residue 509 TYR Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 509 TYR Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 329 SER Chi-restraints excluded: chain D residue 509 TYR Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 329 SER Chi-restraints excluded: chain E residue 509 TYR Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 329 SER Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 329 SER Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 329 SER Chi-restraints excluded: chain H residue 509 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 317 optimal weight: 0.9990 chunk 284 optimal weight: 0.9990 chunk 158 optimal weight: 5.9990 chunk 97 optimal weight: 0.9990 chunk 192 optimal weight: 1.9990 chunk 152 optimal weight: 6.9990 chunk 294 optimal weight: 7.9990 chunk 114 optimal weight: 0.9990 chunk 179 optimal weight: 5.9990 chunk 219 optimal weight: 0.9990 chunk 341 optimal weight: 5.9990 overall best weight: 0.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 21 GLN B 202 GLN ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 GLN C 21 GLN C 33 ASN C 202 GLN C 292 GLN D 21 GLN D 33 ASN D 292 GLN E 202 GLN F 292 GLN ** G 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 202 GLN G 292 GLN G 441 GLN H 202 GLN H 292 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 30008 Z= 0.181 Angle : 0.650 7.382 40728 Z= 0.333 Chirality : 0.044 0.201 4696 Planarity : 0.005 0.053 5064 Dihedral : 20.834 172.011 4694 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.32 % Favored : 97.65 % Rotamer: Outliers : 2.35 % Allowed : 9.01 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.13), residues: 3752 helix: 0.81 (0.13), residues: 1416 sheet: -0.58 (0.25), residues: 360 loop : -0.14 (0.13), residues: 1976 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 507 PHE 0.018 0.002 PHE B 24 TYR 0.017 0.002 TYR G 509 ARG 0.003 0.000 ARG D 356 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Evaluate side-chains 470 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 398 time to evaluate : 3.941 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: A 78 MET cc_start: 0.9067 (tpp) cc_final: 0.8832 (tpp) REVERT: A 82 MET cc_start: 0.9000 (mmm) cc_final: 0.8465 (mmm) REVERT: A 150 MET cc_start: 0.6970 (tpt) cc_final: 0.6498 (tpp) REVERT: A 205 LYS cc_start: 0.7698 (mttp) cc_final: 0.6091 (tptp) REVERT: A 420 MET cc_start: 0.6317 (OUTLIER) cc_final: 0.5947 (tpp) REVERT: A 508 SER cc_start: 0.7575 (t) cc_final: 0.7238 (p) REVERT: A 512 ARG cc_start: 0.6652 (ttt180) cc_final: 0.3951 (mmm160) REVERT: B 82 MET cc_start: 0.8986 (mmm) cc_final: 0.8474 (mmm) REVERT: B 142 ILE cc_start: 0.7747 (OUTLIER) cc_final: 0.7492 (mp) REVERT: B 146 GLU cc_start: 0.5579 (tp30) cc_final: 0.5303 (tp30) REVERT: B 150 MET cc_start: 0.7000 (tpt) cc_final: 0.6565 (tpp) REVERT: B 161 ARG cc_start: 0.7008 (mtt180) cc_final: 0.6417 (mtt-85) REVERT: B 205 LYS cc_start: 0.7832 (mttp) cc_final: 0.6535 (mmtt) REVERT: B 455 LYS cc_start: 0.7956 (mmtt) cc_final: 0.7397 (mtmt) REVERT: B 509 TYR cc_start: 0.5722 (OUTLIER) cc_final: 0.3907 (t80) REVERT: B 512 ARG cc_start: 0.6776 (ttt180) cc_final: 0.3942 (mmm160) REVERT: C 21 GLN cc_start: 0.8036 (tt0) cc_final: 0.7819 (tt0) REVERT: C 78 MET cc_start: 0.9047 (tpp) cc_final: 0.8838 (tpp) REVERT: C 82 MET cc_start: 0.8984 (mmm) cc_final: 0.8672 (mmm) REVERT: C 146 GLU cc_start: 0.5307 (tp30) cc_final: 0.5066 (tp30) REVERT: C 150 MET cc_start: 0.6958 (tpt) cc_final: 0.6515 (tpp) REVERT: C 179 MET cc_start: 0.6801 (mtm) cc_final: 0.6141 (mpt) REVERT: C 205 LYS cc_start: 0.7910 (mttp) cc_final: 0.6315 (tptp) REVERT: C 277 GLN cc_start: 0.9188 (OUTLIER) cc_final: 0.8843 (tm-30) REVERT: C 483 MET cc_start: 0.8998 (tmm) cc_final: 0.8503 (tmm) REVERT: C 508 SER cc_start: 0.7616 (t) cc_final: 0.7302 (p) REVERT: C 512 ARG cc_start: 0.6712 (ttt180) cc_final: 0.3941 (mmm160) REVERT: D 21 GLN cc_start: 0.8098 (tt0) cc_final: 0.7862 (tt0) REVERT: D 78 MET cc_start: 0.9058 (tpp) cc_final: 0.8812 (tpp) REVERT: D 82 MET cc_start: 0.8998 (mmm) cc_final: 0.8667 (mmm) REVERT: D 150 MET cc_start: 0.6940 (tpt) cc_final: 0.6486 (tpp) REVERT: D 205 LYS cc_start: 0.7625 (mttp) cc_final: 0.6263 (mmtt) REVERT: D 286 MET cc_start: 0.8493 (tpt) cc_final: 0.8228 (tpt) REVERT: D 441 GLN cc_start: 0.7465 (mt0) cc_final: 0.7147 (mm-40) REVERT: D 508 SER cc_start: 0.7387 (t) cc_final: 0.7014 (m) REVERT: D 512 ARG cc_start: 0.6823 (ttt180) cc_final: 0.3918 (mmm160) REVERT: E 45 ILE cc_start: 0.8655 (mm) cc_final: 0.8455 (mp) REVERT: E 78 MET cc_start: 0.9049 (tpp) cc_final: 0.8812 (tpp) REVERT: E 82 MET cc_start: 0.8996 (mmm) cc_final: 0.8466 (mmm) REVERT: E 146 GLU cc_start: 0.5405 (tp30) cc_final: 0.5199 (tp30) REVERT: E 150 MET cc_start: 0.7025 (tpt) cc_final: 0.6539 (tpp) REVERT: E 179 MET cc_start: 0.6885 (mtp) cc_final: 0.5992 (mpt) REVERT: E 205 LYS cc_start: 0.7715 (mttp) cc_final: 0.6545 (mmtt) REVERT: E 483 MET cc_start: 0.9004 (tmm) cc_final: 0.8490 (tmm) REVERT: E 508 SER cc_start: 0.7428 (t) cc_final: 0.7047 (m) REVERT: E 510 GLU cc_start: 0.6566 (tt0) cc_final: 0.6169 (tt0) REVERT: E 512 ARG cc_start: 0.6621 (ttt180) cc_final: 0.3856 (mmm160) REVERT: F 82 MET cc_start: 0.9002 (mmm) cc_final: 0.8659 (mmm) REVERT: F 150 MET cc_start: 0.7151 (tpt) cc_final: 0.6719 (tpp) REVERT: F 179 MET cc_start: 0.6827 (mtm) cc_final: 0.6283 (mpt) REVERT: F 205 LYS cc_start: 0.7628 (mttp) cc_final: 0.6452 (mmtt) REVERT: F 286 MET cc_start: 0.8504 (tpt) cc_final: 0.8182 (tpt) REVERT: F 455 LYS cc_start: 0.7933 (mmtt) cc_final: 0.7424 (mtmt) REVERT: F 512 ARG cc_start: 0.6568 (ttt180) cc_final: 0.3798 (mmm160) REVERT: G 82 MET cc_start: 0.8996 (mmm) cc_final: 0.8632 (mmm) REVERT: G 150 MET cc_start: 0.6869 (tpt) cc_final: 0.6368 (tpp) REVERT: G 179 MET cc_start: 0.6804 (mtm) cc_final: 0.6383 (mpt) REVERT: G 205 LYS cc_start: 0.7554 (mttp) cc_final: 0.5951 (tptp) REVERT: G 277 GLN cc_start: 0.9290 (OUTLIER) cc_final: 0.9021 (tm-30) REVERT: G 455 LYS cc_start: 0.7928 (mmtt) cc_final: 0.7356 (mtmt) REVERT: G 483 MET cc_start: 0.8996 (tmm) cc_final: 0.8577 (tmm) REVERT: G 512 ARG cc_start: 0.6563 (ttt180) cc_final: 0.3883 (mmm160) REVERT: H 82 MET cc_start: 0.8996 (mmm) cc_final: 0.8651 (mmm) REVERT: H 150 MET cc_start: 0.6937 (tpt) cc_final: 0.6420 (tpp) REVERT: H 205 LYS cc_start: 0.7600 (mttp) cc_final: 0.5968 (tptp) REVERT: H 255 ASP cc_start: 0.6700 (OUTLIER) cc_final: 0.6475 (p0) REVERT: H 512 ARG cc_start: 0.6365 (ttt180) cc_final: 0.3530 (mmm160) outliers start: 72 outliers final: 30 residues processed: 441 average time/residue: 2.3531 time to fit residues: 1239.4273 Evaluate side-chains 395 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 359 time to evaluate : 3.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 509 TYR Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain B residue 509 TYR Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 509 TYR Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 329 SER Chi-restraints excluded: chain D residue 509 TYR Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 329 SER Chi-restraints excluded: chain E residue 509 TYR Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 329 SER Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 329 SER Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 255 ASP Chi-restraints excluded: chain H residue 329 SER Chi-restraints excluded: chain H residue 509 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 189 optimal weight: 5.9990 chunk 105 optimal weight: 8.9990 chunk 284 optimal weight: 2.9990 chunk 232 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 342 optimal weight: 6.9990 chunk 369 optimal weight: 10.0000 chunk 304 optimal weight: 7.9990 chunk 339 optimal weight: 0.9980 chunk 116 optimal weight: 5.9990 chunk 274 optimal weight: 1.9990 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 94 ASN A 202 GLN A 298 GLN A 303 ASN B 94 ASN ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 298 GLN C 202 GLN C 292 GLN C 303 ASN C 372 HIS D 94 ASN D 202 GLN ** D 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 292 GLN D 298 GLN D 372 HIS E 94 ASN E 202 GLN E 298 GLN F 94 ASN F 202 GLN F 292 GLN F 441 GLN G 94 ASN ** G 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 292 GLN H 94 ASN H 202 GLN H 298 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 30008 Z= 0.273 Angle : 0.633 6.702 40728 Z= 0.326 Chirality : 0.044 0.177 4696 Planarity : 0.005 0.053 5064 Dihedral : 20.014 178.044 4682 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.22 % Allowed : 10.51 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.13), residues: 3752 helix: 1.13 (0.14), residues: 1416 sheet: -0.83 (0.25), residues: 360 loop : 0.01 (0.14), residues: 1976 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 296 PHE 0.016 0.002 PHE B 24 TYR 0.020 0.002 TYR G 514 ARG 0.003 0.001 ARG A 259 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Evaluate side-chains 452 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 384 time to evaluate : 3.439 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: A 150 MET cc_start: 0.6922 (tpt) cc_final: 0.6426 (tpp) REVERT: A 161 ARG cc_start: 0.7152 (mtt180) cc_final: 0.6834 (mtt180) REVERT: A 205 LYS cc_start: 0.7855 (mttp) cc_final: 0.6462 (tptp) REVERT: A 231 ARG cc_start: 0.7656 (OUTLIER) cc_final: 0.6818 (ttm110) REVERT: A 420 MET cc_start: 0.6397 (OUTLIER) cc_final: 0.6043 (tpp) REVERT: A 441 GLN cc_start: 0.7818 (OUTLIER) cc_final: 0.7407 (mm110) REVERT: A 483 MET cc_start: 0.8983 (tmm) cc_final: 0.8635 (tmm) REVERT: A 508 SER cc_start: 0.7333 (t) cc_final: 0.7052 (m) REVERT: A 512 ARG cc_start: 0.6795 (ttt180) cc_final: 0.4024 (mmm160) REVERT: B 117 ASP cc_start: 0.7288 (t0) cc_final: 0.7085 (t0) REVERT: B 142 ILE cc_start: 0.7786 (mt) cc_final: 0.7556 (mp) REVERT: B 146 GLU cc_start: 0.5653 (tp30) cc_final: 0.5372 (tp30) REVERT: B 150 MET cc_start: 0.6926 (tpt) cc_final: 0.6407 (tpp) REVERT: B 161 ARG cc_start: 0.7128 (mtt180) cc_final: 0.6423 (mtt-85) REVERT: B 179 MET cc_start: 0.6601 (mtp) cc_final: 0.5820 (mpt) REVERT: B 205 LYS cc_start: 0.7833 (mttp) cc_final: 0.6665 (mmtt) REVERT: B 483 MET cc_start: 0.9003 (tmm) cc_final: 0.8369 (tmm) REVERT: B 509 TYR cc_start: 0.5682 (OUTLIER) cc_final: 0.3692 (t80) REVERT: B 512 ARG cc_start: 0.6940 (ttt180) cc_final: 0.3878 (mmm160) REVERT: C 82 MET cc_start: 0.8971 (mmm) cc_final: 0.8417 (mmm) REVERT: C 146 GLU cc_start: 0.5331 (tp30) cc_final: 0.5057 (tp30) REVERT: C 150 MET cc_start: 0.6851 (tpt) cc_final: 0.6311 (tpp) REVERT: C 179 MET cc_start: 0.6743 (mtm) cc_final: 0.6187 (mpt) REVERT: C 205 LYS cc_start: 0.7899 (mttp) cc_final: 0.6474 (tptp) REVERT: C 277 GLN cc_start: 0.9235 (OUTLIER) cc_final: 0.8935 (tm-30) REVERT: C 483 MET cc_start: 0.8976 (tmm) cc_final: 0.8603 (tmm) REVERT: C 508 SER cc_start: 0.7401 (t) cc_final: 0.7107 (m) REVERT: C 512 ARG cc_start: 0.6822 (ttt180) cc_final: 0.3895 (mmm160) REVERT: D 70 MET cc_start: 0.8918 (mtp) cc_final: 0.8373 (mtp) REVERT: D 150 MET cc_start: 0.6811 (tpt) cc_final: 0.6320 (tpp) REVERT: D 205 LYS cc_start: 0.7744 (mttp) cc_final: 0.6538 (mmtt) REVERT: D 286 MET cc_start: 0.8533 (tpt) cc_final: 0.8199 (tpt) REVERT: D 508 SER cc_start: 0.7326 (t) cc_final: 0.7074 (m) REVERT: D 509 TYR cc_start: 0.6098 (OUTLIER) cc_final: 0.4359 (t80) REVERT: D 512 ARG cc_start: 0.6905 (ttt180) cc_final: 0.3847 (mmm160) REVERT: E 45 ILE cc_start: 0.8644 (mm) cc_final: 0.8423 (mp) REVERT: E 146 GLU cc_start: 0.5441 (tp30) cc_final: 0.5231 (tp30) REVERT: E 150 MET cc_start: 0.6917 (tpt) cc_final: 0.6373 (tpp) REVERT: E 179 MET cc_start: 0.6736 (mtp) cc_final: 0.5945 (mpt) REVERT: E 205 LYS cc_start: 0.7884 (mttp) cc_final: 0.6828 (mmtt) REVERT: E 441 GLN cc_start: 0.7918 (OUTLIER) cc_final: 0.7436 (mm110) REVERT: E 483 MET cc_start: 0.8988 (tmm) cc_final: 0.8627 (tmm) REVERT: E 495 MET cc_start: 0.6423 (OUTLIER) cc_final: 0.6109 (mtp) REVERT: E 508 SER cc_start: 0.7417 (t) cc_final: 0.7170 (m) REVERT: E 512 ARG cc_start: 0.6845 (ttt180) cc_final: 0.3957 (mmm160) REVERT: F 150 MET cc_start: 0.7062 (tpt) cc_final: 0.6573 (tpp) REVERT: F 179 MET cc_start: 0.6785 (mtm) cc_final: 0.6384 (mpt) REVERT: F 205 LYS cc_start: 0.7813 (mttp) cc_final: 0.6695 (mmtt) REVERT: F 286 MET cc_start: 0.8508 (tpt) cc_final: 0.8198 (tpt) REVERT: F 441 GLN cc_start: 0.7931 (OUTLIER) cc_final: 0.7352 (mm-40) REVERT: F 483 MET cc_start: 0.9009 (tmm) cc_final: 0.8440 (tmm) REVERT: F 512 ARG cc_start: 0.6716 (ttt180) cc_final: 0.3866 (mmm160) REVERT: G 150 MET cc_start: 0.6742 (tpt) cc_final: 0.6233 (tpp) REVERT: G 179 MET cc_start: 0.6770 (mtm) cc_final: 0.6383 (mpt) REVERT: G 185 LEU cc_start: 0.7198 (pp) cc_final: 0.6971 (pp) REVERT: G 205 LYS cc_start: 0.7851 (mttp) cc_final: 0.6291 (tptp) REVERT: G 483 MET cc_start: 0.8980 (tmm) cc_final: 0.8610 (tmm) REVERT: G 509 TYR cc_start: 0.7636 (p90) cc_final: 0.7361 (p90) REVERT: G 512 ARG cc_start: 0.6826 (ttt180) cc_final: 0.3929 (mmm160) REVERT: H 70 MET cc_start: 0.8968 (mtp) cc_final: 0.8572 (mtp) REVERT: H 150 MET cc_start: 0.6943 (tpt) cc_final: 0.6394 (tpp) REVERT: H 179 MET cc_start: 0.6667 (mtp) cc_final: 0.5930 (mpt) REVERT: H 205 LYS cc_start: 0.7864 (mttp) cc_final: 0.6230 (tptp) REVERT: H 334 GLN cc_start: 0.7423 (mt0) cc_final: 0.7212 (mt0) REVERT: H 441 GLN cc_start: 0.7720 (OUTLIER) cc_final: 0.7389 (mm110) REVERT: H 483 MET cc_start: 0.8911 (tmm) cc_final: 0.8586 (tmm) REVERT: H 512 ARG cc_start: 0.6629 (ttt180) cc_final: 0.3836 (mmm160) outliers start: 68 outliers final: 39 residues processed: 415 average time/residue: 2.3883 time to fit residues: 1191.1255 Evaluate side-chains 403 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 354 time to evaluate : 3.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 441 GLN Chi-restraints excluded: chain A residue 509 TYR Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain B residue 509 TYR Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 420 MET Chi-restraints excluded: chain C residue 509 TYR Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 329 SER Chi-restraints excluded: chain D residue 509 TYR Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 329 SER Chi-restraints excluded: chain E residue 441 GLN Chi-restraints excluded: chain E residue 495 MET Chi-restraints excluded: chain E residue 509 TYR Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 117 ASP Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 329 SER Chi-restraints excluded: chain F residue 441 GLN Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain G residue 329 SER Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 135 MET Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 219 VAL Chi-restraints excluded: chain H residue 329 SER Chi-restraints excluded: chain H residue 441 GLN Chi-restraints excluded: chain H residue 509 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 337 optimal weight: 5.9990 chunk 257 optimal weight: 6.9990 chunk 177 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 chunk 163 optimal weight: 6.9990 chunk 229 optimal weight: 5.9990 chunk 343 optimal weight: 9.9990 chunk 363 optimal weight: 5.9990 chunk 179 optimal weight: 6.9990 chunk 325 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 441 GLN ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN C 202 GLN C 298 GLN C 303 ASN D 202 GLN ** D 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 292 GLN E 202 GLN E 441 GLN F 202 GLN F 298 GLN ** G 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 298 GLN H 202 GLN H 441 GLN H 507 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 30008 Z= 0.444 Angle : 0.702 6.603 40728 Z= 0.365 Chirality : 0.047 0.152 4696 Planarity : 0.005 0.056 5064 Dihedral : 20.102 177.458 4679 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.10 % Allowed : 11.26 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.13), residues: 3752 helix: 0.86 (0.14), residues: 1416 sheet: -1.03 (0.23), residues: 360 loop : -0.06 (0.14), residues: 1976 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS A 296 PHE 0.020 0.003 PHE B 24 TYR 0.023 0.003 TYR D 514 ARG 0.007 0.001 ARG D 322 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Evaluate side-chains 454 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 359 time to evaluate : 3.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.8992 (mtp) cc_final: 0.8547 (mtp) REVERT: A 150 MET cc_start: 0.6745 (tpt) cc_final: 0.6269 (tpp) REVERT: A 161 ARG cc_start: 0.7191 (mtt180) cc_final: 0.6870 (mtt180) REVERT: A 205 LYS cc_start: 0.7931 (mttp) cc_final: 0.6521 (tptp) REVERT: A 231 ARG cc_start: 0.7633 (OUTLIER) cc_final: 0.6832 (ttm110) REVERT: A 420 MET cc_start: 0.6438 (OUTLIER) cc_final: 0.6079 (tpp) REVERT: A 441 GLN cc_start: 0.7869 (OUTLIER) cc_final: 0.7305 (mm-40) REVERT: A 483 MET cc_start: 0.8986 (tmm) cc_final: 0.8553 (tmm) REVERT: A 508 SER cc_start: 0.7328 (t) cc_final: 0.6950 (m) REVERT: A 509 TYR cc_start: 0.6143 (OUTLIER) cc_final: 0.4880 (t80) REVERT: A 512 ARG cc_start: 0.6904 (ttt180) cc_final: 0.4380 (mmt-90) REVERT: B 142 ILE cc_start: 0.7770 (mt) cc_final: 0.7565 (mp) REVERT: B 146 GLU cc_start: 0.5752 (tp30) cc_final: 0.5480 (tp30) REVERT: B 150 MET cc_start: 0.6856 (tpt) cc_final: 0.6595 (tpt) REVERT: B 161 ARG cc_start: 0.7002 (mtt180) cc_final: 0.6409 (mtt-85) REVERT: B 179 MET cc_start: 0.6779 (mtp) cc_final: 0.5983 (mpt) REVERT: B 205 LYS cc_start: 0.8032 (mttp) cc_final: 0.6488 (tptp) REVERT: B 441 GLN cc_start: 0.7803 (OUTLIER) cc_final: 0.7133 (mm-40) REVERT: B 483 MET cc_start: 0.8984 (tmm) cc_final: 0.8436 (tmm) REVERT: B 509 TYR cc_start: 0.5824 (OUTLIER) cc_final: 0.3953 (t80) REVERT: B 512 ARG cc_start: 0.6957 (ttt180) cc_final: 0.3803 (mmm160) REVERT: C 70 MET cc_start: 0.8968 (mtp) cc_final: 0.8508 (mtp) REVERT: C 146 GLU cc_start: 0.5389 (tp30) cc_final: 0.5161 (tp30) REVERT: C 150 MET cc_start: 0.6799 (tpt) cc_final: 0.6291 (tpp) REVERT: C 179 MET cc_start: 0.6668 (mtm) cc_final: 0.6171 (mpt) REVERT: C 205 LYS cc_start: 0.8019 (mttp) cc_final: 0.6594 (tptp) REVERT: C 441 GLN cc_start: 0.7896 (OUTLIER) cc_final: 0.7375 (mm110) REVERT: C 508 SER cc_start: 0.7420 (t) cc_final: 0.7155 (m) REVERT: C 509 TYR cc_start: 0.5814 (OUTLIER) cc_final: 0.4049 (t80) REVERT: C 512 ARG cc_start: 0.6895 (ttt180) cc_final: 0.3836 (mmm160) REVERT: D 70 MET cc_start: 0.8979 (mtp) cc_final: 0.8594 (mtp) REVERT: D 150 MET cc_start: 0.6775 (tpt) cc_final: 0.6319 (tpp) REVERT: D 205 LYS cc_start: 0.7958 (mttp) cc_final: 0.6516 (tptp) REVERT: D 286 MET cc_start: 0.8530 (tpt) cc_final: 0.8311 (tpt) REVERT: D 441 GLN cc_start: 0.7904 (OUTLIER) cc_final: 0.7385 (mm110) REVERT: D 483 MET cc_start: 0.9042 (tmm) cc_final: 0.8691 (tmm) REVERT: D 508 SER cc_start: 0.7326 (t) cc_final: 0.7047 (m) REVERT: D 509 TYR cc_start: 0.6327 (OUTLIER) cc_final: 0.4971 (t80) REVERT: E 45 ILE cc_start: 0.8644 (mm) cc_final: 0.8411 (mp) REVERT: E 70 MET cc_start: 0.8939 (mtp) cc_final: 0.8664 (mtp) REVERT: E 146 GLU cc_start: 0.5634 (tp30) cc_final: 0.5401 (tp30) REVERT: E 150 MET cc_start: 0.6877 (tpt) cc_final: 0.6389 (tpp) REVERT: E 179 MET cc_start: 0.6908 (mtp) cc_final: 0.6228 (mpt) REVERT: E 205 LYS cc_start: 0.7916 (mttp) cc_final: 0.6483 (tptp) REVERT: E 441 GLN cc_start: 0.7781 (OUTLIER) cc_final: 0.7184 (mm-40) REVERT: E 483 MET cc_start: 0.8997 (tmm) cc_final: 0.8569 (tmm) REVERT: E 495 MET cc_start: 0.6410 (OUTLIER) cc_final: 0.6129 (mtp) REVERT: E 508 SER cc_start: 0.7425 (t) cc_final: 0.7159 (m) REVERT: E 509 TYR cc_start: 0.5952 (OUTLIER) cc_final: 0.4131 (t80) REVERT: E 512 ARG cc_start: 0.6931 (ttt180) cc_final: 0.3828 (mmm160) REVERT: F 70 MET cc_start: 0.8951 (mtp) cc_final: 0.8543 (mtp) REVERT: F 150 MET cc_start: 0.6881 (tpt) cc_final: 0.6399 (tpp) REVERT: F 179 MET cc_start: 0.6818 (mtm) cc_final: 0.6435 (mpt) REVERT: F 205 LYS cc_start: 0.7866 (mttp) cc_final: 0.6490 (tptp) REVERT: F 231 ARG cc_start: 0.7687 (OUTLIER) cc_final: 0.6819 (ttm110) REVERT: F 356 ARG cc_start: 0.7637 (mtp180) cc_final: 0.7406 (mtm110) REVERT: F 483 MET cc_start: 0.9037 (tmm) cc_final: 0.8516 (tmm) REVERT: G 70 MET cc_start: 0.8976 (mtp) cc_final: 0.8516 (mtp) REVERT: G 150 MET cc_start: 0.6755 (tpt) cc_final: 0.6355 (tpp) REVERT: G 179 MET cc_start: 0.6824 (mtm) cc_final: 0.6407 (mpt) REVERT: G 205 LYS cc_start: 0.7896 (mttp) cc_final: 0.6438 (tptp) REVERT: G 441 GLN cc_start: 0.7873 (OUTLIER) cc_final: 0.7375 (mm110) REVERT: G 483 MET cc_start: 0.8986 (tmm) cc_final: 0.8431 (tmm) REVERT: G 509 TYR cc_start: 0.7897 (p90) cc_final: 0.7649 (p90) REVERT: H 70 MET cc_start: 0.8991 (mtp) cc_final: 0.8642 (mtp) REVERT: H 150 MET cc_start: 0.6843 (tpt) cc_final: 0.6305 (tpp) REVERT: H 179 MET cc_start: 0.6739 (mtp) cc_final: 0.6010 (mpt) REVERT: H 205 LYS cc_start: 0.8003 (mttp) cc_final: 0.6636 (tptp) REVERT: H 255 ASP cc_start: 0.6961 (OUTLIER) cc_final: 0.6428 (p0) REVERT: H 418 ASP cc_start: 0.5440 (m-30) cc_final: 0.5006 (m-30) REVERT: H 441 GLN cc_start: 0.7891 (OUTLIER) cc_final: 0.7354 (mm-40) REVERT: H 509 TYR cc_start: 0.6166 (OUTLIER) cc_final: 0.4784 (t80) outliers start: 95 outliers final: 48 residues processed: 411 average time/residue: 2.4673 time to fit residues: 1213.4028 Evaluate side-chains 401 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 335 time to evaluate : 3.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 441 GLN Chi-restraints excluded: chain A residue 509 TYR Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 441 GLN Chi-restraints excluded: chain B residue 495 MET Chi-restraints excluded: chain B residue 509 TYR Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 420 MET Chi-restraints excluded: chain C residue 441 GLN Chi-restraints excluded: chain C residue 509 TYR Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 441 GLN Chi-restraints excluded: chain D residue 509 TYR Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 329 SER Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 441 GLN Chi-restraints excluded: chain E residue 495 MET Chi-restraints excluded: chain E residue 509 TYR Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 117 ASP Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 231 ARG Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain G residue 420 MET Chi-restraints excluded: chain G residue 441 GLN Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 219 VAL Chi-restraints excluded: chain H residue 255 ASP Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 441 GLN Chi-restraints excluded: chain H residue 509 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 302 optimal weight: 0.6980 chunk 206 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 270 optimal weight: 2.9990 chunk 149 optimal weight: 0.7980 chunk 310 optimal weight: 3.9990 chunk 251 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 185 optimal weight: 1.9990 chunk 326 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN A 303 ASN ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 507 HIS C 202 GLN C 303 ASN D 202 GLN ** D 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 292 GLN E 202 GLN ** G 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 202 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 30008 Z= 0.163 Angle : 0.565 6.942 40728 Z= 0.283 Chirality : 0.043 0.151 4696 Planarity : 0.004 0.046 5064 Dihedral : 18.872 179.431 4671 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.58 % Allowed : 11.95 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.14), residues: 3752 helix: 1.37 (0.14), residues: 1416 sheet: -1.03 (0.23), residues: 360 loop : 0.06 (0.14), residues: 1976 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 296 PHE 0.013 0.001 PHE C 24 TYR 0.016 0.001 TYR F 514 ARG 0.002 0.000 ARG D 322 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Evaluate side-chains 420 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 341 time to evaluate : 3.338 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: A 150 MET cc_start: 0.6739 (tpt) cc_final: 0.6292 (tpp) REVERT: A 161 ARG cc_start: 0.7192 (mtt180) cc_final: 0.6905 (mtt-85) REVERT: A 179 MET cc_start: 0.6707 (mtp) cc_final: 0.5868 (mpt) REVERT: A 205 LYS cc_start: 0.7929 (mttp) cc_final: 0.6461 (tptp) REVERT: A 231 ARG cc_start: 0.7669 (OUTLIER) cc_final: 0.6826 (ttm110) REVERT: A 420 MET cc_start: 0.6286 (OUTLIER) cc_final: 0.6081 (tpp) REVERT: A 483 MET cc_start: 0.8986 (tmm) cc_final: 0.8666 (tmm) REVERT: A 508 SER cc_start: 0.7227 (t) cc_final: 0.6971 (m) REVERT: A 512 ARG cc_start: 0.6918 (ttt180) cc_final: 0.3888 (mmm160) REVERT: B 146 GLU cc_start: 0.5595 (tp30) cc_final: 0.5361 (tp30) REVERT: B 150 MET cc_start: 0.6860 (tpt) cc_final: 0.6372 (tpp) REVERT: B 161 ARG cc_start: 0.7090 (mtt180) cc_final: 0.6477 (mtt-85) REVERT: B 179 MET cc_start: 0.6671 (mtp) cc_final: 0.6017 (mpt) REVERT: B 205 LYS cc_start: 0.8036 (mttp) cc_final: 0.6515 (tptp) REVERT: B 441 GLN cc_start: 0.7686 (mt0) cc_final: 0.6948 (mm-40) REVERT: B 483 MET cc_start: 0.8988 (tmm) cc_final: 0.8360 (tmm) REVERT: B 509 TYR cc_start: 0.5568 (OUTLIER) cc_final: 0.3772 (t80) REVERT: B 512 ARG cc_start: 0.6926 (ttt180) cc_final: 0.3779 (mmm160) REVERT: C 146 GLU cc_start: 0.5455 (tp30) cc_final: 0.5208 (tp30) REVERT: C 150 MET cc_start: 0.6745 (tpt) cc_final: 0.6179 (tpp) REVERT: C 179 MET cc_start: 0.6534 (mtm) cc_final: 0.6183 (mpt) REVERT: C 205 LYS cc_start: 0.7925 (mttp) cc_final: 0.6483 (tptp) REVERT: C 441 GLN cc_start: 0.7670 (OUTLIER) cc_final: 0.7126 (mm-40) REVERT: C 483 MET cc_start: 0.8984 (tmm) cc_final: 0.8489 (tmm) REVERT: C 508 SER cc_start: 0.7308 (t) cc_final: 0.7084 (m) REVERT: C 509 TYR cc_start: 0.5549 (OUTLIER) cc_final: 0.3843 (t80) REVERT: C 512 ARG cc_start: 0.6934 (ttt180) cc_final: 0.3876 (mmm160) REVERT: D 150 MET cc_start: 0.6710 (tpt) cc_final: 0.6277 (tpp) REVERT: D 179 MET cc_start: 0.6617 (mtp) cc_final: 0.5783 (mpt) REVERT: D 205 LYS cc_start: 0.7917 (mttp) cc_final: 0.6808 (mmtt) REVERT: D 286 MET cc_start: 0.8488 (tpt) cc_final: 0.8191 (tpt) REVERT: D 441 GLN cc_start: 0.7726 (OUTLIER) cc_final: 0.7199 (mm-40) REVERT: D 483 MET cc_start: 0.8971 (tmm) cc_final: 0.8419 (tmm) REVERT: D 508 SER cc_start: 0.7125 (t) cc_final: 0.6878 (m) REVERT: D 509 TYR cc_start: 0.6229 (OUTLIER) cc_final: 0.4701 (t80) REVERT: E 146 GLU cc_start: 0.5589 (tp30) cc_final: 0.5341 (tp30) REVERT: E 150 MET cc_start: 0.6802 (tpt) cc_final: 0.6330 (tpp) REVERT: E 179 MET cc_start: 0.7004 (mtp) cc_final: 0.6256 (mpt) REVERT: E 205 LYS cc_start: 0.7916 (mttp) cc_final: 0.6848 (mmtt) REVERT: E 483 MET cc_start: 0.8986 (tmm) cc_final: 0.8658 (tmm) REVERT: E 495 MET cc_start: 0.6270 (OUTLIER) cc_final: 0.5934 (mtp) REVERT: E 509 TYR cc_start: 0.5644 (OUTLIER) cc_final: 0.3891 (t80) REVERT: E 512 ARG cc_start: 0.6923 (ttt180) cc_final: 0.3847 (mmm160) REVERT: F 150 MET cc_start: 0.6860 (tpt) cc_final: 0.6386 (tpp) REVERT: F 179 MET cc_start: 0.6827 (mtm) cc_final: 0.6457 (mpt) REVERT: F 205 LYS cc_start: 0.7844 (mttp) cc_final: 0.6778 (mmtt) REVERT: F 231 ARG cc_start: 0.7675 (OUTLIER) cc_final: 0.6776 (ttm110) REVERT: F 483 MET cc_start: 0.8999 (tmm) cc_final: 0.8400 (tmm) REVERT: G 150 MET cc_start: 0.6753 (tpt) cc_final: 0.6241 (tpp) REVERT: G 179 MET cc_start: 0.6936 (mtm) cc_final: 0.6617 (mpt) REVERT: G 205 LYS cc_start: 0.7880 (mttp) cc_final: 0.6819 (mmtt) REVERT: G 441 GLN cc_start: 0.7698 (OUTLIER) cc_final: 0.7183 (mm-40) REVERT: G 483 MET cc_start: 0.8974 (tmm) cc_final: 0.8634 (tmm) REVERT: G 509 TYR cc_start: 0.7760 (p90) cc_final: 0.7555 (p90) REVERT: H 150 MET cc_start: 0.6902 (tpt) cc_final: 0.6353 (tpp) REVERT: H 179 MET cc_start: 0.6691 (mtp) cc_final: 0.5983 (mpt) REVERT: H 205 LYS cc_start: 0.7900 (mttp) cc_final: 0.6455 (tptp) REVERT: H 418 ASP cc_start: 0.5581 (m-30) cc_final: 0.5152 (m-30) REVERT: H 483 MET cc_start: 0.8919 (tmm) cc_final: 0.8599 (tmm) REVERT: H 509 TYR cc_start: 0.6011 (OUTLIER) cc_final: 0.4181 (t80) outliers start: 79 outliers final: 52 residues processed: 391 average time/residue: 2.4569 time to fit residues: 1140.4707 Evaluate side-chains 388 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 324 time to evaluate : 3.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 509 TYR Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 495 MET Chi-restraints excluded: chain B residue 509 TYR Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 420 MET Chi-restraints excluded: chain C residue 441 GLN Chi-restraints excluded: chain C residue 509 TYR Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 329 SER Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 441 GLN Chi-restraints excluded: chain D residue 509 TYR Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 329 SER Chi-restraints excluded: chain E residue 495 MET Chi-restraints excluded: chain E residue 509 TYR Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 231 ARG Chi-restraints excluded: chain F residue 329 SER Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain G residue 329 SER Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 420 MET Chi-restraints excluded: chain G residue 441 GLN Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 219 VAL Chi-restraints excluded: chain H residue 329 SER Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 509 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 122 optimal weight: 4.9990 chunk 327 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 213 optimal weight: 0.7980 chunk 89 optimal weight: 5.9990 chunk 363 optimal weight: 5.9990 chunk 301 optimal weight: 1.9990 chunk 168 optimal weight: 5.9990 chunk 30 optimal weight: 10.0000 chunk 120 optimal weight: 1.9990 chunk 190 optimal weight: 3.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN A 303 ASN ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN C 202 GLN C 303 ASN D 202 GLN ** D 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 292 GLN D 303 ASN E 202 GLN E 303 ASN ** G 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 202 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 30008 Z= 0.271 Angle : 0.599 6.397 40728 Z= 0.304 Chirality : 0.044 0.150 4696 Planarity : 0.004 0.050 5064 Dihedral : 18.661 177.254 4671 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.68 % Allowed : 12.40 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.14), residues: 3752 helix: 1.31 (0.14), residues: 1416 sheet: -1.09 (0.23), residues: 360 loop : 0.11 (0.14), residues: 1976 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS G 296 PHE 0.016 0.002 PHE D 24 TYR 0.016 0.002 TYR F 514 ARG 0.003 0.001 ARG H 322 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Evaluate side-chains 418 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 336 time to evaluate : 3.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.6657 (tpt) cc_final: 0.6226 (tpp) REVERT: A 161 ARG cc_start: 0.7227 (mtt180) cc_final: 0.6907 (mtt-85) REVERT: A 179 MET cc_start: 0.6636 (mtp) cc_final: 0.5855 (mpt) REVERT: A 205 LYS cc_start: 0.7965 (mttp) cc_final: 0.6483 (tptp) REVERT: A 231 ARG cc_start: 0.7650 (OUTLIER) cc_final: 0.6829 (ttm110) REVERT: A 420 MET cc_start: 0.6346 (OUTLIER) cc_final: 0.6084 (tpp) REVERT: A 483 MET cc_start: 0.8971 (tmm) cc_final: 0.8470 (tmm) REVERT: A 508 SER cc_start: 0.7290 (t) cc_final: 0.7061 (m) REVERT: A 509 TYR cc_start: 0.6031 (OUTLIER) cc_final: 0.4477 (t80) REVERT: A 512 ARG cc_start: 0.6944 (ttt180) cc_final: 0.3890 (mmm160) REVERT: B 146 GLU cc_start: 0.5616 (tp30) cc_final: 0.5381 (tp30) REVERT: B 150 MET cc_start: 0.6817 (tpt) cc_final: 0.6575 (tpt) REVERT: B 161 ARG cc_start: 0.7033 (mtt180) cc_final: 0.6510 (mtt-85) REVERT: B 179 MET cc_start: 0.6774 (mtp) cc_final: 0.6159 (mpt) REVERT: B 205 LYS cc_start: 0.8037 (mttp) cc_final: 0.6522 (tptp) REVERT: B 483 MET cc_start: 0.8980 (tmm) cc_final: 0.8477 (tmm) REVERT: B 509 TYR cc_start: 0.5591 (OUTLIER) cc_final: 0.3834 (t80) REVERT: B 512 ARG cc_start: 0.7006 (ttt180) cc_final: 0.3825 (mmm160) REVERT: C 146 GLU cc_start: 0.5508 (tp30) cc_final: 0.5262 (tp30) REVERT: C 150 MET cc_start: 0.6731 (tpt) cc_final: 0.6264 (tpp) REVERT: C 179 MET cc_start: 0.6629 (mtm) cc_final: 0.6278 (mpt) REVERT: C 205 LYS cc_start: 0.7957 (mttp) cc_final: 0.6585 (tptp) REVERT: C 441 GLN cc_start: 0.7642 (OUTLIER) cc_final: 0.7084 (mm-40) REVERT: C 483 MET cc_start: 0.8977 (tmm) cc_final: 0.8647 (tmm) REVERT: C 509 TYR cc_start: 0.5508 (OUTLIER) cc_final: 0.3782 (t80) REVERT: C 512 ARG cc_start: 0.6980 (ttt180) cc_final: 0.3871 (mmm160) REVERT: D 70 MET cc_start: 0.9025 (mtp) cc_final: 0.8261 (mtp) REVERT: D 150 MET cc_start: 0.6818 (tpt) cc_final: 0.6399 (tpp) REVERT: D 179 MET cc_start: 0.6563 (mtp) cc_final: 0.5756 (mpt) REVERT: D 205 LYS cc_start: 0.7943 (mttp) cc_final: 0.6480 (tptp) REVERT: D 441 GLN cc_start: 0.7714 (OUTLIER) cc_final: 0.7232 (mm110) REVERT: D 483 MET cc_start: 0.8966 (tmm) cc_final: 0.8482 (tmm) REVERT: D 508 SER cc_start: 0.7193 (t) cc_final: 0.6960 (m) REVERT: D 509 TYR cc_start: 0.6222 (OUTLIER) cc_final: 0.4689 (t80) REVERT: E 146 GLU cc_start: 0.5616 (tp30) cc_final: 0.5369 (tp30) REVERT: E 150 MET cc_start: 0.6864 (tpt) cc_final: 0.6435 (tpp) REVERT: E 179 MET cc_start: 0.6984 (mtp) cc_final: 0.6284 (mpt) REVERT: E 205 LYS cc_start: 0.7924 (mttp) cc_final: 0.6489 (tptp) REVERT: E 483 MET cc_start: 0.8989 (tmm) cc_final: 0.8493 (tmm) REVERT: E 495 MET cc_start: 0.6374 (OUTLIER) cc_final: 0.6075 (mtp) REVERT: E 509 TYR cc_start: 0.5633 (OUTLIER) cc_final: 0.4109 (t80) REVERT: E 512 ARG cc_start: 0.7002 (ttt180) cc_final: 0.3875 (mmm160) REVERT: F 150 MET cc_start: 0.6879 (tpt) cc_final: 0.6386 (tpp) REVERT: F 179 MET cc_start: 0.6921 (mtm) cc_final: 0.6521 (mpt) REVERT: F 205 LYS cc_start: 0.7884 (mttp) cc_final: 0.6831 (mmtt) REVERT: F 231 ARG cc_start: 0.7656 (OUTLIER) cc_final: 0.6776 (ttm110) REVERT: F 483 MET cc_start: 0.8978 (tmm) cc_final: 0.8489 (tmm) REVERT: G 150 MET cc_start: 0.6753 (tpt) cc_final: 0.6310 (tpp) REVERT: G 179 MET cc_start: 0.7018 (mtm) cc_final: 0.6637 (mpt) REVERT: G 205 LYS cc_start: 0.7925 (mttp) cc_final: 0.6465 (tptp) REVERT: G 441 GLN cc_start: 0.7686 (OUTLIER) cc_final: 0.7227 (mm110) REVERT: G 483 MET cc_start: 0.8974 (tmm) cc_final: 0.8466 (tmm) REVERT: H 70 MET cc_start: 0.9047 (mtp) cc_final: 0.8364 (mtp) REVERT: H 150 MET cc_start: 0.6884 (tpt) cc_final: 0.6335 (tpp) REVERT: H 179 MET cc_start: 0.6721 (mtp) cc_final: 0.6121 (mpt) REVERT: H 205 LYS cc_start: 0.7935 (mttp) cc_final: 0.6516 (tptp) REVERT: H 418 ASP cc_start: 0.5625 (m-30) cc_final: 0.5178 (m-30) REVERT: H 509 TYR cc_start: 0.5925 (OUTLIER) cc_final: 0.4258 (t80) outliers start: 82 outliers final: 42 residues processed: 383 average time/residue: 2.4632 time to fit residues: 1123.2431 Evaluate side-chains 379 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 324 time to evaluate : 3.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 509 TYR Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 509 TYR Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 420 MET Chi-restraints excluded: chain C residue 441 GLN Chi-restraints excluded: chain C residue 509 TYR Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 441 GLN Chi-restraints excluded: chain D residue 509 TYR Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 329 SER Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 495 MET Chi-restraints excluded: chain E residue 509 TYR Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 231 ARG Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain G residue 420 MET Chi-restraints excluded: chain G residue 441 GLN Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 219 VAL Chi-restraints excluded: chain H residue 230 ASN Chi-restraints excluded: chain H residue 509 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 350 optimal weight: 0.5980 chunk 41 optimal weight: 5.9990 chunk 207 optimal weight: 0.9980 chunk 265 optimal weight: 5.9990 chunk 205 optimal weight: 5.9990 chunk 306 optimal weight: 5.9990 chunk 203 optimal weight: 3.9990 chunk 362 optimal weight: 3.9990 chunk 226 optimal weight: 2.9990 chunk 220 optimal weight: 3.9990 chunk 167 optimal weight: 5.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 507 HIS D 202 GLN ** D 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 292 GLN E 202 GLN F 303 ASN ** G 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 202 GLN H 303 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 30008 Z= 0.257 Angle : 0.585 6.594 40728 Z= 0.295 Chirality : 0.044 0.149 4696 Planarity : 0.004 0.049 5064 Dihedral : 18.213 176.520 4669 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.35 % Allowed : 13.15 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.14), residues: 3752 helix: 1.35 (0.14), residues: 1416 sheet: -0.53 (0.22), residues: 440 loop : 0.05 (0.14), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS G 296 PHE 0.015 0.002 PHE B 24 TYR 0.014 0.002 TYR F 514 ARG 0.004 0.000 ARG A 322 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Evaluate side-chains 417 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 345 time to evaluate : 3.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.6621 (tpt) cc_final: 0.6229 (tpp) REVERT: A 161 ARG cc_start: 0.7236 (mtt180) cc_final: 0.6681 (mtt-85) REVERT: A 179 MET cc_start: 0.6631 (mtp) cc_final: 0.5895 (mpt) REVERT: A 205 LYS cc_start: 0.7963 (mttp) cc_final: 0.6572 (tptp) REVERT: A 231 ARG cc_start: 0.7652 (OUTLIER) cc_final: 0.6826 (ttm110) REVERT: A 420 MET cc_start: 0.6362 (OUTLIER) cc_final: 0.6138 (tpp) REVERT: A 483 MET cc_start: 0.8973 (tmm) cc_final: 0.8490 (tmm) REVERT: A 509 TYR cc_start: 0.6017 (OUTLIER) cc_final: 0.4476 (t80) REVERT: A 512 ARG cc_start: 0.6859 (ttt180) cc_final: 0.3839 (mmm160) REVERT: B 146 GLU cc_start: 0.5628 (tp30) cc_final: 0.5390 (tp30) REVERT: B 150 MET cc_start: 0.6743 (tpt) cc_final: 0.6526 (tpt) REVERT: B 161 ARG cc_start: 0.7106 (mtt180) cc_final: 0.6513 (mtt-85) REVERT: B 179 MET cc_start: 0.6798 (mtp) cc_final: 0.6234 (mpt) REVERT: B 205 LYS cc_start: 0.8041 (mttp) cc_final: 0.6524 (tptp) REVERT: B 441 GLN cc_start: 0.7695 (mt0) cc_final: 0.6900 (mm-40) REVERT: B 483 MET cc_start: 0.8984 (tmm) cc_final: 0.8493 (tmm) REVERT: B 509 TYR cc_start: 0.5523 (OUTLIER) cc_final: 0.3809 (t80) REVERT: B 512 ARG cc_start: 0.7032 (ttt180) cc_final: 0.3825 (mmm160) REVERT: C 146 GLU cc_start: 0.5558 (tp30) cc_final: 0.5307 (tp30) REVERT: C 150 MET cc_start: 0.6696 (tpt) cc_final: 0.6165 (tpp) REVERT: C 179 MET cc_start: 0.6608 (mtm) cc_final: 0.6238 (mpt) REVERT: C 205 LYS cc_start: 0.7969 (mttp) cc_final: 0.6572 (tptp) REVERT: C 441 GLN cc_start: 0.7649 (OUTLIER) cc_final: 0.7089 (mm-40) REVERT: C 509 TYR cc_start: 0.5446 (OUTLIER) cc_final: 0.3948 (t80) REVERT: C 512 ARG cc_start: 0.6995 (ttt180) cc_final: 0.3891 (mmm160) REVERT: D 150 MET cc_start: 0.6726 (tpt) cc_final: 0.6322 (tpp) REVERT: D 179 MET cc_start: 0.6495 (mtp) cc_final: 0.5776 (mpt) REVERT: D 205 LYS cc_start: 0.7948 (mttp) cc_final: 0.6864 (mmtt) REVERT: D 441 GLN cc_start: 0.7700 (OUTLIER) cc_final: 0.7226 (mm110) REVERT: D 483 MET cc_start: 0.8975 (tmm) cc_final: 0.8508 (tmm) REVERT: D 508 SER cc_start: 0.7075 (t) cc_final: 0.6734 (t) REVERT: D 509 TYR cc_start: 0.6179 (OUTLIER) cc_final: 0.4330 (t80) REVERT: E 146 GLU cc_start: 0.5616 (tp30) cc_final: 0.5384 (tp30) REVERT: E 150 MET cc_start: 0.6840 (tpt) cc_final: 0.6372 (tpp) REVERT: E 179 MET cc_start: 0.6943 (mtp) cc_final: 0.6337 (mpt) REVERT: E 205 LYS cc_start: 0.7938 (mttp) cc_final: 0.6504 (tptp) REVERT: E 483 MET cc_start: 0.8991 (tmm) cc_final: 0.8506 (tmm) REVERT: E 495 MET cc_start: 0.6379 (OUTLIER) cc_final: 0.6074 (mtp) REVERT: E 509 TYR cc_start: 0.5602 (OUTLIER) cc_final: 0.3858 (t80) REVERT: E 512 ARG cc_start: 0.7097 (ttt180) cc_final: 0.3912 (mmm160) REVERT: F 150 MET cc_start: 0.6816 (tpt) cc_final: 0.6386 (tpp) REVERT: F 179 MET cc_start: 0.6923 (mtm) cc_final: 0.6567 (mpt) REVERT: F 205 LYS cc_start: 0.7880 (mttp) cc_final: 0.6518 (tptp) REVERT: F 231 ARG cc_start: 0.7649 (OUTLIER) cc_final: 0.6782 (ttm110) REVERT: F 483 MET cc_start: 0.8984 (tmm) cc_final: 0.8507 (tmm) REVERT: F 510 GLU cc_start: 0.6333 (tt0) cc_final: 0.4838 (mm-30) REVERT: G 70 MET cc_start: 0.8925 (mtp) cc_final: 0.8379 (mtp) REVERT: G 150 MET cc_start: 0.6777 (tpt) cc_final: 0.6332 (tpp) REVERT: G 179 MET cc_start: 0.6909 (mtm) cc_final: 0.6640 (mpt) REVERT: G 205 LYS cc_start: 0.7957 (mttp) cc_final: 0.6560 (tptp) REVERT: G 441 GLN cc_start: 0.7674 (OUTLIER) cc_final: 0.7300 (mm-40) REVERT: G 483 MET cc_start: 0.8978 (tmm) cc_final: 0.8483 (tmm) REVERT: H 150 MET cc_start: 0.6859 (tpt) cc_final: 0.6375 (tpp) REVERT: H 179 MET cc_start: 0.6683 (mtp) cc_final: 0.6127 (mpt) REVERT: H 205 LYS cc_start: 0.7996 (mttp) cc_final: 0.6550 (tptp) REVERT: H 418 ASP cc_start: 0.5725 (m-30) cc_final: 0.5239 (m-30) REVERT: H 509 TYR cc_start: 0.5828 (OUTLIER) cc_final: 0.4194 (t80) outliers start: 72 outliers final: 45 residues processed: 387 average time/residue: 2.5431 time to fit residues: 1190.1407 Evaluate side-chains 384 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 326 time to evaluate : 3.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 509 TYR Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 509 TYR Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 420 MET Chi-restraints excluded: chain C residue 441 GLN Chi-restraints excluded: chain C residue 509 TYR Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 441 GLN Chi-restraints excluded: chain D residue 509 TYR Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 329 SER Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 420 MET Chi-restraints excluded: chain E residue 495 MET Chi-restraints excluded: chain E residue 509 TYR Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 231 ARG Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain G residue 420 MET Chi-restraints excluded: chain G residue 441 GLN Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 219 VAL Chi-restraints excluded: chain H residue 509 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 224 optimal weight: 5.9990 chunk 144 optimal weight: 3.9990 chunk 216 optimal weight: 2.9990 chunk 109 optimal weight: 10.0000 chunk 71 optimal weight: 5.9990 chunk 70 optimal weight: 0.9980 chunk 230 optimal weight: 3.9990 chunk 246 optimal weight: 7.9990 chunk 179 optimal weight: 7.9990 chunk 33 optimal weight: 0.0970 chunk 284 optimal weight: 0.7980 overall best weight: 1.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 GLN ** D 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 292 GLN E 202 GLN ** G 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 202 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 30008 Z= 0.201 Angle : 0.558 7.529 40728 Z= 0.278 Chirality : 0.043 0.149 4696 Planarity : 0.004 0.047 5064 Dihedral : 17.375 175.835 4669 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.09 % Allowed : 13.77 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.14), residues: 3752 helix: 1.53 (0.14), residues: 1416 sheet: -0.56 (0.22), residues: 440 loop : 0.08 (0.14), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 92 PHE 0.014 0.001 PHE A 24 TYR 0.015 0.001 TYR F 514 ARG 0.002 0.000 ARG A 322 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Evaluate side-chains 400 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 336 time to evaluate : 3.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.6697 (tpt) cc_final: 0.6274 (tpp) REVERT: A 161 ARG cc_start: 0.7237 (mtt180) cc_final: 0.6693 (mtt-85) REVERT: A 179 MET cc_start: 0.6564 (mtp) cc_final: 0.5918 (mpt) REVERT: A 205 LYS cc_start: 0.7966 (mttp) cc_final: 0.6573 (tptp) REVERT: A 231 ARG cc_start: 0.7669 (OUTLIER) cc_final: 0.6827 (ttm110) REVERT: A 420 MET cc_start: 0.6321 (OUTLIER) cc_final: 0.5969 (tpp) REVERT: A 483 MET cc_start: 0.8969 (tmm) cc_final: 0.8499 (tmm) REVERT: A 509 TYR cc_start: 0.5737 (OUTLIER) cc_final: 0.4127 (t80) REVERT: A 512 ARG cc_start: 0.7018 (ttt180) cc_final: 0.4831 (ttm-80) REVERT: B 146 GLU cc_start: 0.5669 (tp30) cc_final: 0.5429 (tp30) REVERT: B 161 ARG cc_start: 0.7143 (mtt180) cc_final: 0.6620 (mtt-85) REVERT: B 179 MET cc_start: 0.6926 (mtp) cc_final: 0.6362 (mpt) REVERT: B 205 LYS cc_start: 0.8041 (mttp) cc_final: 0.6526 (tptp) REVERT: B 441 GLN cc_start: 0.7591 (mt0) cc_final: 0.6760 (mm-40) REVERT: B 483 MET cc_start: 0.8980 (tmm) cc_final: 0.8512 (tmm) REVERT: B 512 ARG cc_start: 0.7040 (ttt180) cc_final: 0.3675 (mmm160) REVERT: C 146 GLU cc_start: 0.5559 (tp30) cc_final: 0.5303 (tp30) REVERT: C 150 MET cc_start: 0.6686 (tpt) cc_final: 0.6159 (tpp) REVERT: C 179 MET cc_start: 0.6611 (mtm) cc_final: 0.6196 (mpt) REVERT: C 205 LYS cc_start: 0.7970 (mttp) cc_final: 0.6571 (tptp) REVERT: C 441 GLN cc_start: 0.7560 (OUTLIER) cc_final: 0.7116 (mm-40) REVERT: C 512 ARG cc_start: 0.7091 (ttt180) cc_final: 0.3904 (mmm160) REVERT: D 150 MET cc_start: 0.6699 (tpt) cc_final: 0.6298 (tpp) REVERT: D 179 MET cc_start: 0.6531 (mtp) cc_final: 0.5796 (mpt) REVERT: D 205 LYS cc_start: 0.7946 (mttp) cc_final: 0.6859 (mmtt) REVERT: D 441 GLN cc_start: 0.7656 (OUTLIER) cc_final: 0.7245 (mm-40) REVERT: D 483 MET cc_start: 0.8978 (tmm) cc_final: 0.8532 (tmm) REVERT: D 508 SER cc_start: 0.6770 (t) cc_final: 0.6555 (t) REVERT: D 512 ARG cc_start: 0.7055 (ttt180) cc_final: 0.4165 (mpt90) REVERT: E 146 GLU cc_start: 0.5627 (tp30) cc_final: 0.5410 (tp30) REVERT: E 150 MET cc_start: 0.6795 (tpt) cc_final: 0.6360 (tpp) REVERT: E 179 MET cc_start: 0.6878 (mtp) cc_final: 0.6374 (mpt) REVERT: E 205 LYS cc_start: 0.7924 (mttp) cc_final: 0.6450 (tptp) REVERT: E 483 MET cc_start: 0.8981 (tmm) cc_final: 0.8517 (tmm) REVERT: E 495 MET cc_start: 0.6284 (OUTLIER) cc_final: 0.5989 (mtp) REVERT: E 512 ARG cc_start: 0.7119 (ttt180) cc_final: 0.3774 (mmm160) REVERT: F 150 MET cc_start: 0.6787 (tpt) cc_final: 0.6363 (tpp) REVERT: F 179 MET cc_start: 0.6919 (mtm) cc_final: 0.6588 (mpt) REVERT: F 205 LYS cc_start: 0.7908 (mttp) cc_final: 0.6447 (tptp) REVERT: F 231 ARG cc_start: 0.7645 (OUTLIER) cc_final: 0.6771 (ttm110) REVERT: F 483 MET cc_start: 0.8978 (tmm) cc_final: 0.8523 (tmm) REVERT: F 510 GLU cc_start: 0.6323 (tt0) cc_final: 0.4955 (mm-30) REVERT: G 70 MET cc_start: 0.8937 (mtp) cc_final: 0.8365 (mtp) REVERT: G 150 MET cc_start: 0.6718 (tpt) cc_final: 0.6286 (tpp) REVERT: G 179 MET cc_start: 0.6908 (mtm) cc_final: 0.6664 (mpt) REVERT: G 205 LYS cc_start: 0.7926 (mttp) cc_final: 0.6513 (tptp) REVERT: G 441 GLN cc_start: 0.7591 (OUTLIER) cc_final: 0.7240 (mm-40) REVERT: G 483 MET cc_start: 0.8976 (tmm) cc_final: 0.8512 (tmm) REVERT: H 150 MET cc_start: 0.6782 (tpt) cc_final: 0.6252 (tpp) REVERT: H 179 MET cc_start: 0.6759 (mtp) cc_final: 0.6207 (mpt) REVERT: H 205 LYS cc_start: 0.7937 (mttp) cc_final: 0.6511 (tptp) REVERT: H 418 ASP cc_start: 0.5576 (m-30) cc_final: 0.5074 (m-30) REVERT: H 509 TYR cc_start: 0.5725 (OUTLIER) cc_final: 0.3881 (t80) outliers start: 64 outliers final: 46 residues processed: 372 average time/residue: 2.5560 time to fit residues: 1123.0203 Evaluate side-chains 382 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 327 time to evaluate : 3.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 509 TYR Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 420 MET Chi-restraints excluded: chain C residue 441 GLN Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 441 GLN Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 117 ASP Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 420 MET Chi-restraints excluded: chain E residue 495 MET Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 231 ARG Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain G residue 420 MET Chi-restraints excluded: chain G residue 441 GLN Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 219 VAL Chi-restraints excluded: chain H residue 230 ASN Chi-restraints excluded: chain H residue 509 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 329 optimal weight: 3.9990 chunk 347 optimal weight: 5.9990 chunk 316 optimal weight: 5.9990 chunk 337 optimal weight: 4.9990 chunk 203 optimal weight: 0.6980 chunk 147 optimal weight: 3.9990 chunk 265 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 305 optimal weight: 4.9990 chunk 319 optimal weight: 0.9980 chunk 336 optimal weight: 3.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN A 202 GLN ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 202 GLN ** G 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 202 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 30008 Z= 0.252 Angle : 0.582 7.505 40728 Z= 0.292 Chirality : 0.043 0.148 4696 Planarity : 0.004 0.049 5064 Dihedral : 17.164 171.378 4660 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.02 % Allowed : 14.07 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.14), residues: 3752 helix: 1.46 (0.14), residues: 1416 sheet: -0.55 (0.22), residues: 440 loop : 0.10 (0.14), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS G 296 PHE 0.015 0.002 PHE B 24 TYR 0.014 0.002 TYR G 348 ARG 0.003 0.000 ARG A 322 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Evaluate side-chains 393 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 331 time to evaluate : 3.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.6683 (tpt) cc_final: 0.6307 (tpp) REVERT: A 161 ARG cc_start: 0.7235 (mtt180) cc_final: 0.6679 (mtt-85) REVERT: A 179 MET cc_start: 0.6788 (mtp) cc_final: 0.6026 (mpt) REVERT: A 205 LYS cc_start: 0.7982 (mttp) cc_final: 0.6564 (tptp) REVERT: A 231 ARG cc_start: 0.7651 (OUTLIER) cc_final: 0.6822 (ttm110) REVERT: A 483 MET cc_start: 0.8958 (tmm) cc_final: 0.8469 (tmm) REVERT: A 509 TYR cc_start: 0.5704 (OUTLIER) cc_final: 0.4076 (t80) REVERT: A 512 ARG cc_start: 0.6928 (ttt180) cc_final: 0.4770 (ttm-80) REVERT: B 146 GLU cc_start: 0.5720 (tp30) cc_final: 0.5493 (tp30) REVERT: B 161 ARG cc_start: 0.7097 (mtt180) cc_final: 0.6518 (mtt-85) REVERT: B 179 MET cc_start: 0.7004 (mtp) cc_final: 0.6439 (mpt) REVERT: B 205 LYS cc_start: 0.8061 (mttp) cc_final: 0.6520 (tptp) REVERT: B 441 GLN cc_start: 0.7626 (mt0) cc_final: 0.6876 (mm-40) REVERT: B 483 MET cc_start: 0.8969 (tmm) cc_final: 0.8473 (tmm) REVERT: B 512 ARG cc_start: 0.7079 (ttt180) cc_final: 0.3732 (mmm160) REVERT: C 146 GLU cc_start: 0.5551 (tp30) cc_final: 0.5297 (tp30) REVERT: C 150 MET cc_start: 0.6677 (tpt) cc_final: 0.6227 (tpp) REVERT: C 157 ILE cc_start: 0.7662 (tt) cc_final: 0.7359 (tp) REVERT: C 179 MET cc_start: 0.6616 (mtm) cc_final: 0.6229 (mpt) REVERT: C 205 LYS cc_start: 0.7996 (mttp) cc_final: 0.6559 (tptp) REVERT: C 441 GLN cc_start: 0.7556 (OUTLIER) cc_final: 0.7122 (mm-40) REVERT: C 512 ARG cc_start: 0.6967 (ttt180) cc_final: 0.3825 (mmm160) REVERT: D 150 MET cc_start: 0.6673 (tpt) cc_final: 0.6322 (tpp) REVERT: D 179 MET cc_start: 0.6530 (mtp) cc_final: 0.5836 (mpt) REVERT: D 205 LYS cc_start: 0.7967 (mttp) cc_final: 0.6428 (tptp) REVERT: D 441 GLN cc_start: 0.7670 (OUTLIER) cc_final: 0.7277 (mm-40) REVERT: D 483 MET cc_start: 0.8969 (tmm) cc_final: 0.8499 (tmm) REVERT: D 512 ARG cc_start: 0.7048 (ttt180) cc_final: 0.4135 (mpt90) REVERT: E 135 MET cc_start: 0.6700 (ttp) cc_final: 0.6499 (ttm) REVERT: E 146 GLU cc_start: 0.5647 (tp30) cc_final: 0.5430 (tp30) REVERT: E 150 MET cc_start: 0.6711 (tpt) cc_final: 0.6256 (tpp) REVERT: E 179 MET cc_start: 0.6836 (mtp) cc_final: 0.6377 (mpt) REVERT: E 205 LYS cc_start: 0.7941 (mttp) cc_final: 0.6470 (tptp) REVERT: E 483 MET cc_start: 0.8982 (tmm) cc_final: 0.8497 (tmm) REVERT: E 495 MET cc_start: 0.6343 (OUTLIER) cc_final: 0.6039 (mtp) REVERT: E 512 ARG cc_start: 0.7149 (ttt180) cc_final: 0.3797 (mmm160) REVERT: F 150 MET cc_start: 0.6751 (tpt) cc_final: 0.6467 (tpp) REVERT: F 179 MET cc_start: 0.6950 (mtm) cc_final: 0.6640 (mpt) REVERT: F 205 LYS cc_start: 0.7913 (mttp) cc_final: 0.6451 (tptp) REVERT: F 231 ARG cc_start: 0.7644 (OUTLIER) cc_final: 0.6779 (ttm110) REVERT: F 483 MET cc_start: 0.8998 (tmm) cc_final: 0.8484 (tmm) REVERT: F 510 GLU cc_start: 0.6345 (tt0) cc_final: 0.4968 (mm-30) REVERT: G 70 MET cc_start: 0.8953 (mtp) cc_final: 0.8294 (mtp) REVERT: G 150 MET cc_start: 0.6712 (tpt) cc_final: 0.6363 (tpp) REVERT: G 179 MET cc_start: 0.6911 (mtm) cc_final: 0.6670 (mpt) REVERT: G 205 LYS cc_start: 0.7938 (mttp) cc_final: 0.6540 (tptp) REVERT: G 441 GLN cc_start: 0.7588 (OUTLIER) cc_final: 0.7224 (mm-40) REVERT: G 483 MET cc_start: 0.8969 (tmm) cc_final: 0.8471 (tmm) REVERT: H 70 MET cc_start: 0.9060 (mtp) cc_final: 0.8301 (mtp) REVERT: H 150 MET cc_start: 0.6745 (tpt) cc_final: 0.6221 (tpp) REVERT: H 179 MET cc_start: 0.6794 (mtp) cc_final: 0.6248 (mpt) REVERT: H 205 LYS cc_start: 0.8020 (mttp) cc_final: 0.6549 (tptp) REVERT: H 418 ASP cc_start: 0.5707 (m-30) cc_final: 0.5190 (m-30) outliers start: 62 outliers final: 46 residues processed: 361 average time/residue: 2.6176 time to fit residues: 1113.3832 Evaluate side-chains 381 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 328 time to evaluate : 3.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 509 TYR Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 117 ASP Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 420 MET Chi-restraints excluded: chain C residue 441 GLN Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 441 GLN Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 117 ASP Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 420 MET Chi-restraints excluded: chain E residue 495 MET Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 231 ARG Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 117 ASP Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain G residue 420 MET Chi-restraints excluded: chain G residue 441 GLN Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 219 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 221 optimal weight: 2.9990 chunk 357 optimal weight: 1.9990 chunk 217 optimal weight: 0.9980 chunk 169 optimal weight: 1.9990 chunk 248 optimal weight: 0.8980 chunk 374 optimal weight: 0.6980 chunk 344 optimal weight: 2.9990 chunk 298 optimal weight: 10.0000 chunk 30 optimal weight: 7.9990 chunk 230 optimal weight: 2.9990 chunk 182 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 202 GLN ** G 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 202 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 30008 Z= 0.154 Angle : 0.538 7.791 40728 Z= 0.264 Chirality : 0.042 0.149 4696 Planarity : 0.004 0.045 5064 Dihedral : 16.469 177.353 4658 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.76 % Allowed : 14.46 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.14), residues: 3752 helix: 1.76 (0.14), residues: 1416 sheet: -0.58 (0.22), residues: 440 loop : 0.15 (0.14), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 92 PHE 0.012 0.001 PHE C 24 TYR 0.016 0.001 TYR F 514 ARG 0.001 0.000 ARG A 322 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Evaluate side-chains 380 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 326 time to evaluate : 3.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.6630 (tpt) cc_final: 0.6251 (tpp) REVERT: A 161 ARG cc_start: 0.7193 (mtt180) cc_final: 0.6666 (mtt-85) REVERT: A 179 MET cc_start: 0.6692 (mtp) cc_final: 0.6055 (mpt) REVERT: A 205 LYS cc_start: 0.7972 (mttp) cc_final: 0.6554 (tptp) REVERT: A 231 ARG cc_start: 0.7674 (OUTLIER) cc_final: 0.6801 (ttm110) REVERT: A 420 MET cc_start: 0.6308 (OUTLIER) cc_final: 0.6031 (tpp) REVERT: A 483 MET cc_start: 0.8964 (tmm) cc_final: 0.8510 (tmm) REVERT: A 512 ARG cc_start: 0.7033 (ttt180) cc_final: 0.3942 (mmm160) REVERT: B 70 MET cc_start: 0.9066 (mtp) cc_final: 0.8854 (mtp) REVERT: B 146 GLU cc_start: 0.5673 (tp30) cc_final: 0.5458 (tp30) REVERT: B 161 ARG cc_start: 0.7110 (mtt180) cc_final: 0.6593 (mtt-85) REVERT: B 179 MET cc_start: 0.6875 (mtp) cc_final: 0.6421 (mpt) REVERT: B 205 LYS cc_start: 0.8055 (mttp) cc_final: 0.6565 (tptp) REVERT: B 441 GLN cc_start: 0.7560 (mt0) cc_final: 0.6799 (mm-40) REVERT: B 483 MET cc_start: 0.8982 (tmm) cc_final: 0.8545 (tmm) REVERT: B 512 ARG cc_start: 0.6968 (ttt180) cc_final: 0.3727 (mmm160) REVERT: C 146 GLU cc_start: 0.5529 (tp30) cc_final: 0.5282 (tp30) REVERT: C 150 MET cc_start: 0.6671 (tpt) cc_final: 0.6221 (tpp) REVERT: C 179 MET cc_start: 0.6622 (mtm) cc_final: 0.6302 (mpt) REVERT: C 205 LYS cc_start: 0.7988 (mttp) cc_final: 0.6515 (tptp) REVERT: C 441 GLN cc_start: 0.7542 (OUTLIER) cc_final: 0.7140 (mm-40) REVERT: C 483 MET cc_start: 0.8899 (tmm) cc_final: 0.8680 (tmm) REVERT: C 512 ARG cc_start: 0.7106 (ttt180) cc_final: 0.3775 (mmm160) REVERT: D 150 MET cc_start: 0.6657 (tpt) cc_final: 0.6254 (tpp) REVERT: D 179 MET cc_start: 0.6697 (mtp) cc_final: 0.6021 (mpt) REVERT: D 205 LYS cc_start: 0.7987 (mttp) cc_final: 0.6867 (mmtt) REVERT: D 441 GLN cc_start: 0.7564 (OUTLIER) cc_final: 0.7207 (mm-40) REVERT: D 483 MET cc_start: 0.8973 (tmm) cc_final: 0.8557 (tmm) REVERT: D 512 ARG cc_start: 0.7031 (ttt180) cc_final: 0.3995 (mpt90) REVERT: E 146 GLU cc_start: 0.5612 (tp30) cc_final: 0.5393 (tp30) REVERT: E 150 MET cc_start: 0.6653 (tpt) cc_final: 0.6202 (tpp) REVERT: E 179 MET cc_start: 0.6687 (mtp) cc_final: 0.6313 (mpt) REVERT: E 205 LYS cc_start: 0.7924 (mttp) cc_final: 0.6419 (tptt) REVERT: E 483 MET cc_start: 0.8991 (tmm) cc_final: 0.8541 (tmm) REVERT: E 495 MET cc_start: 0.6264 (OUTLIER) cc_final: 0.5921 (mtp) REVERT: E 510 GLU cc_start: 0.6672 (tt0) cc_final: 0.6208 (tt0) REVERT: E 512 ARG cc_start: 0.7136 (ttt180) cc_final: 0.3770 (mmm160) REVERT: F 150 MET cc_start: 0.6727 (tpt) cc_final: 0.6453 (tpp) REVERT: F 205 LYS cc_start: 0.7900 (mttp) cc_final: 0.6492 (tptp) REVERT: F 231 ARG cc_start: 0.7643 (OUTLIER) cc_final: 0.6760 (ttm110) REVERT: F 483 MET cc_start: 0.8986 (tmm) cc_final: 0.8557 (tmm) REVERT: F 510 GLU cc_start: 0.6232 (tt0) cc_final: 0.5013 (mm-30) REVERT: G 150 MET cc_start: 0.6664 (tpt) cc_final: 0.6319 (tpp) REVERT: G 205 LYS cc_start: 0.7926 (mttp) cc_final: 0.6509 (tptp) REVERT: G 441 GLN cc_start: 0.7588 (OUTLIER) cc_final: 0.7130 (mm-40) REVERT: G 483 MET cc_start: 0.8974 (tmm) cc_final: 0.8522 (tmm) REVERT: H 150 MET cc_start: 0.6721 (tpt) cc_final: 0.6254 (tpp) REVERT: H 179 MET cc_start: 0.6870 (mtp) cc_final: 0.6357 (mpt) REVERT: H 205 LYS cc_start: 0.7954 (mttp) cc_final: 0.6511 (tptp) REVERT: H 418 ASP cc_start: 0.5559 (m-30) cc_final: 0.5166 (m-30) REVERT: H 483 MET cc_start: 0.8875 (tmm) cc_final: 0.8561 (tmm) REVERT: H 508 SER cc_start: 0.7363 (m) cc_final: 0.6973 (t) REVERT: H 510 GLU cc_start: 0.6762 (tt0) cc_final: 0.6302 (tt0) outliers start: 54 outliers final: 38 residues processed: 355 average time/residue: 2.6098 time to fit residues: 1091.1745 Evaluate side-chains 363 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 318 time to evaluate : 3.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 420 MET Chi-restraints excluded: chain C residue 441 GLN Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 339 CYS Chi-restraints excluded: chain D residue 441 GLN Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 495 MET Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 231 ARG Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 420 MET Chi-restraints excluded: chain G residue 441 GLN Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 187 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 236 optimal weight: 3.9990 chunk 317 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 275 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 298 optimal weight: 7.9990 chunk 125 optimal weight: 4.9990 chunk 306 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 GLN ** D 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 202 GLN ** G 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 202 GLN ** H 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 292 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.136898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.103514 restraints weight = 93233.384| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 1.30 r_work: 0.2978 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.3427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 30008 Z= 0.284 Angle : 0.598 7.757 40728 Z= 0.299 Chirality : 0.044 0.148 4696 Planarity : 0.004 0.050 5064 Dihedral : 16.711 176.780 4656 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.83 % Allowed : 14.43 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.14), residues: 3752 helix: 1.52 (0.14), residues: 1416 sheet: -0.53 (0.22), residues: 440 loop : 0.14 (0.14), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 296 PHE 0.016 0.002 PHE D 24 TYR 0.015 0.002 TYR C 348 ARG 0.004 0.001 ARG A 322 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18047.76 seconds wall clock time: 311 minutes 13.65 seconds (18673.65 seconds total)