Starting phenix.real_space_refine on Wed Feb 14 13:55:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rfg_24441/02_2024/7rfg_24441_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rfg_24441/02_2024/7rfg_24441.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/7rfg_24441/02_2024/7rfg_24441.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rfg_24441/02_2024/7rfg_24441.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rfg_24441/02_2024/7rfg_24441_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rfg_24441/02_2024/7rfg_24441_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= -0.000 sd= 0.295 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 19040 2.51 5 N 5232 2.21 5 O 6040 1.98 5 H 30240 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 PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 43": "OD1" <-> "OD2" Residue "A ASP 47": "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 114": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 117": "OD1" <-> "OD2" Residue "A GLU 132": "OE1" <-> "OE2" 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 ASP 164": "OD1" <-> "OD2" Residue "A GLU 168": "OE1" <-> "OE2" Residue "A ASP 170": "OD1" <-> "OD2" Residue "A GLU 177": "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 ASP 261": "OD1" <-> "OD2" Residue "A ASP 269": "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 PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 470": "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 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 PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 47": "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 114": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 117": "OD1" <-> "OD2" Residue "B GLU 132": "OE1" <-> "OE2" Residue "B ARG 136": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 164": "OD1" <-> "OD2" Residue "B GLU 168": "OE1" <-> "OE2" Residue "B ASP 170": "OD1" <-> "OD2" Residue "B ARG 182": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 184": "OE1" <-> "OE2" Residue "B ASP 214": "OD1" <-> "OD2" 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 GLU 254": "OE1" <-> "OE2" Residue "B ASP 256": "OD1" <-> "OD2" Residue "B ASP 261": "OD1" <-> "OD2" Residue "B ASP 269": "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 ARG 355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 404": "OD1" <-> "OD2" 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 470": "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 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 PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 43": "OD1" <-> "OD2" Residue "C GLU 48": "OE1" <-> "OE2" 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 114": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 136": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 164": "OD1" <-> "OD2" Residue "C ASP 170": "OD1" <-> "OD2" Residue "C GLU 177": "OE1" <-> "OE2" Residue "C ARG 182": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 184": "OE1" <-> "OE2" Residue "C GLU 199": "OE1" <-> "OE2" Residue "C GLU 217": "OE1" <-> "OE2" 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 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 PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 407": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 421": "OE1" <-> "OE2" 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 PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 47": "OD1" <-> "OD2" Residue "D GLU 48": "OE1" <-> "OE2" 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 114": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 ASP 164": "OD1" <-> "OD2" Residue "D ASP 170": "OD1" <-> "OD2" Residue "D ARG 182": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 184": "OE1" <-> "OE2" Residue "D ASP 214": "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 GLU 254": "OE1" <-> "OE2" Residue "D ASP 256": "OD1" <-> "OD2" Residue "D ASP 261": "OD1" <-> "OD2" Residue "D ASP 269": "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 ARG 355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 407": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 421": "OE1" <-> "OE2" 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 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 PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 47": "OD1" <-> "OD2" Residue "E GLU 48": "OE1" <-> "OE2" Residue "E ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 75": "OE1" <-> "OE2" 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 114": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 129": "OD1" <-> "OD2" Residue "E ARG 136": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 146": "OE1" <-> "OE2" Residue "E ASP 164": "OD1" <-> "OD2" Residue "E GLU 168": "OE1" <-> "OE2" Residue "E GLU 177": "OE1" <-> "OE2" Residue "E ARG 182": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 184": "OE1" <-> "OE2" Residue "E GLU 199": "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 256": "OD1" <-> "OD2" Residue "E ASP 261": "OD1" <-> "OD2" Residue "E ASP 269": "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 ARG 355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 402": "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 418": "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 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 PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 43": "OD1" <-> "OD2" Residue "F ASP 47": "OD1" <-> "OD2" Residue "F GLU 48": "OE1" <-> "OE2" 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 114": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 117": "OD1" <-> "OD2" 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 ASP 164": "OD1" <-> "OD2" Residue "F ASP 170": "OD1" <-> "OD2" Residue "F GLU 177": "OE1" <-> "OE2" Residue "F ARG 182": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F GLU 184": "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 ARG 253": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ASP 256": "OD1" <-> "OD2" Residue "F ASP 261": "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 PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 402": "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 GLU 421": "OE1" <-> "OE2" Residue "F ASP 470": "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 "F TYR 514": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 47": "OD1" <-> "OD2" Residue "G GLU 48": "OE1" <-> "OE2" Residue "G ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G GLU 75": "OE1" <-> "OE2" 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 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 ASP 164": "OD1" <-> "OD2" Residue "G GLU 168": "OE1" <-> "OE2" Residue "G GLU 177": "OE1" <-> "OE2" Residue "G ARG 182": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G GLU 184": "OE1" <-> "OE2" Residue "G GLU 199": "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 256": "OD1" <-> "OD2" Residue "G ASP 261": "OD1" <-> "OD2" Residue "G ASP 269": "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 ARG 355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 402": "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 GLU 421": "OE1" <-> "OE2" Residue "G ASP 470": "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 GLU 491": "OE1" <-> "OE2" Residue "G GLU 510": "OE1" <-> "OE2" Residue "G ARG 512": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G TYR 514": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 43": "OD1" <-> "OD2" Residue "H ASP 47": "OD1" <-> "OD2" Residue "H ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H GLU 75": "OE1" <-> "OE2" 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 ARG 136": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 146": "OE1" <-> "OE2" Residue "H ASP 164": "OD1" <-> "OD2" Residue "H GLU 177": "OE1" <-> "OE2" Residue "H ARG 182": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H GLU 184": "OE1" <-> "OE2" 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 ASP 261": "OD1" <-> "OD2" Residue "H ASP 269": "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 401": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 402": "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 GLU 421": "OE1" <-> "OE2" 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 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: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 60824 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 7485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 7485 Classifications: {'peptide': 491} Link IDs: {'PTRANS': 17, 'TRANS': 473} Chain breaks: 1 Chain: "B" Number of atoms: 7485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 7485 Classifications: {'peptide': 491} Link IDs: {'PTRANS': 17, 'TRANS': 473} Chain breaks: 1 Chain: "C" Number of atoms: 7485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 7485 Classifications: {'peptide': 491} Link IDs: {'PTRANS': 17, 'TRANS': 473} Chain breaks: 1 Chain: "D" Number of atoms: 7485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 7485 Classifications: {'peptide': 491} Link IDs: {'PTRANS': 17, 'TRANS': 473} Chain breaks: 1 Chain: "E" Number of atoms: 7485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 7485 Classifications: {'peptide': 491} Link IDs: {'PTRANS': 17, 'TRANS': 473} Chain breaks: 1 Chain: "F" Number of atoms: 7485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 7485 Classifications: {'peptide': 491} Link IDs: {'PTRANS': 17, 'TRANS': 473} Chain breaks: 1 Chain: "G" Number of atoms: 7485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 7485 Classifications: {'peptide': 491} Link IDs: {'PTRANS': 17, 'TRANS': 473} Chain breaks: 1 Chain: "H" Number of atoms: 7485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 7485 Classifications: {'peptide': 491} Link IDs: {'PTRANS': 17, 'TRANS': 473} Chain breaks: 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: 18.85, per 1000 atoms: 0.31 Number of scatterers: 60824 At special positions: 0 Unit cell: (166.95, 168, 112.35, 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 6040 8.00 N 5232 7.00 C 19040 6.00 H 30240 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: 39.58 Conformation dependent library (CDL) restraints added in 4.6 seconds 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7072 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 156 helices and 51 sheets defined 35.5% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.22 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 109 Processing helix chain 'A' and resid 127 through 137 Processing helix chain 'A' and resid 160 through 163 No H-bonds generated for 'chain 'A' and resid 160 through 163' Processing helix chain 'A' and resid 175 through 177 No H-bonds generated for 'chain 'A' and resid 175 through 177' Processing helix chain 'A' and resid 194 through 204 Processing helix chain 'A' and resid 224 through 232 Processing helix chain 'A' and resid 254 through 265 removed outlier: 3.629A pdb=" N LEU A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 293 Processing helix chain 'A' and resid 307 through 316 removed outlier: 3.636A pdb=" N ASN A 312 " --> pdb=" O ALA A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 337 Processing helix chain 'A' and resid 343 through 357 removed outlier: 4.503A pdb=" N ARG A 356 " --> pdb=" O GLU A 352 " (cutoff:3.500A) removed outlier: 4.270A 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 160 through 163 No H-bonds generated for 'chain 'B' and resid 160 through 163' Processing helix chain 'B' and resid 175 through 177 No H-bonds generated for 'chain 'B' and resid 175 through 177' Processing helix chain 'B' and resid 194 through 204 Processing helix chain 'B' and resid 224 through 232 Processing helix chain 'B' and resid 254 through 265 removed outlier: 3.606A pdb=" N LEU B 260 " --> pdb=" O LYS B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 293 Processing helix chain 'B' and resid 307 through 316 removed outlier: 3.631A pdb=" N ASN B 312 " --> pdb=" O ALA B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 337 Processing helix chain 'B' and resid 343 through 357 removed outlier: 4.504A pdb=" N ARG B 356 " --> pdb=" O GLU B 352 " (cutoff:3.500A) removed outlier: 4.252A 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 417 through 420 No H-bonds generated for 'chain 'B' and resid 417 through 420' 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 163 No H-bonds generated for 'chain 'C' and resid 160 through 163' Processing helix chain 'C' and resid 175 through 177 No H-bonds generated for 'chain 'C' and resid 175 through 177' Processing helix chain 'C' and resid 194 through 204 Processing helix chain 'C' and resid 224 through 232 Processing helix chain 'C' and resid 254 through 265 removed outlier: 3.601A pdb=" N LEU C 260 " --> pdb=" O LYS C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 293 Processing helix chain 'C' and resid 307 through 316 removed outlier: 3.644A pdb=" N ASN C 312 " --> pdb=" O ALA C 308 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU C 313 " --> pdb=" O GLN C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 337 Processing helix chain 'C' and resid 343 through 357 removed outlier: 4.415A pdb=" N ARG C 356 " --> pdb=" O GLU C 352 " (cutoff:3.500A) removed outlier: 4.230A 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 417 through 420 No H-bonds generated for 'chain 'C' and resid 417 through 420' Processing helix chain 'C' and resid 453 through 471 Proline residue: C 458 - end of helix Processing helix chain 'C' and resid 476 through 484 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 163 No H-bonds generated for 'chain 'D' and resid 160 through 163' Processing helix chain 'D' and resid 175 through 177 No H-bonds generated for 'chain 'D' and resid 175 through 177' Processing helix chain 'D' and resid 194 through 204 Processing helix chain 'D' and resid 224 through 232 Processing helix chain 'D' and resid 254 through 265 removed outlier: 3.600A pdb=" N LEU D 260 " --> pdb=" O LYS D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 293 Processing helix chain 'D' and resid 307 through 316 removed outlier: 3.682A pdb=" N ASN D 312 " --> pdb=" O ALA D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 337 Processing helix chain 'D' and resid 343 through 357 removed outlier: 4.430A pdb=" N ARG D 356 " --> pdb=" O GLU D 352 " (cutoff:3.500A) removed outlier: 4.222A 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 500 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 160 through 163 No H-bonds generated for 'chain 'E' and resid 160 through 163' Processing helix chain 'E' and resid 175 through 177 No H-bonds generated for 'chain 'E' and resid 175 through 177' Processing helix chain 'E' and resid 194 through 204 Processing helix chain 'E' and resid 224 through 232 Processing helix chain 'E' and resid 254 through 265 removed outlier: 3.619A pdb=" N LEU E 260 " --> pdb=" O LYS E 257 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR E 264 " --> pdb=" O ASP E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 293 Processing helix chain 'E' and resid 307 through 316 removed outlier: 3.647A pdb=" N ASN E 312 " --> pdb=" O ALA E 308 " (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: 4.449A pdb=" N ARG E 356 " --> pdb=" O GLU E 352 " (cutoff:3.500A) removed outlier: 4.234A 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 417 through 420 No H-bonds generated for 'chain 'E' and resid 417 through 420' Processing helix chain 'E' and resid 453 through 471 Proline residue: E 458 - end of helix Processing helix chain 'E' and resid 476 through 484 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 160 through 163 No H-bonds generated for 'chain 'F' and resid 160 through 163' Processing helix chain 'F' and resid 175 through 177 No H-bonds generated for 'chain 'F' and resid 175 through 177' Processing helix chain 'F' and resid 194 through 204 Processing helix chain 'F' and resid 224 through 232 Processing helix chain 'F' and resid 254 through 265 removed outlier: 3.618A pdb=" N LEU F 260 " --> pdb=" O LYS F 257 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR F 264 " --> pdb=" O ASP F 261 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 293 Processing helix chain 'F' and resid 307 through 316 removed outlier: 3.638A pdb=" N ASN F 312 " --> pdb=" O ALA F 308 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU F 313 " --> pdb=" O GLN F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 337 Processing helix chain 'F' and resid 343 through 357 removed outlier: 4.479A pdb=" N ARG F 356 " --> pdb=" O GLU F 352 " (cutoff:3.500A) removed outlier: 4.273A 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 160 through 163 No H-bonds generated for 'chain 'G' and resid 160 through 163' Processing helix chain 'G' and resid 175 through 177 No H-bonds generated for 'chain 'G' and resid 175 through 177' Processing helix chain 'G' and resid 194 through 204 Processing helix chain 'G' and resid 224 through 232 Processing helix chain 'G' and resid 254 through 265 removed outlier: 3.649A pdb=" N LEU G 260 " --> pdb=" O LYS G 257 " (cutoff:3.500A) Processing helix chain 'G' and resid 281 through 293 Processing helix chain 'G' and resid 307 through 316 removed outlier: 3.657A pdb=" N ASN G 312 " --> pdb=" O ALA G 308 " (cutoff:3.500A) Processing helix chain 'G' and resid 333 through 337 Processing helix chain 'G' and resid 343 through 357 removed outlier: 4.455A pdb=" N ARG G 356 " --> pdb=" O GLU G 352 " (cutoff:3.500A) removed outlier: 4.226A 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 109 Processing helix chain 'H' and resid 127 through 137 Processing helix chain 'H' and resid 160 through 163 No H-bonds generated for 'chain 'H' and resid 160 through 163' Processing helix chain 'H' and resid 175 through 177 No H-bonds generated for 'chain 'H' and resid 175 through 177' Processing helix chain 'H' and resid 194 through 204 Processing helix chain 'H' and resid 224 through 232 Processing helix chain 'H' and resid 254 through 265 removed outlier: 3.611A pdb=" N LEU H 260 " --> pdb=" O LYS H 257 " (cutoff:3.500A) Processing helix chain 'H' and resid 281 through 293 Processing helix chain 'H' and resid 307 through 316 removed outlier: 3.622A pdb=" N ASN H 312 " --> pdb=" O ALA H 308 " (cutoff:3.500A) Processing helix chain 'H' and resid 333 through 337 Processing helix chain 'H' and resid 343 through 357 removed outlier: 4.477A pdb=" N ARG H 356 " --> pdb=" O GLU H 352 " (cutoff:3.500A) removed outlier: 4.259A 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 417 through 420 No H-bonds generated for 'chain 'H' and resid 417 through 420' 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: 6.471A pdb=" N VAL A 384 " --> pdb=" O ILE A 66 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASN A 303 " --> pdb=" O ARG A 322 " (cutoff:3.500A) removed outlier: 4.148A 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: 8.061A pdb=" N ALA A 188 " --> pdb=" O LYS A 208 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 408 through 411 Processing sheet with id= E, first strand: chain 'A' and resid 53 through 56 removed outlier: 6.632A pdb=" N ILE A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 142 through 145 Processing sheet with id= G, first strand: chain 'B' and resid 35 through 37 Processing sheet with id= H, first strand: chain 'B' and resid 65 through 67 removed outlier: 6.465A pdb=" N VAL B 384 " --> pdb=" O ILE B 66 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 187 through 189 removed outlier: 8.053A pdb=" N ALA B 188 " --> pdb=" O LYS B 208 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 247 through 250 removed outlier: 6.612A pdb=" N VAL B 270 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N VAL B 250 " --> pdb=" O VAL B 270 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N VAL B 272 " --> pdb=" O VAL B 250 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N GLN B 298 " --> pdb=" O ILE B 271 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N LEU B 273 " --> pdb=" O GLN B 298 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N ILE B 300 " --> pdb=" O LEU B 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'B' and resid 408 through 411 Processing sheet with id= L, first strand: chain 'B' and resid 142 through 145 Processing sheet with id= M, first strand: chain 'C' and resid 35 through 37 Processing sheet with id= N, first strand: chain 'C' and resid 65 through 67 removed outlier: 6.437A pdb=" N VAL C 384 " --> pdb=" O ILE C 66 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ASN C 303 " --> pdb=" O ARG C 322 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLY C 302 " --> pdb=" O LEU C 273 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 187 through 189 removed outlier: 8.093A pdb=" N ALA C 188 " --> pdb=" O LYS C 208 " (cutoff:3.500A) 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 53 through 56 removed outlier: 6.632A pdb=" N ILE C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 142 through 145 Processing sheet with id= S, first strand: chain 'D' and resid 35 through 37 Processing sheet with id= T, first strand: chain 'D' and resid 65 through 67 removed outlier: 6.453A pdb=" N VAL D 384 " --> pdb=" O ILE D 66 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 187 through 189 removed outlier: 8.056A pdb=" N ALA D 188 " --> pdb=" O LYS D 208 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 247 through 250 removed outlier: 6.604A pdb=" N VAL D 270 " --> pdb=" O ALA D 248 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N VAL D 250 " --> pdb=" O VAL D 270 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N VAL D 272 " --> pdb=" O VAL D 250 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N GLN D 298 " --> pdb=" O ILE D 271 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N LEU D 273 " --> pdb=" O GLN D 298 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N ILE D 300 " --> pdb=" O LEU D 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'D' and resid 408 through 411 Processing sheet with id= X, first strand: chain 'D' and resid 53 through 56 removed outlier: 6.620A pdb=" N ILE D 59 " --> pdb=" O LEU D 55 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'D' and resid 142 through 145 Processing sheet with id= Z, first strand: chain 'E' and resid 35 through 37 Processing sheet with id= AA, first strand: chain 'E' and resid 65 through 67 removed outlier: 6.463A pdb=" N VAL E 384 " --> pdb=" O ILE E 66 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ASN E 303 " --> pdb=" O ARG E 322 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLY E 302 " --> pdb=" O LEU E 273 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'E' and resid 187 through 189 removed outlier: 8.030A pdb=" N ALA E 188 " --> pdb=" O LYS E 208 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'E' and resid 408 through 411 Processing sheet with id= AD, first strand: chain 'E' and resid 53 through 56 removed outlier: 6.622A 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: 6.434A pdb=" N VAL F 384 " --> pdb=" O ILE F 66 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ASN F 303 " --> pdb=" O ARG F 322 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLY F 302 " --> pdb=" O LEU F 273 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'F' and resid 187 through 189 removed outlier: 8.141A pdb=" N ALA F 188 " --> pdb=" O LYS F 208 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'F' and resid 408 through 411 Processing sheet with id= AJ, first strand: chain 'F' and resid 53 through 56 removed outlier: 6.612A pdb=" N ILE F 59 " --> pdb=" O LEU F 55 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'F' and resid 142 through 145 Processing sheet with id= AL, first strand: chain 'G' and resid 35 through 37 Processing sheet with id= AM, first strand: chain 'G' and resid 65 through 67 removed outlier: 6.423A pdb=" N VAL G 384 " --> pdb=" O ILE G 66 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'G' and resid 187 through 189 removed outlier: 8.036A pdb=" N ALA G 188 " --> pdb=" O LYS G 208 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'G' and resid 247 through 250 removed outlier: 6.606A pdb=" N VAL G 270 " --> pdb=" O ALA G 248 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N VAL G 250 " --> pdb=" O VAL G 270 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N VAL G 272 " --> pdb=" O VAL G 250 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N GLN G 298 " --> pdb=" O ILE G 271 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N LEU G 273 " --> pdb=" O GLN G 298 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N ILE G 300 " --> pdb=" O LEU G 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= AO Processing sheet with id= AP, first strand: chain 'G' and resid 408 through 411 Processing sheet with id= AQ, first strand: chain 'G' and resid 53 through 56 removed outlier: 6.622A pdb=" N ILE G 59 " --> pdb=" O LEU G 55 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'G' and resid 142 through 145 Processing sheet with id= AS, first strand: chain 'H' and resid 35 through 37 Processing sheet with id= AT, first strand: chain 'H' and resid 65 through 67 removed outlier: 6.455A pdb=" N VAL H 384 " --> pdb=" O ILE H 66 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'H' and resid 187 through 189 removed outlier: 8.071A pdb=" N ALA H 188 " --> pdb=" O LYS H 208 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'H' and resid 247 through 250 removed outlier: 6.581A pdb=" N VAL H 270 " --> pdb=" O ALA H 248 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N VAL H 250 " --> pdb=" O VAL H 270 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N VAL H 272 " --> pdb=" O VAL H 250 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N GLN H 298 " --> pdb=" O ILE H 271 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N LEU H 273 " --> pdb=" O GLN H 298 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N ILE H 300 " --> pdb=" O LEU H 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= AV Processing sheet with id= AW, first strand: chain 'H' and resid 408 through 411 Processing sheet with id= AX, first strand: chain 'H' and resid 53 through 56 removed outlier: 6.630A pdb=" N ILE H 59 " --> pdb=" O LEU H 55 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'H' and resid 142 through 145 969 hydrogen bonds defined for protein. 2616 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: 22.14 Time building geometry restraints manager: 41.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.90 - 1.09: 7965 1.09 - 1.27: 27284 1.27 - 1.45: 8171 1.45 - 1.64: 17588 1.64 - 1.82: 328 Bond restraints: 61336 Sorted by residual: bond pdb=" CB SER A 416 " pdb=" OG SER A 416 " ideal model delta sigma weight residual 1.417 1.180 0.237 2.00e-02 2.50e+03 1.41e+02 bond pdb=" CE1 HIS A 137 " pdb=" HE1 HIS A 137 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.73e+01 bond pdb=" N LYS A 349 " pdb=" H LYS A 349 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" N GLY A 405 " pdb=" H GLY A 405 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" N LYS D 153 " pdb=" H LYS D 153 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 ... (remaining 61331 not shown) Histogram of bond angle deviations from ideal: 73.28 - 85.32: 9 85.32 - 97.35: 41 97.35 - 109.39: 42641 109.39 - 121.43: 59418 121.43 - 133.47: 8923 Bond angle restraints: 111032 Sorted by residual: angle pdb=" PB ATP A 603 " pdb=" O3B ATP A 603 " pdb=" PG ATP A 603 " ideal model delta sigma weight residual 139.87 124.00 15.87 1.00e+00 1.00e+00 2.52e+02 angle pdb=" PB ATP G 603 " pdb=" O3B ATP G 603 " pdb=" PG ATP G 603 " ideal model delta sigma weight residual 139.87 124.32 15.55 1.00e+00 1.00e+00 2.42e+02 angle pdb=" PB ATP C 603 " pdb=" O3B ATP C 603 " pdb=" PG ATP C 603 " ideal model delta sigma weight residual 139.87 124.32 15.55 1.00e+00 1.00e+00 2.42e+02 angle pdb=" PB ATP B 603 " pdb=" O3B ATP B 603 " pdb=" PG ATP B 603 " ideal model delta sigma weight residual 139.87 124.33 15.54 1.00e+00 1.00e+00 2.42e+02 angle pdb=" PB ATP E 603 " pdb=" O3B ATP E 603 " pdb=" PG ATP E 603 " ideal model delta sigma weight residual 139.87 124.91 14.96 1.00e+00 1.00e+00 2.24e+02 ... (remaining 111027 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.51: 27063 34.51 - 69.03: 1503 69.03 - 103.54: 84 103.54 - 138.06: 57 138.06 - 172.57: 13 Dihedral angle restraints: 28720 sinusoidal: 16272 harmonic: 12448 Sorted by residual: dihedral pdb=" CA ASP G 418 " pdb=" C ASP G 418 " pdb=" N ALA G 419 " pdb=" CA ALA G 419 " ideal model delta harmonic sigma weight residual -180.00 -143.77 -36.23 0 5.00e+00 4.00e-02 5.25e+01 dihedral pdb=" O5' GTP C 601 " pdb=" O3A GTP C 601 " pdb=" PA GTP C 601 " pdb=" PB GTP C 601 " ideal model delta sinusoidal sigma weight residual 274.12 101.55 172.57 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" C5' GTP B 601 " pdb=" O5' GTP B 601 " pdb=" PA GTP B 601 " pdb=" O3A GTP B 601 " ideal model delta sinusoidal sigma weight residual 69.27 -99.92 169.19 1 2.00e+01 2.50e-03 4.76e+01 ... (remaining 28717 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.308: 4844 0.308 - 0.617: 25 0.617 - 0.925: 0 0.925 - 1.234: 0 1.234 - 1.542: 3 Chirality restraints: 4872 Sorted by residual: chirality pdb=" CB VAL F 437 " pdb=" CA VAL F 437 " pdb=" CG1 VAL F 437 " pdb=" CG2 VAL F 437 " both_signs ideal model delta sigma weight residual False -2.63 -1.09 -1.54 2.00e-01 2.50e+01 5.95e+01 chirality pdb=" CB VAL C 437 " pdb=" CA VAL C 437 " pdb=" CG1 VAL C 437 " pdb=" CG2 VAL C 437 " both_signs ideal model delta sigma weight residual False -2.63 -1.19 -1.44 2.00e-01 2.50e+01 5.20e+01 chirality pdb=" CB VAL E 437 " pdb=" CA VAL E 437 " pdb=" CG1 VAL E 437 " pdb=" CG2 VAL E 437 " both_signs ideal model delta sigma weight residual False -2.63 -1.23 -1.40 2.00e-01 2.50e+01 4.91e+01 ... (remaining 4869 not shown) Planarity restraints: 9024 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 412 " 0.432 9.50e-02 1.11e+02 1.83e-01 3.10e+02 pdb=" NE ARG D 412 " 0.080 2.00e-02 2.50e+03 pdb=" CZ ARG D 412 " 0.030 2.00e-02 2.50e+03 pdb=" NH1 ARG D 412 " 0.044 2.00e-02 2.50e+03 pdb=" NH2 ARG D 412 " -0.031 2.00e-02 2.50e+03 pdb="HH11 ARG D 412 " -0.236 2.00e-02 2.50e+03 pdb="HH12 ARG D 412 " 0.203 2.00e-02 2.50e+03 pdb="HH21 ARG D 412 " -0.020 2.00e-02 2.50e+03 pdb="HH22 ARG D 412 " -0.089 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 230 " 0.143 2.00e-02 2.50e+03 1.42e-01 3.04e+02 pdb=" CG ASN B 230 " -0.061 2.00e-02 2.50e+03 pdb=" OD1 ASN B 230 " -0.085 2.00e-02 2.50e+03 pdb=" ND2 ASN B 230 " -0.160 2.00e-02 2.50e+03 pdb="HD21 ASN B 230 " -0.078 2.00e-02 2.50e+03 pdb="HD22 ASN B 230 " 0.242 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 412 " -0.419 9.50e-02 1.11e+02 1.74e-01 2.66e+02 pdb=" NE ARG A 412 " -0.073 2.00e-02 2.50e+03 pdb=" CZ ARG A 412 " -0.039 2.00e-02 2.50e+03 pdb=" NH1 ARG A 412 " -0.074 2.00e-02 2.50e+03 pdb=" NH2 ARG A 412 " 0.018 2.00e-02 2.50e+03 pdb="HH11 ARG A 412 " 0.234 2.00e-02 2.50e+03 pdb="HH12 ARG A 412 " -0.158 2.00e-02 2.50e+03 pdb="HH21 ARG A 412 " 0.047 2.00e-02 2.50e+03 pdb="HH22 ARG A 412 " 0.064 2.00e-02 2.50e+03 ... (remaining 9021 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 4958 2.19 - 2.79: 115862 2.79 - 3.39: 188097 3.39 - 4.00: 259390 4.00 - 4.60: 374343 Nonbonded interactions: 942650 Sorted by model distance: nonbonded pdb=" HG1 THR D 159 " pdb=" O1B ATP D 603 " model vdw 1.587 1.850 nonbonded pdb=" HG SER D 140 " pdb=" O2G GTP D 602 " model vdw 1.604 1.850 nonbonded pdb=" HG SER E 140 " pdb=" O2G GTP E 602 " model vdw 1.604 1.850 nonbonded pdb=" HG SER H 140 " pdb=" O1G GTP H 602 " model vdw 1.605 1.850 nonbonded pdb=" HG1 THR F 159 " pdb=" O1B ATP F 603 " model vdw 1.608 1.850 ... (remaining 942645 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: 1.300 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: 0.670 Extract box with map and model: 8.340 Check model and map are aligned: 0.650 Set scattering table: 0.400 Process input model: 152.150 Find NCS groups from input model: 2.290 Set up NCS constraints: 0.310 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:11.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 177.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 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 0.237 31096 Z= 0.830 Angle : 2.031 23.065 42200 Z= 1.299 Chirality : 0.110 1.542 4872 Planarity : 0.017 0.161 5248 Dihedral : 19.280 172.571 11744 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 1.16 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.18 % Favored : 95.64 % Rotamer: Outliers : 1.84 % Allowed : 5.19 % Favored : 92.97 % Cbeta Deviations : 0.76 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -0.50 (0.12), residues: 3896 helix: -0.43 (0.12), residues: 1504 sheet: -1.14 (0.29), residues: 296 loop : 0.04 (0.13), residues: 2096 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.014 0.004 HIS A 466 PHE 0.099 0.017 PHE F 357 TYR 0.126 0.025 TYR H 459 ARG 0.012 0.002 ARG H 512 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 868 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 809 time to evaluate : 3.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 LEU cc_start: 0.9180 (mt) cc_final: 0.8976 (mt) REVERT: A 129 ASP cc_start: 0.7155 (m-30) cc_final: 0.6884 (m-30) REVERT: A 140 SER cc_start: 0.7958 (t) cc_final: 0.7682 (t) REVERT: A 206 LYS cc_start: 0.8234 (mmtm) cc_final: 0.7972 (mmmt) REVERT: A 385 MET cc_start: 0.9047 (ttm) cc_final: 0.8830 (ttm) REVERT: A 399 GLU cc_start: 0.6824 (mp0) cc_final: 0.6377 (tm-30) REVERT: A 410 LYS cc_start: 0.7700 (tptt) cc_final: 0.6436 (pttp) REVERT: A 447 ILE cc_start: 0.8370 (mm) cc_final: 0.8097 (mm) REVERT: B 102 ASN cc_start: 0.8676 (t0) cc_final: 0.8451 (t0) REVERT: B 129 ASP cc_start: 0.7149 (m-30) cc_final: 0.6862 (m-30) REVERT: B 206 LYS cc_start: 0.8298 (mmtm) cc_final: 0.7959 (mmmt) REVERT: B 322 ARG cc_start: 0.9125 (OUTLIER) cc_final: 0.7204 (ttm170) REVERT: B 325 MET cc_start: 0.9001 (ttt) cc_final: 0.8740 (ttt) REVERT: B 399 GLU cc_start: 0.6914 (mp0) cc_final: 0.6440 (tm-30) REVERT: B 492 LYS cc_start: 0.8685 (mtmt) cc_final: 0.8478 (mtpp) REVERT: B 493 ARG cc_start: 0.8630 (mtp180) cc_final: 0.8405 (mtp180) REVERT: B 509 TYR cc_start: 0.7806 (p90) cc_final: 0.7507 (p90) REVERT: C 102 ASN cc_start: 0.8664 (t0) cc_final: 0.8425 (t0) REVERT: C 129 ASP cc_start: 0.7255 (m-30) cc_final: 0.6954 (m-30) REVERT: C 201 LEU cc_start: 0.8588 (tp) cc_final: 0.8364 (tp) REVERT: C 206 LYS cc_start: 0.8265 (mmtm) cc_final: 0.7997 (mmtt) REVERT: C 322 ARG cc_start: 0.9142 (OUTLIER) cc_final: 0.7217 (ttm170) REVERT: C 325 MET cc_start: 0.9017 (ttt) cc_final: 0.8749 (ttt) REVERT: C 385 MET cc_start: 0.9030 (ttm) cc_final: 0.8822 (ttm) REVERT: C 399 GLU cc_start: 0.6904 (mp0) cc_final: 0.6298 (tm-30) REVERT: C 410 LYS cc_start: 0.7611 (tptt) cc_final: 0.6203 (pttp) REVERT: C 437 VAL cc_start: 0.6039 (OUTLIER) cc_final: 0.5803 (p) REVERT: C 447 ILE cc_start: 0.8156 (mm) cc_final: 0.7848 (mp) REVERT: D 18 LEU cc_start: 0.9169 (mt) cc_final: 0.8966 (mt) REVERT: D 102 ASN cc_start: 0.8566 (t0) cc_final: 0.8243 (t0) REVERT: D 129 ASP cc_start: 0.7277 (m-30) cc_final: 0.7052 (m-30) REVERT: D 134 LYS cc_start: 0.7982 (tmtm) cc_final: 0.7746 (tmtm) REVERT: D 206 LYS cc_start: 0.8308 (mmtm) cc_final: 0.8078 (mmtt) REVERT: D 322 ARG cc_start: 0.9128 (OUTLIER) cc_final: 0.7128 (ttm170) REVERT: D 325 MET cc_start: 0.9032 (ttt) cc_final: 0.8777 (ttt) REVERT: D 399 GLU cc_start: 0.6758 (mp0) cc_final: 0.6427 (tm-30) REVERT: D 410 LYS cc_start: 0.7609 (tptt) cc_final: 0.6489 (pttp) REVERT: D 447 ILE cc_start: 0.8350 (mm) cc_final: 0.7975 (mp) REVERT: D 493 ARG cc_start: 0.8638 (mtp180) cc_final: 0.8415 (mtp180) REVERT: D 510 GLU cc_start: 0.6718 (mt-10) cc_final: 0.6413 (mt-10) REVERT: E 18 LEU cc_start: 0.9193 (mt) cc_final: 0.8974 (mt) REVERT: E 129 ASP cc_start: 0.7095 (m-30) cc_final: 0.6865 (m-30) REVERT: E 201 LEU cc_start: 0.8624 (tp) cc_final: 0.8420 (tp) REVERT: E 206 LYS cc_start: 0.8298 (mmtm) cc_final: 0.8047 (mmmt) REVERT: E 242 LYS cc_start: 0.8892 (mmtt) cc_final: 0.8674 (mmtp) REVERT: E 322 ARG cc_start: 0.9161 (OUTLIER) cc_final: 0.7235 (ttm170) REVERT: E 325 MET cc_start: 0.9008 (ttt) cc_final: 0.8736 (ttt) REVERT: E 368 GLN cc_start: 0.7827 (mt0) cc_final: 0.7577 (mt0) REVERT: E 399 GLU cc_start: 0.6713 (mp0) cc_final: 0.6444 (tm-30) REVERT: E 410 LYS cc_start: 0.7735 (mptt) cc_final: 0.6634 (pttp) REVERT: E 447 ILE cc_start: 0.8319 (mm) cc_final: 0.8025 (mm) REVERT: E 509 TYR cc_start: 0.7876 (p90) cc_final: 0.7589 (p90) REVERT: E 510 GLU cc_start: 0.6685 (mt-10) cc_final: 0.6462 (mt-10) REVERT: F 18 LEU cc_start: 0.9190 (mt) cc_final: 0.8987 (mt) REVERT: F 102 ASN cc_start: 0.8678 (t0) cc_final: 0.8316 (t0) REVERT: F 129 ASP cc_start: 0.7325 (m-30) cc_final: 0.7002 (m-30) REVERT: F 201 LEU cc_start: 0.8583 (tp) cc_final: 0.8331 (tp) REVERT: F 206 LYS cc_start: 0.8332 (mmtm) cc_final: 0.8040 (mmtt) REVERT: F 228 LYS cc_start: 0.8075 (mtpp) cc_final: 0.7862 (mtpm) REVERT: F 322 ARG cc_start: 0.9168 (OUTLIER) cc_final: 0.7274 (ttm170) REVERT: F 325 MET cc_start: 0.8987 (ttt) cc_final: 0.8734 (ttt) REVERT: F 410 LYS cc_start: 0.7880 (mptt) cc_final: 0.6270 (pttp) REVERT: F 447 ILE cc_start: 0.8396 (mm) cc_final: 0.8174 (mm) REVERT: G 18 LEU cc_start: 0.9181 (mt) cc_final: 0.8965 (mt) REVERT: G 102 ASN cc_start: 0.8530 (t0) cc_final: 0.8241 (t0) REVERT: G 129 ASP cc_start: 0.7245 (m-30) cc_final: 0.6999 (m-30) REVERT: G 201 LEU cc_start: 0.8565 (tp) cc_final: 0.8346 (tp) REVERT: G 206 LYS cc_start: 0.8274 (mmtm) cc_final: 0.8001 (mmmt) REVERT: G 322 ARG cc_start: 0.9097 (OUTLIER) cc_final: 0.7177 (ttm170) REVERT: G 325 MET cc_start: 0.9011 (ttt) cc_final: 0.8755 (ttt) REVERT: G 399 GLU cc_start: 0.6843 (mp0) cc_final: 0.6362 (tm-30) REVERT: G 410 LYS cc_start: 0.7879 (mptt) cc_final: 0.6395 (pttp) REVERT: G 446 SER cc_start: 0.8789 (p) cc_final: 0.8576 (p) REVERT: G 447 ILE cc_start: 0.8347 (mm) cc_final: 0.8039 (mm) REVERT: H 82 MET cc_start: 0.9247 (mmm) cc_final: 0.9008 (mmm) REVERT: H 102 ASN cc_start: 0.8591 (t0) cc_final: 0.8321 (t0) REVERT: H 129 ASP cc_start: 0.7312 (m-30) cc_final: 0.7102 (m-30) REVERT: H 201 LEU cc_start: 0.8625 (tp) cc_final: 0.8384 (tp) REVERT: H 206 LYS cc_start: 0.8320 (mmtm) cc_final: 0.8053 (mmmt) REVERT: H 242 LYS cc_start: 0.8927 (mmtt) cc_final: 0.8709 (mmtp) REVERT: H 253 ARG cc_start: 0.6100 (mmt180) cc_final: 0.5392 (mtt-85) REVERT: H 322 ARG cc_start: 0.9174 (OUTLIER) cc_final: 0.7229 (ttm170) REVERT: H 325 MET cc_start: 0.9038 (ttt) cc_final: 0.8789 (ttt) REVERT: H 399 GLU cc_start: 0.6856 (mp0) cc_final: 0.6242 (tm-30) REVERT: H 410 LYS cc_start: 0.7819 (tptt) cc_final: 0.6513 (pttp) REVERT: H 496 SER cc_start: 0.8331 (m) cc_final: 0.8097 (m) outliers start: 59 outliers final: 27 residues processed: 844 average time/residue: 2.6165 time to fit residues: 2606.7810 Evaluate side-chains 747 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 712 time to evaluate : 3.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 337 MET Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 322 ARG Chi-restraints excluded: chain C residue 337 MET Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 322 ARG Chi-restraints excluded: chain D residue 337 MET Chi-restraints excluded: chain D residue 339 CYS Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 322 ARG Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 322 ARG Chi-restraints excluded: chain F residue 337 MET Chi-restraints excluded: chain F residue 437 VAL Chi-restraints excluded: chain G residue 152 SER Chi-restraints excluded: chain G residue 172 THR Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 322 ARG Chi-restraints excluded: chain G residue 337 MET Chi-restraints excluded: chain H residue 164 ASP Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 322 ARG Chi-restraints excluded: chain H residue 339 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 331 optimal weight: 0.8980 chunk 297 optimal weight: 0.8980 chunk 164 optimal weight: 0.8980 chunk 101 optimal weight: 0.7980 chunk 200 optimal weight: 0.9990 chunk 158 optimal weight: 0.9990 chunk 307 optimal weight: 1.9990 chunk 118 optimal weight: 0.7980 chunk 186 optimal weight: 0.8980 chunk 228 optimal weight: 2.9990 chunk 355 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN A 441 GLN B 202 GLN B 283 GLN C 303 ASN D 202 GLN E 94 ASN ** E 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 303 ASN F 21 GLN F 94 ASN F 112 GLN F 198 ASN F 243 GLN F 303 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 31096 Z= 0.205 Angle : 0.670 10.719 42200 Z= 0.346 Chirality : 0.062 1.586 4872 Planarity : 0.005 0.048 5248 Dihedral : 20.264 179.501 4858 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.77 % Favored : 97.18 % Rotamer: Outliers : 3.09 % Allowed : 10.06 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 0.01 (0.13), residues: 3896 helix: 0.31 (0.13), residues: 1512 sheet: -0.41 (0.25), residues: 408 loop : 0.01 (0.13), residues: 1976 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS B 92 PHE 0.015 0.002 PHE A 24 TYR 0.019 0.002 TYR A 282 ARG 0.006 0.001 ARG G 474 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 868 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 769 time to evaluate : 3.458 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: A 129 ASP cc_start: 0.7174 (m-30) cc_final: 0.6945 (m-30) REVERT: A 140 SER cc_start: 0.8148 (t) cc_final: 0.7868 (t) REVERT: A 202 GLN cc_start: 0.7958 (mt0) cc_final: 0.7706 (mt0) REVERT: A 399 GLU cc_start: 0.6887 (mp0) cc_final: 0.6334 (tm-30) REVERT: A 410 LYS cc_start: 0.7465 (tptt) cc_final: 0.6193 (pttp) REVERT: B 34 ASP cc_start: 0.8692 (m-30) cc_final: 0.8440 (m-30) REVERT: B 206 LYS cc_start: 0.8305 (mmtm) cc_final: 0.8082 (mmmt) REVERT: B 322 ARG cc_start: 0.9106 (OUTLIER) cc_final: 0.7326 (ttm170) REVERT: B 325 MET cc_start: 0.8933 (ttt) cc_final: 0.8702 (ttt) REVERT: B 399 GLU cc_start: 0.6839 (mp0) cc_final: 0.6144 (tm-30) REVERT: B 410 LYS cc_start: 0.7505 (tptt) cc_final: 0.6091 (pttp) REVERT: B 495 MET cc_start: 0.6742 (OUTLIER) cc_final: 0.6390 (tmm) REVERT: B 510 GLU cc_start: 0.6304 (mt-10) cc_final: 0.5951 (mt-10) REVERT: C 34 ASP cc_start: 0.8694 (m-30) cc_final: 0.8182 (m-30) REVERT: C 129 ASP cc_start: 0.7276 (m-30) cc_final: 0.6971 (m-30) REVERT: C 203 ARG cc_start: 0.7306 (OUTLIER) cc_final: 0.7084 (mtm110) REVERT: C 206 LYS cc_start: 0.8297 (mmtm) cc_final: 0.8083 (mmtt) REVERT: C 322 ARG cc_start: 0.8919 (OUTLIER) cc_final: 0.7017 (ttm170) REVERT: C 325 MET cc_start: 0.8899 (ttt) cc_final: 0.8690 (ttt) REVERT: C 399 GLU cc_start: 0.6852 (mp0) cc_final: 0.6201 (tm-30) REVERT: C 410 LYS cc_start: 0.7460 (tptt) cc_final: 0.6041 (pttp) REVERT: C 420 MET cc_start: 0.7556 (mtp) cc_final: 0.7351 (mtm) REVERT: C 454 GLN cc_start: 0.8323 (mt0) cc_final: 0.8075 (mt0) REVERT: D 206 LYS cc_start: 0.8372 (mmtm) cc_final: 0.8144 (mmtt) REVERT: D 322 ARG cc_start: 0.9129 (OUTLIER) cc_final: 0.7347 (ttm170) REVERT: D 325 MET cc_start: 0.8966 (ttt) cc_final: 0.8741 (ttt) REVERT: D 399 GLU cc_start: 0.6845 (mp0) cc_final: 0.6333 (tm-30) REVERT: D 410 LYS cc_start: 0.7325 (tptt) cc_final: 0.6201 (pttp) REVERT: D 510 GLU cc_start: 0.6491 (mt-10) cc_final: 0.6197 (mt-10) REVERT: E 34 ASP cc_start: 0.8738 (m-30) cc_final: 0.8430 (m-30) REVERT: E 322 ARG cc_start: 0.8907 (OUTLIER) cc_final: 0.7017 (ttm170) REVERT: E 325 MET cc_start: 0.8942 (ttt) cc_final: 0.8723 (ttt) REVERT: E 399 GLU cc_start: 0.6679 (mp0) cc_final: 0.6212 (tm-30) REVERT: E 410 LYS cc_start: 0.7501 (mptt) cc_final: 0.6325 (pttp) REVERT: E 420 MET cc_start: 0.7776 (mtp) cc_final: 0.7540 (mtt) REVERT: E 447 ILE cc_start: 0.8152 (mm) cc_final: 0.7858 (mm) REVERT: E 495 MET cc_start: 0.6799 (OUTLIER) cc_final: 0.6353 (tmm) REVERT: F 34 ASP cc_start: 0.8666 (m-30) cc_final: 0.8350 (m-30) REVERT: F 129 ASP cc_start: 0.7349 (m-30) cc_final: 0.7003 (m-30) REVERT: F 201 LEU cc_start: 0.8548 (tp) cc_final: 0.8334 (tp) REVERT: F 202 GLN cc_start: 0.7993 (mt0) cc_final: 0.7656 (mt0) REVERT: F 206 LYS cc_start: 0.8358 (mmtm) cc_final: 0.8131 (mmmt) REVERT: F 322 ARG cc_start: 0.9086 (OUTLIER) cc_final: 0.7155 (ttm170) REVERT: F 410 LYS cc_start: 0.7716 (mptt) cc_final: 0.6036 (pttp) REVERT: F 447 ILE cc_start: 0.8258 (mm) cc_final: 0.8002 (mm) REVERT: G 206 LYS cc_start: 0.8343 (mmtm) cc_final: 0.8105 (mmtt) REVERT: G 303 ASN cc_start: 0.6939 (OUTLIER) cc_final: 0.6538 (t0) REVERT: G 322 ARG cc_start: 0.9092 (OUTLIER) cc_final: 0.7352 (ttm170) REVERT: G 325 MET cc_start: 0.8924 (ttt) cc_final: 0.8693 (ttt) REVERT: G 399 GLU cc_start: 0.6732 (mp0) cc_final: 0.6171 (tm-30) REVERT: G 410 LYS cc_start: 0.7591 (mptt) cc_final: 0.6078 (pttp) REVERT: G 447 ILE cc_start: 0.8283 (mm) cc_final: 0.8037 (mm) REVERT: G 496 SER cc_start: 0.8249 (m) cc_final: 0.8017 (m) REVERT: H 134 LYS cc_start: 0.7906 (tmtm) cc_final: 0.7671 (tmtm) REVERT: H 201 LEU cc_start: 0.8551 (tp) cc_final: 0.8347 (tp) REVERT: H 202 GLN cc_start: 0.8009 (mt0) cc_final: 0.7677 (mt0) REVERT: H 215 CYS cc_start: 0.7329 (t) cc_final: 0.7059 (t) REVERT: H 253 ARG cc_start: 0.6011 (mmt180) cc_final: 0.5286 (mtt-85) REVERT: H 322 ARG cc_start: 0.9133 (OUTLIER) cc_final: 0.7206 (ttm170) REVERT: H 325 MET cc_start: 0.8986 (ttt) cc_final: 0.8769 (ttt) REVERT: H 399 GLU cc_start: 0.6852 (mp0) cc_final: 0.6142 (tm-30) REVERT: H 410 LYS cc_start: 0.7557 (tptt) cc_final: 0.6224 (pttp) REVERT: H 447 ILE cc_start: 0.8049 (mm) cc_final: 0.7830 (mm) REVERT: H 495 MET cc_start: 0.6768 (OUTLIER) cc_final: 0.6298 (tmm) outliers start: 99 outliers final: 39 residues processed: 807 average time/residue: 2.5554 time to fit residues: 2456.6209 Evaluate side-chains 766 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 715 time to evaluate : 3.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 495 MET Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 203 ARG Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 322 ARG Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain D residue 179 MET Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 322 ARG Chi-restraints excluded: chain D residue 337 MET Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 283 GLN Chi-restraints excluded: chain E residue 322 ARG Chi-restraints excluded: chain E residue 495 MET Chi-restraints excluded: chain F residue 164 ASP Chi-restraints excluded: chain F residue 179 MET Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 322 ARG Chi-restraints excluded: chain F residue 337 MET Chi-restraints excluded: chain F residue 437 VAL Chi-restraints excluded: chain G residue 152 SER Chi-restraints excluded: chain G residue 172 THR Chi-restraints excluded: chain G residue 179 MET Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 303 ASN Chi-restraints excluded: chain G residue 322 ARG Chi-restraints excluded: chain H residue 135 MET Chi-restraints excluded: chain H residue 164 ASP Chi-restraints excluded: chain H residue 179 MET Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 322 ARG Chi-restraints excluded: chain H residue 339 CYS Chi-restraints excluded: chain H residue 495 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 197 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 296 optimal weight: 0.3980 chunk 242 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 356 optimal weight: 3.9990 chunk 385 optimal weight: 0.9990 chunk 317 optimal weight: 1.9990 chunk 353 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 286 optimal weight: 5.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN B 198 ASN C 94 ASN D 94 ASN D 283 GLN D 441 GLN D 498 GLN E 94 ASN E 498 GLN F 94 ASN ** F 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 441 GLN F 498 GLN G 94 ASN G 498 GLN H 94 ASN H 303 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 31096 Z= 0.254 Angle : 0.632 10.825 42200 Z= 0.325 Chirality : 0.062 1.696 4872 Planarity : 0.005 0.058 5248 Dihedral : 19.723 179.197 4842 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.93 % Favored : 98.05 % Rotamer: Outliers : 2.66 % Allowed : 11.78 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.13), residues: 3896 helix: 0.34 (0.13), residues: 1560 sheet: -0.27 (0.25), residues: 408 loop : 0.06 (0.14), residues: 1928 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS G 504 PHE 0.015 0.002 PHE A 24 TYR 0.017 0.002 TYR A 282 ARG 0.008 0.001 ARG C 231 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 840 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 755 time to evaluate : 3.487 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: A 18 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8882 (mt) REVERT: A 140 SER cc_start: 0.8175 (t) cc_final: 0.7874 (t) REVERT: A 202 GLN cc_start: 0.7984 (mt0) cc_final: 0.7730 (mt0) REVERT: A 255 ASP cc_start: 0.7604 (p0) cc_final: 0.7387 (p0) REVERT: A 322 ARG cc_start: 0.8899 (OUTLIER) cc_final: 0.7019 (ttm170) REVERT: A 399 GLU cc_start: 0.6998 (mp0) cc_final: 0.6166 (tm-30) REVERT: A 410 LYS cc_start: 0.7408 (tptt) cc_final: 0.6192 (pttp) REVERT: A 447 ILE cc_start: 0.8257 (mm) cc_final: 0.7850 (mp) REVERT: A 495 MET cc_start: 0.6851 (OUTLIER) cc_final: 0.6391 (tmm) REVERT: B 129 ASP cc_start: 0.7414 (m-30) cc_final: 0.7206 (m-30) REVERT: B 206 LYS cc_start: 0.8328 (mmtm) cc_final: 0.8100 (mmmt) REVERT: B 303 ASN cc_start: 0.7408 (OUTLIER) cc_final: 0.6953 (t0) REVERT: B 322 ARG cc_start: 0.9121 (OUTLIER) cc_final: 0.7293 (ttm170) REVERT: B 410 LYS cc_start: 0.7533 (tptt) cc_final: 0.6164 (pttp) REVERT: B 510 GLU cc_start: 0.6436 (mt-10) cc_final: 0.6141 (mt-10) REVERT: C 18 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8893 (mt) REVERT: C 180 THR cc_start: 0.8345 (m) cc_final: 0.8111 (m) REVERT: C 205 LYS cc_start: 0.8281 (mttp) cc_final: 0.7996 (mttt) REVERT: C 206 LYS cc_start: 0.8269 (mmtm) cc_final: 0.8044 (mmmt) REVERT: C 225 THR cc_start: 0.8896 (m) cc_final: 0.8661 (m) REVERT: C 322 ARG cc_start: 0.8920 (OUTLIER) cc_final: 0.7040 (ttm170) REVERT: C 410 LYS cc_start: 0.7519 (tptt) cc_final: 0.6026 (pttp) REVERT: C 441 GLN cc_start: 0.7221 (OUTLIER) cc_final: 0.6939 (mm110) REVERT: C 454 GLN cc_start: 0.8384 (mt0) cc_final: 0.8120 (mt0) REVERT: C 510 GLU cc_start: 0.6696 (mt-10) cc_final: 0.6385 (mt-10) REVERT: D 18 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8880 (mt) REVERT: D 206 LYS cc_start: 0.8336 (mmtm) cc_final: 0.8096 (mmmt) REVERT: D 303 ASN cc_start: 0.7381 (OUTLIER) cc_final: 0.7010 (t0) REVERT: D 322 ARG cc_start: 0.9140 (OUTLIER) cc_final: 0.7262 (ttm170) REVERT: D 399 GLU cc_start: 0.6908 (mp0) cc_final: 0.6107 (tm-30) REVERT: D 410 LYS cc_start: 0.7213 (tptt) cc_final: 0.6163 (pttp) REVERT: D 447 ILE cc_start: 0.8251 (mm) cc_final: 0.7899 (mp) REVERT: D 454 GLN cc_start: 0.8380 (mt0) cc_final: 0.8078 (mt0) REVERT: D 510 GLU cc_start: 0.6635 (mt-10) cc_final: 0.6392 (mt-10) REVERT: E 18 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8878 (mt) REVERT: E 322 ARG cc_start: 0.8922 (OUTLIER) cc_final: 0.7042 (ttm170) REVERT: E 399 GLU cc_start: 0.6900 (mp0) cc_final: 0.6125 (tm-30) REVERT: E 410 LYS cc_start: 0.7564 (mptt) cc_final: 0.6387 (pttp) REVERT: E 447 ILE cc_start: 0.8240 (mm) cc_final: 0.7925 (mm) REVERT: E 454 GLN cc_start: 0.8370 (mt0) cc_final: 0.8093 (mt0) REVERT: E 509 TYR cc_start: 0.7902 (p90) cc_final: 0.7623 (p90) REVERT: F 18 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8877 (mt) REVERT: F 129 ASP cc_start: 0.7356 (m-30) cc_final: 0.7040 (m-30) REVERT: F 202 GLN cc_start: 0.8021 (mt0) cc_final: 0.7670 (mt0) REVERT: F 206 LYS cc_start: 0.8314 (mmtm) cc_final: 0.8074 (mmmt) REVERT: F 255 ASP cc_start: 0.7678 (p0) cc_final: 0.7371 (p0) REVERT: F 322 ARG cc_start: 0.9013 (OUTLIER) cc_final: 0.7167 (ttm170) REVERT: F 410 LYS cc_start: 0.7736 (mptt) cc_final: 0.6118 (pttp) REVERT: F 447 ILE cc_start: 0.8372 (mm) cc_final: 0.8049 (mm) REVERT: F 454 GLN cc_start: 0.8263 (mt0) cc_final: 0.8051 (mt0) REVERT: F 495 MET cc_start: 0.6741 (OUTLIER) cc_final: 0.6307 (tmm) REVERT: F 510 GLU cc_start: 0.6358 (mt-10) cc_final: 0.6151 (mt-10) REVERT: G 18 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8887 (mt) REVERT: G 206 LYS cc_start: 0.8275 (mmtm) cc_final: 0.8053 (mmmt) REVERT: G 225 THR cc_start: 0.8917 (m) cc_final: 0.8688 (m) REVERT: G 303 ASN cc_start: 0.7319 (OUTLIER) cc_final: 0.6881 (t0) REVERT: G 322 ARG cc_start: 0.9131 (OUTLIER) cc_final: 0.7303 (ttm170) REVERT: G 399 GLU cc_start: 0.6914 (mp0) cc_final: 0.6180 (tm-30) REVERT: G 410 LYS cc_start: 0.7722 (mptt) cc_final: 0.6268 (pttp) REVERT: G 447 ILE cc_start: 0.8334 (mm) cc_final: 0.7919 (mp) REVERT: G 454 GLN cc_start: 0.8454 (mt0) cc_final: 0.8158 (mt0) REVERT: H 202 GLN cc_start: 0.8017 (mt0) cc_final: 0.7673 (mt0) REVERT: H 206 LYS cc_start: 0.8239 (mmtt) cc_final: 0.7916 (mmmt) REVERT: H 253 ARG cc_start: 0.6161 (mmt180) cc_final: 0.5404 (mtt-85) REVERT: H 322 ARG cc_start: 0.9125 (OUTLIER) cc_final: 0.7182 (ttm170) REVERT: H 399 GLU cc_start: 0.6976 (mp0) cc_final: 0.5973 (tm-30) REVERT: H 410 LYS cc_start: 0.7567 (tptt) cc_final: 0.6256 (pttp) REVERT: H 447 ILE cc_start: 0.8144 (mm) cc_final: 0.7852 (mm) REVERT: H 454 GLN cc_start: 0.8324 (mt0) cc_final: 0.8091 (mt0) REVERT: H 510 GLU cc_start: 0.6365 (mt-10) cc_final: 0.6110 (mt-10) outliers start: 85 outliers final: 35 residues processed: 793 average time/residue: 2.6100 time to fit residues: 2454.6779 Evaluate side-chains 784 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 729 time to evaluate : 3.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 322 ARG Chi-restraints excluded: chain A residue 495 MET Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 303 ASN Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 135 MET Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 322 ARG Chi-restraints excluded: chain C residue 441 GLN Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 135 MET Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 303 ASN Chi-restraints excluded: chain D residue 322 ARG Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 322 ARG Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 283 GLN Chi-restraints excluded: chain F residue 322 ARG Chi-restraints excluded: chain F residue 337 MET Chi-restraints excluded: chain F residue 437 VAL Chi-restraints excluded: chain F residue 495 MET Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 152 SER Chi-restraints excluded: chain G residue 170 ASP Chi-restraints excluded: chain G residue 172 THR Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 303 ASN Chi-restraints excluded: chain G residue 322 ARG Chi-restraints excluded: chain H residue 163 ILE Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 322 ARG Chi-restraints excluded: chain H residue 446 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 352 optimal weight: 1.9990 chunk 268 optimal weight: 3.9990 chunk 185 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 170 optimal weight: 3.9990 chunk 239 optimal weight: 0.9980 chunk 357 optimal weight: 4.9990 chunk 378 optimal weight: 0.9980 chunk 186 optimal weight: 0.9980 chunk 339 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 198 ASN D 94 ASN D 198 ASN D 283 GLN E 94 ASN E 368 GLN F 94 ASN ** F 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN H 94 ASN ** H 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 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 : 0.004 0.042 31096 Z= 0.244 Angle : 0.602 10.923 42200 Z= 0.306 Chirality : 0.061 1.692 4872 Planarity : 0.005 0.050 5248 Dihedral : 19.524 176.973 4833 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.52 % Favored : 97.46 % Rotamer: Outliers : 2.66 % Allowed : 12.97 % Favored : 84.38 % 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: 0.18 (0.13), residues: 3896 helix: 0.45 (0.13), residues: 1568 sheet: -0.24 (0.25), residues: 408 loop : 0.09 (0.14), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 504 PHE 0.013 0.001 PHE A 24 TYR 0.017 0.002 TYR A 282 ARG 0.008 0.001 ARG B 231 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 803 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 718 time to evaluate : 3.469 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 18 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8884 (mp) REVERT: A 129 ASP cc_start: 0.7457 (m-30) cc_final: 0.7247 (m-30) REVERT: A 140 SER cc_start: 0.8199 (t) cc_final: 0.7903 (t) REVERT: A 202 GLN cc_start: 0.7978 (mt0) cc_final: 0.7733 (mt0) REVERT: A 255 ASP cc_start: 0.7651 (p0) cc_final: 0.7391 (p0) REVERT: A 322 ARG cc_start: 0.8912 (OUTLIER) cc_final: 0.7067 (ttm170) REVERT: A 410 LYS cc_start: 0.7562 (tptt) cc_final: 0.6250 (pttp) REVERT: A 447 ILE cc_start: 0.8294 (mm) cc_final: 0.7954 (mp) REVERT: A 495 MET cc_start: 0.6884 (OUTLIER) cc_final: 0.6397 (tmm) REVERT: B 18 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8868 (mt) REVERT: B 201 LEU cc_start: 0.8546 (tp) cc_final: 0.8329 (tp) REVERT: B 206 LYS cc_start: 0.8320 (mmtm) cc_final: 0.8074 (mmmt) REVERT: B 303 ASN cc_start: 0.7356 (OUTLIER) cc_final: 0.6956 (t0) REVERT: B 322 ARG cc_start: 0.9114 (OUTLIER) cc_final: 0.7288 (ttm170) REVERT: B 399 GLU cc_start: 0.6997 (mp0) cc_final: 0.6134 (tm-30) REVERT: B 410 LYS cc_start: 0.7391 (tptt) cc_final: 0.6025 (pttp) REVERT: B 495 MET cc_start: 0.6754 (OUTLIER) cc_final: 0.6219 (tmm) REVERT: B 510 GLU cc_start: 0.6448 (mt-10) cc_final: 0.6215 (mt-10) REVERT: C 18 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8908 (mp) REVERT: C 132 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.6738 (tm-30) REVERT: C 205 LYS cc_start: 0.8222 (mttp) cc_final: 0.8013 (mttt) REVERT: C 206 LYS cc_start: 0.8249 (mmtm) cc_final: 0.8035 (mmmt) REVERT: C 225 THR cc_start: 0.8911 (m) cc_final: 0.8667 (m) REVERT: C 322 ARG cc_start: 0.8955 (OUTLIER) cc_final: 0.7098 (ttm170) REVERT: C 410 LYS cc_start: 0.7591 (tptt) cc_final: 0.6075 (pttp) REVERT: C 416 SER cc_start: 0.8204 (t) cc_final: 0.7715 (m) REVERT: C 441 GLN cc_start: 0.7173 (OUTLIER) cc_final: 0.6885 (mm110) REVERT: C 447 ILE cc_start: 0.8068 (mm) cc_final: 0.7753 (mp) REVERT: C 454 GLN cc_start: 0.8408 (mt0) cc_final: 0.8096 (mt0) REVERT: C 495 MET cc_start: 0.6762 (OUTLIER) cc_final: 0.6260 (tmm) REVERT: C 510 GLU cc_start: 0.6773 (mt-10) cc_final: 0.6534 (mt-10) REVERT: D 13 VAL cc_start: 0.8709 (p) cc_final: 0.8435 (t) REVERT: D 18 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8913 (mp) REVERT: D 201 LEU cc_start: 0.8571 (tp) cc_final: 0.8362 (tp) REVERT: D 206 LYS cc_start: 0.8337 (mmtm) cc_final: 0.8090 (mmmt) REVERT: D 303 ASN cc_start: 0.7468 (OUTLIER) cc_final: 0.7166 (t0) REVERT: D 322 ARG cc_start: 0.9129 (OUTLIER) cc_final: 0.7261 (ttm170) REVERT: D 399 GLU cc_start: 0.6930 (mp0) cc_final: 0.6096 (tm-30) REVERT: D 410 LYS cc_start: 0.7317 (tptt) cc_final: 0.6248 (pttp) REVERT: D 447 ILE cc_start: 0.8288 (mm) cc_final: 0.7961 (mp) REVERT: D 454 GLN cc_start: 0.8486 (mt0) cc_final: 0.8185 (mt0) REVERT: E 18 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8889 (mp) REVERT: E 322 ARG cc_start: 0.8969 (OUTLIER) cc_final: 0.7103 (ttm170) REVERT: E 399 GLU cc_start: 0.6916 (mp0) cc_final: 0.6111 (tm-30) REVERT: E 410 LYS cc_start: 0.7524 (mptt) cc_final: 0.6332 (pttp) REVERT: E 447 ILE cc_start: 0.8260 (mm) cc_final: 0.7955 (mm) REVERT: E 454 GLN cc_start: 0.8392 (mt0) cc_final: 0.8084 (mt0) REVERT: E 495 MET cc_start: 0.6843 (OUTLIER) cc_final: 0.6316 (tmm) REVERT: E 509 TYR cc_start: 0.7928 (p90) cc_final: 0.7634 (p90) REVERT: F 129 ASP cc_start: 0.7312 (m-30) cc_final: 0.6976 (m-30) REVERT: F 202 GLN cc_start: 0.8030 (mt0) cc_final: 0.7681 (mt0) REVERT: F 206 LYS cc_start: 0.8305 (mmtm) cc_final: 0.8071 (mmmt) REVERT: F 255 ASP cc_start: 0.7606 (p0) cc_final: 0.7323 (p0) REVERT: F 322 ARG cc_start: 0.8969 (OUTLIER) cc_final: 0.7121 (ttm170) REVERT: F 410 LYS cc_start: 0.7862 (mptt) cc_final: 0.6197 (pttp) REVERT: F 447 ILE cc_start: 0.8318 (mm) cc_final: 0.8011 (mm) REVERT: F 454 GLN cc_start: 0.8326 (mt0) cc_final: 0.8100 (mt0) REVERT: F 495 MET cc_start: 0.6790 (OUTLIER) cc_final: 0.6366 (tmm) REVERT: G 18 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8925 (mp) REVERT: G 206 LYS cc_start: 0.8274 (mmtm) cc_final: 0.8043 (mmmt) REVERT: G 225 THR cc_start: 0.8924 (m) cc_final: 0.8680 (m) REVERT: G 322 ARG cc_start: 0.9128 (OUTLIER) cc_final: 0.7301 (ttm170) REVERT: G 410 LYS cc_start: 0.7719 (mptt) cc_final: 0.6229 (pttp) REVERT: G 447 ILE cc_start: 0.8289 (mm) cc_final: 0.7996 (mm) REVERT: G 454 GLN cc_start: 0.8441 (mt0) cc_final: 0.8133 (mt0) REVERT: H 18 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8904 (mt) REVERT: H 202 GLN cc_start: 0.8000 (mt0) cc_final: 0.7662 (mt0) REVERT: H 206 LYS cc_start: 0.8295 (mmtt) cc_final: 0.8087 (mmmt) REVERT: H 253 ARG cc_start: 0.6139 (mmt180) cc_final: 0.5403 (mtt-85) REVERT: H 322 ARG cc_start: 0.9141 (OUTLIER) cc_final: 0.7246 (ttm170) REVERT: H 399 GLU cc_start: 0.7093 (mp0) cc_final: 0.6031 (tm-30) REVERT: H 410 LYS cc_start: 0.7420 (tptt) cc_final: 0.6135 (pttp) REVERT: H 447 ILE cc_start: 0.8178 (mm) cc_final: 0.7908 (mm) REVERT: H 454 GLN cc_start: 0.8372 (mt0) cc_final: 0.8106 (mt0) REVERT: H 510 GLU cc_start: 0.6411 (mt-10) cc_final: 0.6197 (mt-10) outliers start: 85 outliers final: 43 residues processed: 761 average time/residue: 2.7549 time to fit residues: 2519.4661 Evaluate side-chains 772 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 705 time to evaluate : 3.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 322 ARG Chi-restraints excluded: chain A residue 450 LYS Chi-restraints excluded: chain A residue 495 MET Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 303 ASN Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 337 MET Chi-restraints excluded: chain B residue 495 MET Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 322 ARG Chi-restraints excluded: chain C residue 441 GLN Chi-restraints excluded: chain C residue 495 MET Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 135 MET Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 303 ASN Chi-restraints excluded: chain D residue 322 ARG Chi-restraints excluded: chain D residue 339 CYS Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 322 ARG Chi-restraints excluded: chain E residue 495 MET Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 283 GLN Chi-restraints excluded: chain F residue 322 ARG Chi-restraints excluded: chain F residue 337 MET Chi-restraints excluded: chain F residue 437 VAL Chi-restraints excluded: chain F residue 450 LYS Chi-restraints excluded: chain F residue 495 MET Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 135 MET Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 172 THR Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 322 ARG Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 163 ILE Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 322 ARG Chi-restraints excluded: chain H residue 446 SER Chi-restraints excluded: chain H residue 450 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 315 optimal weight: 2.9990 chunk 215 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 282 optimal weight: 3.9990 chunk 156 optimal weight: 2.9990 chunk 323 optimal weight: 0.5980 chunk 261 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 chunk 193 optimal weight: 1.9990 chunk 340 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 198 ASN B 202 GLN B 283 GLN C 112 GLN D 94 ASN E 94 ASN E 198 ASN F 94 ASN ** F 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN H 94 ASN ** H 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 31096 Z= 0.291 Angle : 0.618 10.902 42200 Z= 0.315 Chirality : 0.062 1.692 4872 Planarity : 0.005 0.067 5248 Dihedral : 19.459 179.362 4830 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.93 % Favored : 97.05 % Rotamer: Outliers : 3.06 % Allowed : 13.59 % Favored : 83.34 % Cbeta Deviations : 0.00 % 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: 0.10 (0.13), residues: 3896 helix: 0.43 (0.13), residues: 1568 sheet: -0.30 (0.27), residues: 352 loop : -0.01 (0.14), residues: 1976 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 92 PHE 0.014 0.002 PHE A 24 TYR 0.018 0.002 TYR F 282 ARG 0.010 0.001 ARG C 231 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 805 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 707 time to evaluate : 3.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8880 (mp) REVERT: A 140 SER cc_start: 0.8209 (t) cc_final: 0.7901 (t) REVERT: A 202 GLN cc_start: 0.7982 (mt0) cc_final: 0.7737 (mt0) REVERT: A 255 ASP cc_start: 0.7573 (p0) cc_final: 0.7359 (p0) REVERT: A 322 ARG cc_start: 0.9003 (OUTLIER) cc_final: 0.7169 (ttm170) REVERT: A 410 LYS cc_start: 0.7644 (tptt) cc_final: 0.6246 (pttp) REVERT: A 447 ILE cc_start: 0.8311 (mm) cc_final: 0.7963 (mp) REVERT: A 495 MET cc_start: 0.6882 (OUTLIER) cc_final: 0.6356 (tmm) REVERT: B 18 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8845 (mt) REVERT: B 201 LEU cc_start: 0.8580 (tp) cc_final: 0.8367 (tp) REVERT: B 206 LYS cc_start: 0.8313 (mmtm) cc_final: 0.8068 (mmmt) REVERT: B 303 ASN cc_start: 0.7557 (OUTLIER) cc_final: 0.7156 (t0) REVERT: B 322 ARG cc_start: 0.9131 (OUTLIER) cc_final: 0.7303 (ttm170) REVERT: B 410 LYS cc_start: 0.7767 (tptt) cc_final: 0.6247 (pttp) REVERT: B 450 LYS cc_start: 0.7548 (mttm) cc_final: 0.7336 (ttmm) REVERT: B 495 MET cc_start: 0.6772 (OUTLIER) cc_final: 0.6221 (tmm) REVERT: B 510 GLU cc_start: 0.6453 (mt-10) cc_final: 0.6201 (mt-10) REVERT: C 18 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8896 (mp) REVERT: C 206 LYS cc_start: 0.8281 (mmtm) cc_final: 0.8078 (mmmt) REVERT: C 225 THR cc_start: 0.8945 (m) cc_final: 0.8690 (m) REVERT: C 322 ARG cc_start: 0.9059 (OUTLIER) cc_final: 0.7216 (ttm170) REVERT: C 410 LYS cc_start: 0.7727 (tptt) cc_final: 0.6125 (pttp) REVERT: C 416 SER cc_start: 0.8102 (t) cc_final: 0.7664 (m) REVERT: C 441 GLN cc_start: 0.7376 (OUTLIER) cc_final: 0.7004 (mm110) REVERT: C 447 ILE cc_start: 0.8118 (mm) cc_final: 0.7803 (mp) REVERT: C 454 GLN cc_start: 0.8396 (mt0) cc_final: 0.8093 (mt0) REVERT: C 495 MET cc_start: 0.6746 (OUTLIER) cc_final: 0.6233 (tmm) REVERT: C 510 GLU cc_start: 0.6737 (mt-10) cc_final: 0.6534 (mt-10) REVERT: D 13 VAL cc_start: 0.8725 (p) cc_final: 0.8471 (t) REVERT: D 18 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8884 (mp) REVERT: D 206 LYS cc_start: 0.8347 (mmtm) cc_final: 0.8097 (mmmt) REVERT: D 255 ASP cc_start: 0.7208 (p0) cc_final: 0.6992 (p0) REVERT: D 303 ASN cc_start: 0.7795 (OUTLIER) cc_final: 0.7509 (t0) REVERT: D 322 ARG cc_start: 0.9115 (OUTLIER) cc_final: 0.7148 (ttm170) REVERT: D 410 LYS cc_start: 0.7350 (tptt) cc_final: 0.6268 (pttp) REVERT: D 447 ILE cc_start: 0.8312 (mm) cc_final: 0.7989 (mp) REVERT: E 13 VAL cc_start: 0.8720 (p) cc_final: 0.8454 (t) REVERT: E 18 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8885 (mp) REVERT: E 322 ARG cc_start: 0.9070 (OUTLIER) cc_final: 0.7223 (ttm170) REVERT: E 410 LYS cc_start: 0.7694 (mptt) cc_final: 0.6387 (pttp) REVERT: E 447 ILE cc_start: 0.8308 (mm) cc_final: 0.7991 (mm) REVERT: E 454 GLN cc_start: 0.8461 (mt0) cc_final: 0.8159 (mt0) REVERT: E 495 MET cc_start: 0.6844 (OUTLIER) cc_final: 0.6329 (tmm) REVERT: F 13 VAL cc_start: 0.8735 (p) cc_final: 0.8460 (t) REVERT: F 18 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8893 (mp) REVERT: F 129 ASP cc_start: 0.7310 (m-30) cc_final: 0.6958 (m-30) REVERT: F 202 GLN cc_start: 0.8020 (mt0) cc_final: 0.7679 (mt0) REVERT: F 206 LYS cc_start: 0.8298 (mmtm) cc_final: 0.8075 (mmmt) REVERT: F 303 ASN cc_start: 0.6965 (OUTLIER) cc_final: 0.6580 (t0) REVERT: F 322 ARG cc_start: 0.8969 (OUTLIER) cc_final: 0.7026 (ttm170) REVERT: F 410 LYS cc_start: 0.7730 (mptt) cc_final: 0.6091 (pttp) REVERT: F 447 ILE cc_start: 0.8404 (mm) cc_final: 0.8106 (mm) REVERT: F 454 GLN cc_start: 0.8318 (mt0) cc_final: 0.8072 (mt0) REVERT: G 18 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8902 (mp) REVERT: G 206 LYS cc_start: 0.8251 (mmtm) cc_final: 0.8027 (mmmt) REVERT: G 303 ASN cc_start: 0.7709 (OUTLIER) cc_final: 0.7493 (t0) REVERT: G 322 ARG cc_start: 0.9140 (OUTLIER) cc_final: 0.7283 (ttm170) REVERT: G 410 LYS cc_start: 0.7764 (mptt) cc_final: 0.6268 (pttp) REVERT: G 447 ILE cc_start: 0.8317 (mm) cc_final: 0.8002 (mm) REVERT: G 450 LYS cc_start: 0.7878 (mtpm) cc_final: 0.7587 (ttmm) REVERT: H 18 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8865 (mt) REVERT: H 202 GLN cc_start: 0.7997 (mt0) cc_final: 0.7651 (mt0) REVERT: H 253 ARG cc_start: 0.6207 (mmt180) cc_final: 0.5447 (mtt-85) REVERT: H 322 ARG cc_start: 0.9142 (OUTLIER) cc_final: 0.7213 (ttm170) REVERT: H 410 LYS cc_start: 0.7593 (tptt) cc_final: 0.6173 (pttp) REVERT: H 447 ILE cc_start: 0.8257 (mm) cc_final: 0.7964 (mm) REVERT: H 454 GLN cc_start: 0.8397 (mt0) cc_final: 0.8133 (mt0) outliers start: 98 outliers final: 54 residues processed: 761 average time/residue: 2.6105 time to fit residues: 2350.8823 Evaluate side-chains 779 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 700 time to evaluate : 3.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 322 ARG Chi-restraints excluded: chain A residue 450 LYS Chi-restraints excluded: chain A residue 495 MET Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 303 ASN Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 495 MET Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 135 MET Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 322 ARG Chi-restraints excluded: chain C residue 441 GLN Chi-restraints excluded: chain C residue 495 MET Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 135 MET Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 303 ASN Chi-restraints excluded: chain D residue 322 ARG Chi-restraints excluded: chain D residue 339 CYS Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 322 ARG Chi-restraints excluded: chain E residue 495 MET Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 170 ASP Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 283 GLN Chi-restraints excluded: chain F residue 303 ASN Chi-restraints excluded: chain F residue 322 ARG Chi-restraints excluded: chain F residue 437 VAL Chi-restraints excluded: chain F residue 450 LYS Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 135 MET Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 170 ASP Chi-restraints excluded: chain G residue 172 THR Chi-restraints excluded: chain G residue 176 SER Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 303 ASN Chi-restraints excluded: chain G residue 322 ARG Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 163 ILE Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 264 THR Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 322 ARG Chi-restraints excluded: chain H residue 446 SER Chi-restraints excluded: chain H residue 450 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 127 optimal weight: 1.9990 chunk 341 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 222 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 379 optimal weight: 1.9990 chunk 314 optimal weight: 1.9990 chunk 175 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 chunk 199 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 198 ASN B 202 GLN D 94 ASN D 372 HIS E 94 ASN ** F 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 372 HIS ** H 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 31096 Z= 0.330 Angle : 0.632 11.111 42200 Z= 0.323 Chirality : 0.063 1.693 4872 Planarity : 0.005 0.080 5248 Dihedral : 19.481 179.496 4827 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.11 % Favored : 96.87 % Rotamer: Outliers : 2.94 % Allowed : 13.94 % Favored : 83.12 % 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: -0.00 (0.13), residues: 3896 helix: 0.37 (0.13), residues: 1568 sheet: -0.38 (0.27), residues: 352 loop : -0.09 (0.14), residues: 1976 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 92 PHE 0.016 0.002 PHE A 24 TYR 0.019 0.002 TYR A 282 ARG 0.013 0.001 ARG D 253 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 791 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 697 time to evaluate : 3.509 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 140 SER cc_start: 0.8218 (t) cc_final: 0.7893 (t) REVERT: A 202 GLN cc_start: 0.7949 (mt0) cc_final: 0.7708 (mt0) REVERT: A 322 ARG cc_start: 0.9068 (OUTLIER) cc_final: 0.7246 (ttm170) REVERT: A 368 GLN cc_start: 0.8151 (mt0) cc_final: 0.7813 (mt0) REVERT: A 410 LYS cc_start: 0.7680 (tptt) cc_final: 0.6256 (pttp) REVERT: A 447 ILE cc_start: 0.8332 (mm) cc_final: 0.7992 (mp) REVERT: A 495 MET cc_start: 0.6872 (OUTLIER) cc_final: 0.6335 (tmm) REVERT: B 18 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.8780 (mt) REVERT: B 201 LEU cc_start: 0.8582 (tp) cc_final: 0.8355 (tp) REVERT: B 206 LYS cc_start: 0.8293 (mmtm) cc_final: 0.8039 (mmmt) REVERT: B 322 ARG cc_start: 0.9112 (OUTLIER) cc_final: 0.7111 (ttm170) REVERT: B 355 ARG cc_start: 0.8688 (OUTLIER) cc_final: 0.8467 (ptt-90) REVERT: B 410 LYS cc_start: 0.7806 (tptt) cc_final: 0.6260 (pttp) REVERT: B 495 MET cc_start: 0.6774 (OUTLIER) cc_final: 0.6213 (tmm) REVERT: B 510 GLU cc_start: 0.6371 (mt-10) cc_final: 0.6166 (mt-10) REVERT: C 18 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8881 (mp) REVERT: C 202 GLN cc_start: 0.7978 (mt0) cc_final: 0.7702 (mt0) REVERT: C 206 LYS cc_start: 0.8320 (mmtm) cc_final: 0.8104 (mmmt) REVERT: C 322 ARG cc_start: 0.9072 (OUTLIER) cc_final: 0.7172 (ttm170) REVERT: C 410 LYS cc_start: 0.7847 (tptt) cc_final: 0.6192 (pttp) REVERT: C 416 SER cc_start: 0.8092 (t) cc_final: 0.7670 (m) REVERT: C 441 GLN cc_start: 0.7538 (OUTLIER) cc_final: 0.7087 (mm110) REVERT: C 447 ILE cc_start: 0.8214 (mm) cc_final: 0.7900 (mp) REVERT: C 454 GLN cc_start: 0.8404 (mt0) cc_final: 0.8065 (mt0) REVERT: C 495 MET cc_start: 0.6744 (OUTLIER) cc_final: 0.6224 (tmm) REVERT: D 13 VAL cc_start: 0.8720 (p) cc_final: 0.8476 (t) REVERT: D 18 LEU cc_start: 0.9203 (OUTLIER) cc_final: 0.8870 (mp) REVERT: D 206 LYS cc_start: 0.8332 (mmtm) cc_final: 0.8081 (mmmt) REVERT: D 255 ASP cc_start: 0.7459 (p0) cc_final: 0.7240 (p0) REVERT: D 303 ASN cc_start: 0.8077 (OUTLIER) cc_final: 0.7730 (t0) REVERT: D 311 LYS cc_start: 0.8938 (tttm) cc_final: 0.8733 (tttp) REVERT: D 322 ARG cc_start: 0.9123 (OUTLIER) cc_final: 0.7133 (ttm170) REVERT: D 410 LYS cc_start: 0.7407 (tptt) cc_final: 0.6291 (pttp) REVERT: D 447 ILE cc_start: 0.8285 (mm) cc_final: 0.7958 (mp) REVERT: D 450 LYS cc_start: 0.7773 (mttm) cc_final: 0.7546 (mtmm) REVERT: E 13 VAL cc_start: 0.8697 (p) cc_final: 0.8441 (t) REVERT: E 322 ARG cc_start: 0.9104 (OUTLIER) cc_final: 0.7237 (ttm170) REVERT: E 410 LYS cc_start: 0.7759 (mptt) cc_final: 0.6423 (pttp) REVERT: E 447 ILE cc_start: 0.8320 (mm) cc_final: 0.8010 (mm) REVERT: E 454 GLN cc_start: 0.8443 (mt0) cc_final: 0.8133 (mt0) REVERT: E 495 MET cc_start: 0.6844 (OUTLIER) cc_final: 0.6326 (tmm) REVERT: F 13 VAL cc_start: 0.8705 (p) cc_final: 0.8442 (t) REVERT: F 18 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8767 (mt) REVERT: F 132 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.6728 (tm-30) REVERT: F 206 LYS cc_start: 0.8297 (mmtm) cc_final: 0.8074 (mmmt) REVERT: F 283 GLN cc_start: 0.8996 (OUTLIER) cc_final: 0.8743 (tt0) REVERT: F 303 ASN cc_start: 0.7357 (OUTLIER) cc_final: 0.6930 (t0) REVERT: F 311 LYS cc_start: 0.8914 (tttm) cc_final: 0.8662 (tttp) REVERT: F 322 ARG cc_start: 0.9002 (OUTLIER) cc_final: 0.7058 (ttm170) REVERT: F 410 LYS cc_start: 0.7737 (mptt) cc_final: 0.6129 (pttp) REVERT: F 447 ILE cc_start: 0.8410 (mm) cc_final: 0.8115 (mm) REVERT: F 454 GLN cc_start: 0.8318 (mt0) cc_final: 0.8058 (mt0) REVERT: G 18 LEU cc_start: 0.9203 (OUTLIER) cc_final: 0.8883 (mp) REVERT: G 179 MET cc_start: 0.7599 (mtm) cc_final: 0.7341 (mtm) REVERT: G 206 LYS cc_start: 0.8269 (mmtm) cc_final: 0.8037 (mmmt) REVERT: G 303 ASN cc_start: 0.7806 (OUTLIER) cc_final: 0.7582 (t0) REVERT: G 322 ARG cc_start: 0.9131 (OUTLIER) cc_final: 0.7159 (ttm170) REVERT: G 410 LYS cc_start: 0.7813 (mptt) cc_final: 0.6325 (pttp) REVERT: G 447 ILE cc_start: 0.8372 (mm) cc_final: 0.8072 (mm) REVERT: H 18 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.8807 (mt) REVERT: H 202 GLN cc_start: 0.7990 (mt0) cc_final: 0.7664 (mt0) REVERT: H 253 ARG cc_start: 0.6182 (mmt180) cc_final: 0.5468 (mtt-85) REVERT: H 322 ARG cc_start: 0.9157 (OUTLIER) cc_final: 0.7224 (ttm170) REVERT: H 410 LYS cc_start: 0.7585 (tptt) cc_final: 0.6210 (pttp) REVERT: H 447 ILE cc_start: 0.8284 (mm) cc_final: 0.7973 (mm) REVERT: H 454 GLN cc_start: 0.8333 (mt0) cc_final: 0.8071 (mt0) outliers start: 94 outliers final: 58 residues processed: 751 average time/residue: 2.6428 time to fit residues: 2345.1680 Evaluate side-chains 776 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 693 time to evaluate : 3.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 322 ARG Chi-restraints excluded: chain A residue 495 MET Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 495 MET Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 135 MET Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 322 ARG Chi-restraints excluded: chain C residue 441 GLN Chi-restraints excluded: chain C residue 450 LYS Chi-restraints excluded: chain C residue 495 MET Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 135 MET Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 303 ASN Chi-restraints excluded: chain D residue 322 ARG Chi-restraints excluded: chain D residue 339 CYS Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 322 ARG Chi-restraints excluded: chain E residue 495 MET Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 170 ASP Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 283 GLN Chi-restraints excluded: chain F residue 303 ASN Chi-restraints excluded: chain F residue 322 ARG Chi-restraints excluded: chain F residue 437 VAL Chi-restraints excluded: chain F residue 450 LYS Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 135 MET Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 170 ASP Chi-restraints excluded: chain G residue 172 THR Chi-restraints excluded: chain G residue 176 SER Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 303 ASN Chi-restraints excluded: chain G residue 322 ARG Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 163 ILE Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 264 THR Chi-restraints excluded: chain H residue 268 VAL Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 322 ARG Chi-restraints excluded: chain H residue 446 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 365 optimal weight: 0.8980 chunk 42 optimal weight: 6.9990 chunk 216 optimal weight: 2.9990 chunk 276 optimal weight: 2.9990 chunk 214 optimal weight: 3.9990 chunk 319 optimal weight: 2.9990 chunk 211 optimal weight: 4.9990 chunk 377 optimal weight: 1.9990 chunk 236 optimal weight: 5.9990 chunk 230 optimal weight: 0.8980 chunk 174 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 198 ASN B 202 GLN B 303 ASN C 372 HIS D 33 ASN D 94 ASN E 94 ASN F 33 ASN ** F 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 372 HIS ** H 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 31096 Z= 0.326 Angle : 0.629 11.195 42200 Z= 0.320 Chirality : 0.062 1.693 4872 Planarity : 0.005 0.077 5248 Dihedral : 19.442 179.397 4825 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.26 % Favored : 96.71 % Rotamer: Outliers : 2.81 % Allowed : 14.62 % Favored : 82.56 % 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: -0.02 (0.13), residues: 3896 helix: 0.37 (0.13), residues: 1568 sheet: -0.37 (0.26), residues: 352 loop : -0.12 (0.14), residues: 1976 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 504 PHE 0.015 0.002 PHE A 24 TYR 0.020 0.002 TYR B 282 ARG 0.014 0.001 ARG G 253 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 777 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 687 time to evaluate : 3.489 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 132 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.6685 (tm-30) REVERT: A 140 SER cc_start: 0.8207 (t) cc_final: 0.7887 (t) REVERT: A 202 GLN cc_start: 0.7969 (mt0) cc_final: 0.7721 (mt0) REVERT: A 255 ASP cc_start: 0.7525 (p0) cc_final: 0.7284 (p0) REVERT: A 322 ARG cc_start: 0.9080 (OUTLIER) cc_final: 0.7254 (ttm170) REVERT: A 368 GLN cc_start: 0.8136 (mt0) cc_final: 0.7854 (mt0) REVERT: A 410 LYS cc_start: 0.7689 (tptt) cc_final: 0.6272 (pttp) REVERT: A 447 ILE cc_start: 0.8322 (mm) cc_final: 0.7996 (mp) REVERT: A 495 MET cc_start: 0.6856 (OUTLIER) cc_final: 0.6330 (tmm) REVERT: B 18 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.8770 (mt) REVERT: B 201 LEU cc_start: 0.8574 (tp) cc_final: 0.8367 (tp) REVERT: B 206 LYS cc_start: 0.8287 (mmtm) cc_final: 0.8033 (mmmt) REVERT: B 322 ARG cc_start: 0.9124 (OUTLIER) cc_final: 0.7201 (ttm170) REVERT: B 355 ARG cc_start: 0.8667 (OUTLIER) cc_final: 0.8438 (ptt-90) REVERT: B 368 GLN cc_start: 0.8106 (mt0) cc_final: 0.7812 (mt0) REVERT: B 410 LYS cc_start: 0.7782 (tptt) cc_final: 0.6250 (pttp) REVERT: B 441 GLN cc_start: 0.7246 (mt0) cc_final: 0.7035 (mp10) REVERT: B 495 MET cc_start: 0.6772 (OUTLIER) cc_final: 0.6210 (tmm) REVERT: B 510 GLU cc_start: 0.6493 (mt-10) cc_final: 0.6256 (mt-10) REVERT: C 129 ASP cc_start: 0.7293 (m-30) cc_final: 0.6982 (m-30) REVERT: C 206 LYS cc_start: 0.8303 (mmtm) cc_final: 0.8084 (mmmt) REVERT: C 322 ARG cc_start: 0.9081 (OUTLIER) cc_final: 0.7186 (ttm170) REVERT: C 410 LYS cc_start: 0.7888 (tptt) cc_final: 0.6226 (pttp) REVERT: C 416 SER cc_start: 0.8164 (t) cc_final: 0.7762 (m) REVERT: C 447 ILE cc_start: 0.8236 (mm) cc_final: 0.7911 (mp) REVERT: C 454 GLN cc_start: 0.8390 (mt0) cc_final: 0.8080 (mt0) REVERT: C 495 MET cc_start: 0.6749 (OUTLIER) cc_final: 0.6222 (tmm) REVERT: D 13 VAL cc_start: 0.8687 (p) cc_final: 0.8449 (t) REVERT: D 18 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8862 (mp) REVERT: D 206 LYS cc_start: 0.8329 (mmtm) cc_final: 0.8080 (mmmt) REVERT: D 303 ASN cc_start: 0.8061 (OUTLIER) cc_final: 0.7684 (t0) REVERT: D 322 ARG cc_start: 0.9108 (OUTLIER) cc_final: 0.7110 (ttm170) REVERT: D 410 LYS cc_start: 0.7455 (tptt) cc_final: 0.6326 (pttp) REVERT: D 447 ILE cc_start: 0.8294 (mm) cc_final: 0.7976 (mp) REVERT: D 450 LYS cc_start: 0.7747 (mttm) cc_final: 0.7530 (mtmm) REVERT: E 13 VAL cc_start: 0.8699 (p) cc_final: 0.8442 (t) REVERT: E 322 ARG cc_start: 0.9099 (OUTLIER) cc_final: 0.7193 (ttm170) REVERT: E 410 LYS cc_start: 0.7807 (mptt) cc_final: 0.6433 (pttp) REVERT: E 416 SER cc_start: 0.8129 (t) cc_final: 0.7715 (p) REVERT: E 447 ILE cc_start: 0.8340 (mm) cc_final: 0.8043 (mm) REVERT: E 495 MET cc_start: 0.6845 (OUTLIER) cc_final: 0.6316 (tmm) REVERT: F 13 VAL cc_start: 0.8695 (p) cc_final: 0.8433 (t) REVERT: F 202 GLN cc_start: 0.8047 (mt0) cc_final: 0.7760 (mt0) REVERT: F 206 LYS cc_start: 0.8311 (mmtm) cc_final: 0.8096 (mmmt) REVERT: F 311 LYS cc_start: 0.8910 (tttm) cc_final: 0.8687 (tttp) REVERT: F 322 ARG cc_start: 0.9006 (OUTLIER) cc_final: 0.7065 (ttm170) REVERT: F 410 LYS cc_start: 0.7731 (mptt) cc_final: 0.6130 (pttp) REVERT: F 447 ILE cc_start: 0.8450 (mm) cc_final: 0.8164 (mm) REVERT: F 454 GLN cc_start: 0.8341 (mt0) cc_final: 0.8076 (mt0) REVERT: G 18 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8874 (mp) REVERT: G 206 LYS cc_start: 0.8290 (mmtm) cc_final: 0.8056 (mmmt) REVERT: G 303 ASN cc_start: 0.7862 (OUTLIER) cc_final: 0.7483 (t0) REVERT: G 322 ARG cc_start: 0.9110 (OUTLIER) cc_final: 0.7167 (ttm170) REVERT: G 410 LYS cc_start: 0.7936 (mptt) cc_final: 0.6354 (pttp) REVERT: G 447 ILE cc_start: 0.8375 (mm) cc_final: 0.8086 (mm) REVERT: H 18 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8798 (mt) REVERT: H 202 GLN cc_start: 0.7990 (mt0) cc_final: 0.7653 (mt0) REVERT: H 253 ARG cc_start: 0.6166 (mmt180) cc_final: 0.5480 (mtt-85) REVERT: H 322 ARG cc_start: 0.9157 (OUTLIER) cc_final: 0.7219 (ttm170) REVERT: H 368 GLN cc_start: 0.8140 (mt0) cc_final: 0.7788 (mt0) REVERT: H 410 LYS cc_start: 0.7644 (mptt) cc_final: 0.6238 (pttp) REVERT: H 447 ILE cc_start: 0.8303 (mm) cc_final: 0.7979 (mm) REVERT: H 454 GLN cc_start: 0.8381 (mt0) cc_final: 0.8102 (mt0) outliers start: 90 outliers final: 57 residues processed: 739 average time/residue: 2.6565 time to fit residues: 2329.9592 Evaluate side-chains 763 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 686 time to evaluate : 3.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 322 ARG Chi-restraints excluded: chain A residue 495 MET Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 495 MET Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 135 MET Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 322 ARG Chi-restraints excluded: chain C residue 450 LYS Chi-restraints excluded: chain C residue 495 MET Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 135 MET Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 303 ASN Chi-restraints excluded: chain D residue 322 ARG Chi-restraints excluded: chain D residue 339 CYS Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 322 ARG Chi-restraints excluded: chain E residue 495 MET Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 170 ASP Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 322 ARG Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 135 MET Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 170 ASP Chi-restraints excluded: chain G residue 172 THR Chi-restraints excluded: chain G residue 176 SER Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 303 ASN Chi-restraints excluded: chain G residue 322 ARG Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 264 THR Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 322 ARG Chi-restraints excluded: chain H residue 446 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 233 optimal weight: 2.9990 chunk 150 optimal weight: 0.5980 chunk 225 optimal weight: 0.9980 chunk 113 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 240 optimal weight: 2.9990 chunk 257 optimal weight: 3.9990 chunk 186 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 296 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 198 ASN C 33 ASN ** F 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 33 ASN ** H 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 31096 Z= 0.169 Angle : 0.568 10.977 42200 Z= 0.282 Chirality : 0.061 1.738 4872 Planarity : 0.004 0.088 5248 Dihedral : 18.534 179.292 4824 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.85 % Favored : 97.13 % Rotamer: Outliers : 2.22 % Allowed : 15.06 % Favored : 82.72 % 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: 0.26 (0.13), residues: 3896 helix: 0.67 (0.14), residues: 1568 sheet: -0.26 (0.27), residues: 352 loop : -0.02 (0.14), residues: 1976 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 92 PHE 0.009 0.001 PHE A 24 TYR 0.017 0.001 TYR H 282 ARG 0.012 0.000 ARG D 253 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 764 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 693 time to evaluate : 3.475 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 132 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.6617 (tm-30) REVERT: A 140 SER cc_start: 0.8131 (t) cc_final: 0.7838 (t) REVERT: A 146 GLU cc_start: 0.6693 (pt0) cc_final: 0.6425 (mt-10) REVERT: A 202 GLN cc_start: 0.7949 (mt0) cc_final: 0.7694 (mt0) REVERT: A 255 ASP cc_start: 0.7433 (p0) cc_final: 0.7231 (p0) REVERT: A 322 ARG cc_start: 0.8993 (OUTLIER) cc_final: 0.7138 (ttm170) REVERT: A 368 GLN cc_start: 0.8126 (mt0) cc_final: 0.7839 (mt0) REVERT: A 410 LYS cc_start: 0.7690 (tptt) cc_final: 0.6299 (pttp) REVERT: A 447 ILE cc_start: 0.8289 (mm) cc_final: 0.7950 (mp) REVERT: B 196 GLU cc_start: 0.7472 (mt-10) cc_final: 0.7230 (pt0) REVERT: B 201 LEU cc_start: 0.8559 (tp) cc_final: 0.8348 (tp) REVERT: B 206 LYS cc_start: 0.8307 (mmtm) cc_final: 0.8059 (mmmt) REVERT: B 322 ARG cc_start: 0.9076 (OUTLIER) cc_final: 0.7210 (ttm170) REVERT: B 355 ARG cc_start: 0.8617 (OUTLIER) cc_final: 0.8393 (ptt-90) REVERT: B 410 LYS cc_start: 0.7701 (tptt) cc_final: 0.6185 (pttp) REVERT: B 441 GLN cc_start: 0.7273 (mt0) cc_final: 0.7047 (mp10) REVERT: B 495 MET cc_start: 0.6819 (OUTLIER) cc_final: 0.6253 (tmm) REVERT: B 510 GLU cc_start: 0.6632 (mt-10) cc_final: 0.6372 (mt-10) REVERT: C 13 VAL cc_start: 0.8659 (p) cc_final: 0.8444 (t) REVERT: C 129 ASP cc_start: 0.7307 (m-30) cc_final: 0.6979 (m-30) REVERT: C 202 GLN cc_start: 0.7933 (mt0) cc_final: 0.7630 (mt0) REVERT: C 206 LYS cc_start: 0.8297 (mmtm) cc_final: 0.8085 (mmmt) REVERT: C 322 ARG cc_start: 0.9013 (OUTLIER) cc_final: 0.7125 (ttm170) REVERT: C 410 LYS cc_start: 0.7590 (tptt) cc_final: 0.6047 (pttp) REVERT: C 416 SER cc_start: 0.8072 (t) cc_final: 0.7636 (m) REVERT: C 441 GLN cc_start: 0.7427 (mt0) cc_final: 0.7043 (mm110) REVERT: C 447 ILE cc_start: 0.8113 (mm) cc_final: 0.7795 (mp) REVERT: C 454 GLN cc_start: 0.8349 (mt0) cc_final: 0.8027 (mt0) REVERT: C 495 MET cc_start: 0.6747 (OUTLIER) cc_final: 0.6239 (tmm) REVERT: D 13 VAL cc_start: 0.8693 (p) cc_final: 0.8479 (t) REVERT: D 206 LYS cc_start: 0.8324 (mmtm) cc_final: 0.8073 (mmmt) REVERT: D 303 ASN cc_start: 0.7589 (OUTLIER) cc_final: 0.7249 (t0) REVERT: D 322 ARG cc_start: 0.9048 (OUTLIER) cc_final: 0.7169 (ttm170) REVERT: D 410 LYS cc_start: 0.7508 (tptt) cc_final: 0.6280 (pttp) REVERT: D 414 MET cc_start: 0.7756 (OUTLIER) cc_final: 0.7070 (mmm) REVERT: D 447 ILE cc_start: 0.8297 (mm) cc_final: 0.7979 (mp) REVERT: D 450 LYS cc_start: 0.7786 (mttm) cc_final: 0.7584 (ttmm) REVERT: E 13 VAL cc_start: 0.8685 (p) cc_final: 0.8452 (t) REVERT: E 322 ARG cc_start: 0.9038 (OUTLIER) cc_final: 0.7148 (ttm170) REVERT: E 410 LYS cc_start: 0.7781 (mptt) cc_final: 0.6426 (pttp) REVERT: E 416 SER cc_start: 0.8117 (t) cc_final: 0.7836 (p) REVERT: E 447 ILE cc_start: 0.8267 (mm) cc_final: 0.7995 (mm) REVERT: E 495 MET cc_start: 0.6841 (OUTLIER) cc_final: 0.6322 (tmm) REVERT: E 509 TYR cc_start: 0.7972 (p90) cc_final: 0.7639 (p90) REVERT: F 13 VAL cc_start: 0.8700 (p) cc_final: 0.8474 (t) REVERT: F 117 ASP cc_start: 0.7817 (t70) cc_final: 0.7543 (t70) REVERT: F 202 GLN cc_start: 0.8020 (mt0) cc_final: 0.7705 (mt0) REVERT: F 206 LYS cc_start: 0.8321 (mmtm) cc_final: 0.8090 (mmmt) REVERT: F 303 ASN cc_start: 0.7186 (OUTLIER) cc_final: 0.6752 (t0) REVERT: F 311 LYS cc_start: 0.8960 (tttm) cc_final: 0.8723 (tttp) REVERT: F 322 ARG cc_start: 0.8966 (OUTLIER) cc_final: 0.7053 (ttm170) REVERT: F 410 LYS cc_start: 0.7638 (mptt) cc_final: 0.6074 (pttp) REVERT: F 447 ILE cc_start: 0.8363 (mm) cc_final: 0.8100 (mm) REVERT: F 454 GLN cc_start: 0.8340 (mt0) cc_final: 0.8065 (mt0) REVERT: G 206 LYS cc_start: 0.8270 (mmtm) cc_final: 0.8017 (mmtt) REVERT: G 303 ASN cc_start: 0.7402 (OUTLIER) cc_final: 0.7040 (t0) REVERT: G 322 ARG cc_start: 0.9056 (OUTLIER) cc_final: 0.7219 (ttm170) REVERT: G 410 LYS cc_start: 0.7579 (mptt) cc_final: 0.6173 (pttp) REVERT: G 447 ILE cc_start: 0.8309 (mm) cc_final: 0.8028 (mm) REVERT: G 450 LYS cc_start: 0.7932 (mtpm) cc_final: 0.7707 (ttmm) REVERT: H 13 VAL cc_start: 0.8689 (p) cc_final: 0.8472 (t) REVERT: H 131 LEU cc_start: 0.8699 (mt) cc_final: 0.8498 (mm) REVERT: H 202 GLN cc_start: 0.7952 (mt0) cc_final: 0.7655 (mt0) REVERT: H 253 ARG cc_start: 0.6230 (mmt180) cc_final: 0.5568 (mtt-85) REVERT: H 322 ARG cc_start: 0.9141 (OUTLIER) cc_final: 0.7297 (ttm170) REVERT: H 337 MET cc_start: 0.7326 (mmt) cc_final: 0.7008 (mmt) REVERT: H 368 GLN cc_start: 0.8122 (mt0) cc_final: 0.7748 (mt0) REVERT: H 410 LYS cc_start: 0.7618 (mptt) cc_final: 0.6160 (pttp) REVERT: H 447 ILE cc_start: 0.8251 (mm) cc_final: 0.7960 (mm) REVERT: H 454 GLN cc_start: 0.8394 (mt0) cc_final: 0.8116 (mt0) outliers start: 71 outliers final: 38 residues processed: 741 average time/residue: 2.6298 time to fit residues: 2295.9725 Evaluate side-chains 742 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 687 time to evaluate : 3.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 322 ARG Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 495 MET Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 322 ARG Chi-restraints excluded: chain C residue 495 MET Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 303 ASN Chi-restraints excluded: chain D residue 322 ARG Chi-restraints excluded: chain D residue 339 CYS Chi-restraints excluded: chain D residue 414 MET Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 322 ARG Chi-restraints excluded: chain E residue 495 MET Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 303 ASN Chi-restraints excluded: chain F residue 322 ARG Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 172 THR Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 303 ASN Chi-restraints excluded: chain G residue 322 ARG Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 322 ARG Chi-restraints excluded: chain H residue 446 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 343 optimal weight: 2.9990 chunk 361 optimal weight: 5.9990 chunk 330 optimal weight: 1.9990 chunk 352 optimal weight: 2.9990 chunk 211 optimal weight: 4.9990 chunk 153 optimal weight: 3.9990 chunk 276 optimal weight: 2.9990 chunk 108 optimal weight: 0.8980 chunk 318 optimal weight: 0.0870 chunk 332 optimal weight: 1.9990 chunk 350 optimal weight: 2.9990 overall best weight: 1.5964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 198 ASN B 202 GLN D 94 ASN E 498 GLN ** F 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 498 GLN ** H 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 31096 Z= 0.271 Angle : 0.603 10.935 42200 Z= 0.303 Chirality : 0.062 1.727 4872 Planarity : 0.005 0.092 5248 Dihedral : 18.596 179.778 4822 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.13 % Favored : 96.84 % Rotamer: Outliers : 2.09 % Allowed : 15.28 % Favored : 82.62 % 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: 3896 helix: 0.60 (0.14), residues: 1568 sheet: -0.30 (0.26), residues: 352 loop : -0.04 (0.14), residues: 1976 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 504 PHE 0.013 0.001 PHE A 24 TYR 0.018 0.002 TYR H 282 ARG 0.011 0.001 ARG F 253 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 748 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 681 time to evaluate : 3.457 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 132 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.6618 (tm-30) REVERT: A 140 SER cc_start: 0.8153 (t) cc_final: 0.7859 (t) REVERT: A 146 GLU cc_start: 0.6729 (pt0) cc_final: 0.6457 (mt-10) REVERT: A 202 GLN cc_start: 0.7935 (mt0) cc_final: 0.7685 (mt0) REVERT: A 322 ARG cc_start: 0.9068 (OUTLIER) cc_final: 0.7233 (ttm170) REVERT: A 368 GLN cc_start: 0.8128 (mt0) cc_final: 0.7835 (mt0) REVERT: A 410 LYS cc_start: 0.7745 (tptt) cc_final: 0.6323 (pttp) REVERT: A 447 ILE cc_start: 0.8337 (mm) cc_final: 0.8001 (mp) REVERT: A 454 GLN cc_start: 0.8059 (OUTLIER) cc_final: 0.7804 (mt0) REVERT: B 201 LEU cc_start: 0.8537 (tp) cc_final: 0.8316 (tp) REVERT: B 206 LYS cc_start: 0.8289 (mmtm) cc_final: 0.8041 (mmmt) REVERT: B 322 ARG cc_start: 0.9112 (OUTLIER) cc_final: 0.7262 (ttm170) REVERT: B 355 ARG cc_start: 0.8655 (OUTLIER) cc_final: 0.8436 (ptt-90) REVERT: B 410 LYS cc_start: 0.7724 (tptt) cc_final: 0.6195 (pttp) REVERT: B 441 GLN cc_start: 0.7322 (mt0) cc_final: 0.7121 (mp10) REVERT: B 495 MET cc_start: 0.6803 (OUTLIER) cc_final: 0.6245 (tmm) REVERT: B 510 GLU cc_start: 0.6572 (mt-10) cc_final: 0.6297 (mt-10) REVERT: C 13 VAL cc_start: 0.8679 (p) cc_final: 0.8459 (t) REVERT: C 18 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.8742 (mt) REVERT: C 117 ASP cc_start: 0.7793 (t70) cc_final: 0.7499 (t70) REVERT: C 129 ASP cc_start: 0.7289 (m-30) cc_final: 0.7008 (m-30) REVERT: C 202 GLN cc_start: 0.7940 (mt0) cc_final: 0.7638 (mt0) REVERT: C 206 LYS cc_start: 0.8297 (mmtm) cc_final: 0.8081 (mmmt) REVERT: C 322 ARG cc_start: 0.9091 (OUTLIER) cc_final: 0.7238 (ttm170) REVERT: C 410 LYS cc_start: 0.7864 (tptt) cc_final: 0.6198 (pttp) REVERT: C 416 SER cc_start: 0.8072 (t) cc_final: 0.7632 (m) REVERT: C 441 GLN cc_start: 0.7458 (mt0) cc_final: 0.7073 (mm110) REVERT: C 447 ILE cc_start: 0.8228 (mm) cc_final: 0.7919 (mp) REVERT: C 454 GLN cc_start: 0.8367 (mt0) cc_final: 0.8041 (mt0) REVERT: C 495 MET cc_start: 0.6777 (OUTLIER) cc_final: 0.6248 (tmm) REVERT: D 13 VAL cc_start: 0.8685 (p) cc_final: 0.8464 (t) REVERT: D 18 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8743 (mt) REVERT: D 206 LYS cc_start: 0.8286 (mmtm) cc_final: 0.8045 (mmmt) REVERT: D 303 ASN cc_start: 0.8037 (OUTLIER) cc_final: 0.7598 (t0) REVERT: D 322 ARG cc_start: 0.9078 (OUTLIER) cc_final: 0.7214 (ttm170) REVERT: D 410 LYS cc_start: 0.7511 (tptt) cc_final: 0.6338 (pttp) REVERT: D 447 ILE cc_start: 0.8308 (mm) cc_final: 0.7987 (mp) REVERT: D 450 LYS cc_start: 0.7796 (mttm) cc_final: 0.7589 (ttmm) REVERT: E 13 VAL cc_start: 0.8686 (p) cc_final: 0.8451 (t) REVERT: E 322 ARG cc_start: 0.9103 (OUTLIER) cc_final: 0.7231 (ttm170) REVERT: E 410 LYS cc_start: 0.7723 (mptt) cc_final: 0.6482 (pttp) REVERT: E 416 SER cc_start: 0.8132 (t) cc_final: 0.7808 (p) REVERT: E 447 ILE cc_start: 0.8323 (mm) cc_final: 0.8042 (mm) REVERT: E 495 MET cc_start: 0.6854 (OUTLIER) cc_final: 0.6327 (tmm) REVERT: E 509 TYR cc_start: 0.7962 (p90) cc_final: 0.7618 (p90) REVERT: F 13 VAL cc_start: 0.8671 (p) cc_final: 0.8460 (t) REVERT: F 117 ASP cc_start: 0.7762 (t70) cc_final: 0.7485 (t70) REVERT: F 202 GLN cc_start: 0.8023 (mt0) cc_final: 0.7734 (mt0) REVERT: F 206 LYS cc_start: 0.8303 (mmtm) cc_final: 0.8089 (mmmt) REVERT: F 311 LYS cc_start: 0.8919 (tttm) cc_final: 0.8675 (tttp) REVERT: F 322 ARG cc_start: 0.9024 (OUTLIER) cc_final: 0.7143 (ttm170) REVERT: F 410 LYS cc_start: 0.7674 (mptt) cc_final: 0.6085 (pttp) REVERT: F 447 ILE cc_start: 0.8397 (mm) cc_final: 0.8093 (mm) REVERT: F 454 GLN cc_start: 0.8340 (mt0) cc_final: 0.8055 (mt0) REVERT: F 495 MET cc_start: 0.6829 (OUTLIER) cc_final: 0.6330 (tmm) REVERT: G 206 LYS cc_start: 0.8257 (mmtm) cc_final: 0.8026 (mmmt) REVERT: G 303 ASN cc_start: 0.7695 (OUTLIER) cc_final: 0.7326 (t0) REVERT: G 322 ARG cc_start: 0.9086 (OUTLIER) cc_final: 0.7264 (ttm170) REVERT: G 410 LYS cc_start: 0.7600 (mptt) cc_final: 0.6196 (pttp) REVERT: G 447 ILE cc_start: 0.8359 (mm) cc_final: 0.8049 (mm) REVERT: G 450 LYS cc_start: 0.7940 (mtpm) cc_final: 0.7718 (ttmm) REVERT: H 13 VAL cc_start: 0.8687 (p) cc_final: 0.8467 (t) REVERT: H 131 LEU cc_start: 0.8701 (mt) cc_final: 0.8501 (mm) REVERT: H 146 GLU cc_start: 0.6695 (mp0) cc_final: 0.6483 (mp0) REVERT: H 202 GLN cc_start: 0.7967 (mt0) cc_final: 0.7639 (mt0) REVERT: H 253 ARG cc_start: 0.6235 (mmt180) cc_final: 0.5568 (mtt-85) REVERT: H 322 ARG cc_start: 0.9131 (OUTLIER) cc_final: 0.7216 (ttm170) REVERT: H 368 GLN cc_start: 0.8124 (mt0) cc_final: 0.7826 (mt0) REVERT: H 410 LYS cc_start: 0.7646 (mptt) cc_final: 0.6215 (pttp) REVERT: H 447 ILE cc_start: 0.8291 (mm) cc_final: 0.7982 (mm) REVERT: H 454 GLN cc_start: 0.8394 (mt0) cc_final: 0.8131 (mt0) outliers start: 67 outliers final: 40 residues processed: 728 average time/residue: 2.6499 time to fit residues: 2280.8868 Evaluate side-chains 738 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 679 time to evaluate : 3.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 322 ARG Chi-restraints excluded: chain A residue 454 GLN Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 495 MET Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 135 MET Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 322 ARG Chi-restraints excluded: chain C residue 495 MET Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 303 ASN Chi-restraints excluded: chain D residue 322 ARG Chi-restraints excluded: chain D residue 339 CYS Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 322 ARG Chi-restraints excluded: chain E residue 495 MET Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 322 ARG Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 495 MET Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 172 THR Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 303 ASN Chi-restraints excluded: chain G residue 322 ARG Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 322 ARG Chi-restraints excluded: chain H residue 446 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 231 optimal weight: 1.9990 chunk 372 optimal weight: 2.9990 chunk 227 optimal weight: 2.9990 chunk 176 optimal weight: 2.9990 chunk 258 optimal weight: 0.9980 chunk 390 optimal weight: 3.9990 chunk 359 optimal weight: 7.9990 chunk 310 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 240 optimal weight: 2.9990 chunk 190 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 198 ASN B 202 GLN D 94 ASN ** F 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 31096 Z= 0.266 Angle : 0.605 10.930 42200 Z= 0.304 Chirality : 0.062 1.723 4872 Planarity : 0.005 0.092 5248 Dihedral : 18.139 178.800 4822 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.16 % Favored : 96.82 % Rotamer: Outliers : 1.94 % Allowed : 15.53 % Favored : 82.53 % 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: 0.18 (0.13), residues: 3896 helix: 0.60 (0.14), residues: 1568 sheet: -0.30 (0.26), residues: 352 loop : -0.07 (0.14), residues: 1976 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 92 PHE 0.013 0.001 PHE A 24 TYR 0.020 0.002 TYR B 282 ARG 0.013 0.001 ARG D 253 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 744 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 682 time to evaluate : 3.478 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 140 SER cc_start: 0.8170 (t) cc_final: 0.7877 (t) REVERT: A 146 GLU cc_start: 0.6825 (pt0) cc_final: 0.6602 (mt-10) REVERT: A 202 GLN cc_start: 0.7933 (mt0) cc_final: 0.7682 (mt0) REVERT: A 311 LYS cc_start: 0.8904 (tttm) cc_final: 0.8692 (tttp) REVERT: A 322 ARG cc_start: 0.9089 (OUTLIER) cc_final: 0.7257 (ttm170) REVERT: A 368 GLN cc_start: 0.8131 (mt0) cc_final: 0.7834 (mt0) REVERT: A 399 GLU cc_start: 0.7009 (mp0) cc_final: 0.5977 (tm-30) REVERT: A 410 LYS cc_start: 0.7696 (tptt) cc_final: 0.6265 (pttp) REVERT: A 447 ILE cc_start: 0.8354 (mm) cc_final: 0.8009 (mp) REVERT: B 201 LEU cc_start: 0.8573 (tp) cc_final: 0.8367 (tp) REVERT: B 206 LYS cc_start: 0.8259 (mmtm) cc_final: 0.8027 (mmmt) REVERT: B 322 ARG cc_start: 0.9107 (OUTLIER) cc_final: 0.7200 (ttm170) REVERT: B 410 LYS cc_start: 0.7507 (tptt) cc_final: 0.6053 (pttp) REVERT: B 441 GLN cc_start: 0.7450 (mt0) cc_final: 0.7237 (mp10) REVERT: B 495 MET cc_start: 0.6797 (OUTLIER) cc_final: 0.6249 (tmm) REVERT: C 13 VAL cc_start: 0.8708 (p) cc_final: 0.8487 (t) REVERT: C 117 ASP cc_start: 0.7797 (t70) cc_final: 0.7523 (t70) REVERT: C 129 ASP cc_start: 0.7282 (m-30) cc_final: 0.7002 (m-30) REVERT: C 202 GLN cc_start: 0.7941 (mt0) cc_final: 0.7643 (mt0) REVERT: C 206 LYS cc_start: 0.8295 (mmtm) cc_final: 0.8075 (mmmt) REVERT: C 322 ARG cc_start: 0.9116 (OUTLIER) cc_final: 0.7260 (ttm170) REVERT: C 410 LYS cc_start: 0.7860 (tptt) cc_final: 0.6185 (pttp) REVERT: C 416 SER cc_start: 0.8074 (t) cc_final: 0.7640 (m) REVERT: C 441 GLN cc_start: 0.7453 (mt0) cc_final: 0.7088 (mm110) REVERT: C 447 ILE cc_start: 0.8226 (mm) cc_final: 0.7897 (mp) REVERT: C 454 GLN cc_start: 0.8363 (mt0) cc_final: 0.8044 (mt0) REVERT: C 495 MET cc_start: 0.6766 (OUTLIER) cc_final: 0.6247 (tmm) REVERT: D 13 VAL cc_start: 0.8680 (p) cc_final: 0.8467 (t) REVERT: D 202 GLN cc_start: 0.7961 (mt0) cc_final: 0.7736 (mt0) REVERT: D 206 LYS cc_start: 0.8297 (mmtm) cc_final: 0.8045 (mmmt) REVERT: D 303 ASN cc_start: 0.8000 (OUTLIER) cc_final: 0.7517 (t0) REVERT: D 322 ARG cc_start: 0.9066 (OUTLIER) cc_final: 0.7186 (ttm170) REVERT: D 410 LYS cc_start: 0.7545 (tptt) cc_final: 0.6349 (pttp) REVERT: D 414 MET cc_start: 0.7728 (mmm) cc_final: 0.6855 (mmm) REVERT: D 447 ILE cc_start: 0.8318 (mm) cc_final: 0.7998 (mp) REVERT: D 450 LYS cc_start: 0.7791 (mttm) cc_final: 0.7582 (ttmm) REVERT: E 13 VAL cc_start: 0.8678 (p) cc_final: 0.8438 (t) REVERT: E 322 ARG cc_start: 0.9123 (OUTLIER) cc_final: 0.7241 (ttm170) REVERT: E 368 GLN cc_start: 0.8093 (mt0) cc_final: 0.7735 (mt0) REVERT: E 410 LYS cc_start: 0.7762 (mptt) cc_final: 0.6472 (pttp) REVERT: E 416 SER cc_start: 0.8114 (t) cc_final: 0.7789 (p) REVERT: E 447 ILE cc_start: 0.8330 (mm) cc_final: 0.8045 (mm) REVERT: E 509 TYR cc_start: 0.7968 (p90) cc_final: 0.7668 (p90) REVERT: F 13 VAL cc_start: 0.8669 (p) cc_final: 0.8461 (t) REVERT: F 117 ASP cc_start: 0.7769 (t70) cc_final: 0.7524 (t70) REVERT: F 202 GLN cc_start: 0.8041 (mt0) cc_final: 0.7760 (mt0) REVERT: F 206 LYS cc_start: 0.8314 (mmtm) cc_final: 0.8084 (mmtt) REVERT: F 311 LYS cc_start: 0.8916 (tttm) cc_final: 0.8705 (tttp) REVERT: F 322 ARG cc_start: 0.9045 (OUTLIER) cc_final: 0.7156 (ttm170) REVERT: F 368 GLN cc_start: 0.8111 (mt0) cc_final: 0.7907 (mt0) REVERT: F 410 LYS cc_start: 0.7665 (mptt) cc_final: 0.6088 (pttp) REVERT: F 447 ILE cc_start: 0.8393 (mm) cc_final: 0.8116 (mm) REVERT: F 454 GLN cc_start: 0.8335 (mt0) cc_final: 0.8053 (mt0) REVERT: F 495 MET cc_start: 0.6816 (OUTLIER) cc_final: 0.6310 (tmm) REVERT: G 206 LYS cc_start: 0.8257 (mmtm) cc_final: 0.8023 (mmmt) REVERT: G 303 ASN cc_start: 0.7763 (OUTLIER) cc_final: 0.7370 (t0) REVERT: G 322 ARG cc_start: 0.9075 (OUTLIER) cc_final: 0.7241 (ttm170) REVERT: G 410 LYS cc_start: 0.7680 (mptt) cc_final: 0.6203 (pttp) REVERT: G 447 ILE cc_start: 0.8363 (mm) cc_final: 0.8048 (mm) REVERT: G 450 LYS cc_start: 0.7937 (mtpm) cc_final: 0.7714 (ttmm) REVERT: G 454 GLN cc_start: 0.8456 (mt0) cc_final: 0.8151 (mt0) REVERT: H 13 VAL cc_start: 0.8681 (p) cc_final: 0.8464 (t) REVERT: H 202 GLN cc_start: 0.7967 (mt0) cc_final: 0.7641 (mt0) REVERT: H 253 ARG cc_start: 0.6244 (mmt180) cc_final: 0.5575 (mtt-85) REVERT: H 322 ARG cc_start: 0.9132 (OUTLIER) cc_final: 0.7210 (ttm170) REVERT: H 368 GLN cc_start: 0.8131 (mt0) cc_final: 0.7830 (mt0) REVERT: H 410 LYS cc_start: 0.7676 (mptt) cc_final: 0.6237 (pttp) REVERT: H 447 ILE cc_start: 0.8287 (mm) cc_final: 0.7976 (mm) REVERT: H 454 GLN cc_start: 0.8398 (mt0) cc_final: 0.8117 (mt0) outliers start: 62 outliers final: 42 residues processed: 729 average time/residue: 2.6487 time to fit residues: 2280.6297 Evaluate side-chains 737 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 682 time to evaluate : 3.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 322 ARG Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 495 MET Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 135 MET Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 322 ARG Chi-restraints excluded: chain C residue 495 MET Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 303 ASN Chi-restraints excluded: chain D residue 322 ARG Chi-restraints excluded: chain D residue 339 CYS Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 322 ARG Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 170 ASP Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 322 ARG Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 495 MET Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 172 THR Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 303 ASN Chi-restraints excluded: chain G residue 322 ARG Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 322 ARG Chi-restraints excluded: chain H residue 446 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 247 optimal weight: 1.9990 chunk 331 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 286 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 311 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 319 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 ASN B 198 ASN B 202 GLN ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN F 198 ASN ** H 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.133048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.099854 restraints weight = 87371.738| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 1.45 r_work: 0.2817 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2691 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 31096 Z= 0.365 Angle : 0.657 10.990 42200 Z= 0.333 Chirality : 0.063 1.738 4872 Planarity : 0.006 0.096 5248 Dihedral : 18.067 177.746 4822 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.21 % Favored : 96.77 % Rotamer: Outliers : 1.78 % Allowed : 15.97 % Favored : 82.25 % 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: -0.00 (0.13), residues: 3896 helix: 0.43 (0.13), residues: 1568 sheet: -0.44 (0.24), residues: 392 loop : -0.13 (0.14), residues: 1936 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 504 PHE 0.017 0.002 PHE A 24 TYR 0.021 0.002 TYR E 282 ARG 0.013 0.001 ARG G 253 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 29611.16 seconds wall clock time: 506 minutes 30.19 seconds (30390.19 seconds total)