Starting phenix.real_space_refine on Thu Feb 15 09:03:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rgd_24448/02_2024/7rgd_24448_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rgd_24448/02_2024/7rgd_24448.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rgd_24448/02_2024/7rgd_24448.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rgd_24448/02_2024/7rgd_24448.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rgd_24448/02_2024/7rgd_24448_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rgd_24448/02_2024/7rgd_24448_trim_updated.pdb" } resolution = 3.0 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= 0.305 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 96 5.49 5 S 200 5.16 5 C 20272 2.51 5 N 5568 2.21 5 O 6448 1.98 5 H 31840 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 3": "OD1" <-> "OD2" Residue "A TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 28": "OD1" <-> "OD2" Residue "A ASP 34": "OD1" <-> "OD2" Residue "A GLU 48": "OE1" <-> "OE2" Residue "A ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 71": "OD1" <-> "OD2" Residue "A PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 103": "OE1" <-> "OE2" Residue "A ARG 105": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 136": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 162": "OD1" <-> "OD2" Residue "A PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 182": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 196": "OE1" <-> "OE2" Residue "A GLU 199": "OE1" <-> "OE2" Residue "A GLU 217": "OE1" <-> "OE2" Residue "A TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 253": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 256": "OD1" <-> "OD2" Residue "A ASP 274": "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 GLU 335": "OE1" <-> "OE2" Residue "A ARG 355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 404": "OD1" <-> "OD2" Residue "A ARG 407": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 418": "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 GLU 491": "OE1" <-> "OE2" Residue "A TYR 509": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 511": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 3": "OD1" <-> "OD2" Residue "B TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 15": "OE1" <-> "OE2" Residue "B PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 28": "OD1" <-> "OD2" Residue "B ASP 34": "OD1" <-> "OD2" Residue "B GLU 48": "OE1" <-> "OE2" Residue "B ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 103": "OE1" <-> "OE2" Residue "B ARG 105": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 136": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 146": "OE1" <-> "OE2" Residue "B ASP 162": "OD1" <-> "OD2" Residue "B PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 182": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 184": "OE1" <-> "OE2" Residue "B GLU 199": "OE1" <-> "OE2" Residue "B ASP 216": "OD1" <-> "OD2" Residue "B GLU 217": "OE1" <-> "OE2" Residue "B TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 253": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 256": "OD1" <-> "OD2" Residue "B TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 335": "OE1" <-> "OE2" Residue "B ARG 355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" 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 ASP 418": "OD1" <-> "OD2" 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 GLU 491": "OE1" <-> "OE2" Residue "B TYR 509": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 511": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 3": "OD1" <-> "OD2" Residue "C TYR 4": "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 28": "OD1" <-> "OD2" Residue "C ASP 34": "OD1" <-> "OD2" Residue "C ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ASP 71": "OD1" <-> "OD2" 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 ASP 129": "OD1" <-> "OD2" Residue "C GLU 132": "OE1" <-> "OE2" Residue "C ARG 136": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 146": "OE1" <-> "OE2" Residue "C ASP 162": "OD1" <-> "OD2" Residue "C PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 182": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 184": "OE1" <-> "OE2" Residue "C TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 253": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ASP 255": "OD1" <-> "OD2" Residue "C ASP 256": "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 GLU 335": "OE1" <-> "OE2" Residue "C ARG 355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" 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 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 GLU 491": "OE1" <-> "OE2" Residue "C TYR 509": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 511": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 4": "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 28": "OD1" <-> "OD2" Residue "D ASP 34": "OD1" <-> "OD2" Residue "D GLU 48": "OE1" <-> "OE2" Residue "D ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 103": "OE1" <-> "OE2" Residue "D ARG 105": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 129": "OD1" <-> "OD2" Residue "D ARG 136": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ASP 162": "OD1" <-> "OD2" Residue "D PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 182": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 184": "OE1" <-> "OE2" Residue "D ASP 216": "OD1" <-> "OD2" Residue "D GLU 217": "OE1" <-> "OE2" Residue "D TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 253": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ASP 256": "OD1" <-> "OD2" Residue "D TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 335": "OE1" <-> "OE2" Residue "D ARG 355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 407": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" 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 491": "OE1" <-> "OE2" Residue "D TYR 509": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 511": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 3": "OD1" <-> "OD2" Residue "E TYR 4": "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 28": "OD1" <-> "OD2" Residue "E ASP 34": "OD1" <-> "OD2" Residue "E GLU 48": "OE1" <-> "OE2" Residue "E ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ASP 71": "OD1" <-> "OD2" Residue "E PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 103": "OE1" <-> "OE2" Residue "E ARG 105": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 129": "OD1" <-> "OD2" Residue "E GLU 132": "OE1" <-> "OE2" Residue "E ARG 136": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 146": "OE1" <-> "OE2" Residue "E ASP 162": "OD1" <-> "OD2" Residue "E PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 182": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 184": "OE1" <-> "OE2" Residue "E GLU 196": "OE1" <-> "OE2" Residue "E GLU 217": "OE1" <-> "OE2" Residue "E TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 253": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ASP 256": "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 GLU 335": "OE1" <-> "OE2" Residue "E ARG 355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E TYR 400": "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 ARG 407": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" 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 491": "OE1" <-> "OE2" Residue "E TYR 509": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 511": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 3": "OD1" <-> "OD2" Residue "F TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 15": "OE1" <-> "OE2" Residue "F PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 28": "OD1" <-> "OD2" Residue "F ASP 34": "OD1" <-> "OD2" Residue "F ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 103": "OE1" <-> "OE2" Residue "F ARG 105": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 136": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F GLU 146": "OE1" <-> "OE2" Residue "F PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 177": "OE1" <-> "OE2" Residue "F ARG 182": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F GLU 184": "OE1" <-> "OE2" Residue "F GLU 199": "OE1" <-> "OE2" 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 TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 335": "OE1" <-> "OE2" Residue "F ARG 355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 407": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ASP 418": "OD1" <-> "OD2" 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 GLU 491": "OE1" <-> "OE2" Residue "F TYR 509": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 511": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 3": "OD1" <-> "OD2" Residue "G TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 15": "OE1" <-> "OE2" Residue "G PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 28": "OD1" <-> "OD2" Residue "G ASP 34": "OD1" <-> "OD2" Residue "G ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" 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 110": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ARG 136": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ARG 182": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G GLU 184": "OE1" <-> "OE2" Residue "G GLU 199": "OE1" <-> "OE2" Residue "G ASP 216": "OD1" <-> "OD2" Residue "G GLU 217": "OE1" <-> "OE2" Residue "G TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ARG 253": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ASP 256": "OD1" <-> "OD2" Residue "G TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 335": "OE1" <-> "OE2" Residue "G ARG 355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" 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 ASP 418": "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 TYR 509": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 511": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 4": "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 28": "OD1" <-> "OD2" Residue "H ASP 34": "OD1" <-> "OD2" Residue "H ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ASP 71": "OD1" <-> "OD2" Residue "H PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 103": "OE1" <-> "OE2" Residue "H ARG 105": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ARG 136": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ASP 162": "OD1" <-> "OD2" Residue "H PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ARG 182": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H GLU 184": "OE1" <-> "OE2" Residue "H GLU 199": "OE1" <-> "OE2" Residue "H GLU 217": "OE1" <-> "OE2" Residue "H TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ARG 253": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ASP 256": "OD1" <-> "OD2" Residue "H TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H 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 ARG 407": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" 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 491": "OE1" <-> "OE2" Residue "H TYR 509": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 511": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 64424 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 7891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 519, 7891 Classifications: {'peptide': 519} Link IDs: {'PTRANS': 18, 'TRANS': 500} Chain breaks: 2 Chain: "B" Number of atoms: 7891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 519, 7891 Classifications: {'peptide': 519} Link IDs: {'PTRANS': 18, 'TRANS': 500} Chain breaks: 2 Chain: "C" Number of atoms: 7891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 519, 7891 Classifications: {'peptide': 519} Link IDs: {'PTRANS': 18, 'TRANS': 500} Chain breaks: 2 Chain: "D" Number of atoms: 7891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 519, 7891 Classifications: {'peptide': 519} Link IDs: {'PTRANS': 18, 'TRANS': 500} Chain breaks: 2 Chain: "E" Number of atoms: 7891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 519, 7891 Classifications: {'peptide': 519} Link IDs: {'PTRANS': 18, 'TRANS': 500} Chain breaks: 2 Chain: "F" Number of atoms: 7891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 519, 7891 Classifications: {'peptide': 519} Link IDs: {'PTRANS': 18, 'TRANS': 500} Chain breaks: 2 Chain: "G" Number of atoms: 7891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 519, 7891 Classifications: {'peptide': 519} Link IDs: {'PTRANS': 18, 'TRANS': 500} Chain breaks: 2 Chain: "H" Number of atoms: 7891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 519, 7891 Classifications: {'peptide': 519} Link IDs: {'PTRANS': 18, 'TRANS': 500} Chain breaks: 2 Chain: "A" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Chain: "B" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Chain: "C" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Chain: "D" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Chain: "E" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Chain: "F" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Chain: "G" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Chain: "H" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Time building chain proxies: 20.95, per 1000 atoms: 0.33 Number of scatterers: 64424 At special positions: 0 Unit cell: (172.815, 172.815, 135.723, 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 200 16.00 P 96 15.00 O 6448 8.00 N 5568 7.00 C 20272 6.00 H 31840 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 42.61 Conformation dependent library (CDL) restraints added in 5.2 seconds 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7456 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 170 helices and 46 sheets defined 35.8% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.63 Creating SS restraints... Processing helix chain 'A' and resid -17 through -8 Processing helix chain 'A' and resid 3 through 6 No H-bonds generated for 'chain 'A' and resid 3 through 6' 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 76 through 84 Processing helix chain 'A' and resid 97 through 109 Processing helix chain 'A' and resid 127 through 136 Processing helix chain 'A' and resid 160 through 162 No H-bonds generated for 'chain 'A' and resid 160 through 162' Processing helix chain 'A' and resid 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: 3.689A 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: 3.955A pdb=" N ASN A 312 " --> pdb=" O ALA A 308 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU A 313 " --> pdb=" O GLN A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 337 Processing helix chain 'A' and resid 343 through 357 removed outlier: 4.382A pdb=" N ARG A 356 " --> pdb=" O GLU A 352 " (cutoff:3.500A) removed outlier: 4.477A 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 484 Processing helix chain 'A' and resid 495 through 500 Processing helix chain 'B' and resid -17 through -8 Processing helix chain 'B' and resid 2 through 6 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 109 Processing helix chain 'B' and resid 127 through 136 Processing helix chain 'B' and resid 160 through 162 No H-bonds generated for 'chain 'B' and resid 160 through 162' 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 182 through 184 No H-bonds generated for 'chain 'B' and resid 182 through 184' 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: 3.694A pdb=" N LEU B 260 " --> pdb=" O LYS B 257 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR B 264 " --> pdb=" O ASP B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 293 Processing helix chain 'B' and resid 307 through 316 removed outlier: 3.981A pdb=" N ASN B 312 " --> pdb=" O ALA B 308 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU B 313 " --> pdb=" O GLN B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 337 Processing helix chain 'B' and resid 343 through 357 removed outlier: 4.327A pdb=" N ARG B 356 " --> pdb=" O GLU B 352 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N PHE B 357 " --> pdb=" O TYR B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 378 Processing helix chain 'B' and resid 453 through 471 Proline residue: B 458 - end of helix Processing helix chain 'B' and resid 476 through 485 Processing helix chain 'B' and resid 495 through 501 Processing helix chain 'C' and resid -17 through -8 Processing helix chain 'C' and resid 2 through 6 Processing helix chain 'C' and resid 20 through 26 removed outlier: 3.895A pdb=" N SER C 26 " --> pdb=" O GLN C 22 " (cutoff:3.500A) 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 109 Processing helix chain 'C' and resid 127 through 136 Processing helix chain 'C' and resid 160 through 162 No H-bonds generated for 'chain 'C' and resid 160 through 162' Processing helix chain 'C' and resid 175 through 177 No H-bonds generated for 'chain 'C' and resid 175 through 177' Processing helix chain 'C' and resid 182 through 184 No H-bonds generated for 'chain 'C' and resid 182 through 184' 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 Processing helix chain 'C' and resid 281 through 293 Processing helix chain 'C' and resid 307 through 316 removed outlier: 3.987A pdb=" N ASN C 312 " --> pdb=" O ALA C 308 " (cutoff:3.500A) removed outlier: 3.643A 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: 4.328A pdb=" N ARG C 356 " --> pdb=" O GLU C 352 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N PHE C 357 " --> pdb=" O TYR C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 378 Processing helix chain 'C' and resid 453 through 471 Proline residue: C 458 - end of helix Processing helix chain 'C' and resid 476 through 485 Processing helix chain 'C' and resid 495 through 501 Processing helix chain 'D' and resid -17 through -8 Processing helix chain 'D' and resid 3 through 6 No H-bonds generated for 'chain 'D' and resid 3 through 6' 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 76 through 84 Processing helix chain 'D' and resid 97 through 109 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 182 through 184 No H-bonds generated for 'chain 'D' and resid 182 through 184' 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 Processing helix chain 'D' and resid 281 through 293 Processing helix chain 'D' and resid 307 through 316 removed outlier: 3.980A pdb=" N ASN D 312 " --> pdb=" O ALA D 308 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU D 313 " --> pdb=" O GLN D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 337 Processing helix chain 'D' and resid 343 through 357 removed outlier: 4.362A pdb=" N ARG D 356 " --> pdb=" O GLU D 352 " (cutoff:3.500A) removed outlier: 4.365A 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 -17 through -8 Processing helix chain 'E' and resid 2 through 6 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 109 Processing helix chain 'E' and resid 127 through 136 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 182 through 184 No H-bonds generated for 'chain 'E' and resid 182 through 184' 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 Processing helix chain 'E' and resid 281 through 293 Processing helix chain 'E' and resid 307 through 316 removed outlier: 4.035A pdb=" N ASN E 312 " --> pdb=" O ALA E 308 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU E 313 " --> pdb=" O GLN E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 333 through 337 Processing helix chain 'E' and resid 343 through 357 removed outlier: 4.335A pdb=" N ARG E 356 " --> pdb=" O GLU E 352 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N PHE E 357 " --> pdb=" O TYR E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 370 through 378 Processing helix chain 'E' and resid 453 through 471 Proline residue: E 458 - end of helix Processing helix chain 'E' and resid 476 through 485 Processing helix chain 'E' and resid 495 through 501 Processing helix chain 'F' and resid -17 through -8 Processing helix chain 'F' and resid 2 through 6 removed outlier: 3.535A pdb=" N ILE F 6 " --> pdb=" O ALA F 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 2 through 6' Processing helix chain 'F' and resid 20 through 26 removed outlier: 3.834A pdb=" N SER F 26 " --> pdb=" O GLN F 22 " (cutoff:3.500A) 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 109 Processing helix chain 'F' and resid 127 through 136 Processing helix chain 'F' and resid 160 through 162 No H-bonds generated for 'chain 'F' and resid 160 through 162' 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: 3.502A pdb=" N ARG F 259 " --> pdb=" O ASP F 256 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 293 Processing helix chain 'F' and resid 307 through 316 removed outlier: 3.987A pdb=" N ASN F 312 " --> pdb=" O ALA F 308 " (cutoff:3.500A) removed outlier: 3.664A 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: 4.342A pdb=" N ARG F 356 " --> pdb=" O GLU F 352 " (cutoff:3.500A) removed outlier: 4.468A 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 -17 through -8 Processing helix chain 'G' and resid 2 through 6 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 109 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 182 through 184 No H-bonds generated for 'chain 'G' and resid 182 through 184' 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 Processing helix chain 'G' and resid 281 through 293 Processing helix chain 'G' and resid 307 through 316 removed outlier: 4.018A pdb=" N ASN G 312 " --> pdb=" O ALA G 308 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU G 313 " --> pdb=" O GLN G 309 " (cutoff:3.500A) Processing helix chain 'G' and resid 333 through 336 No H-bonds generated for 'chain 'G' and resid 333 through 336' Processing helix chain 'G' and resid 343 through 357 removed outlier: 4.307A pdb=" N ARG G 356 " --> pdb=" O GLU G 352 " (cutoff:3.500A) removed outlier: 4.483A 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 500 Processing helix chain 'H' and resid -17 through -8 Processing helix chain 'H' and resid 3 through 6 No H-bonds generated for 'chain 'H' and resid 3 through 6' 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 76 through 84 Processing helix chain 'H' and resid 97 through 109 Processing helix chain 'H' and resid 127 through 136 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 182 through 184 No H-bonds generated for 'chain 'H' and resid 182 through 184' 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: 3.514A pdb=" N ARG H 259 " --> pdb=" O ASP H 256 " (cutoff:3.500A) Processing helix chain 'H' and resid 281 through 293 Processing helix chain 'H' and resid 307 through 316 removed outlier: 4.001A pdb=" N ASN H 312 " --> pdb=" O ALA H 308 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU H 313 " --> pdb=" O GLN H 309 " (cutoff:3.500A) Processing helix chain 'H' and resid 333 through 337 Processing helix chain 'H' and resid 343 through 357 removed outlier: 4.399A pdb=" N ARG H 356 " --> pdb=" O GLU H 352 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N PHE H 357 " --> pdb=" O TYR H 353 " (cutoff:3.500A) Processing helix chain 'H' and resid 370 through 378 Processing helix chain 'H' and resid 453 through 471 Proline residue: H 458 - end of helix Processing helix chain 'H' and resid 476 through 485 Processing helix chain 'H' and resid 495 through 501 Processing sheet with id= A, first strand: chain 'A' and resid 35 through 37 Processing sheet with id= B, first strand: chain 'A' and resid 65 through 67 removed outlier: 6.489A pdb=" N VAL A 384 " --> pdb=" O ILE A 66 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 187 through 189 removed outlier: 8.145A pdb=" N ALA A 188 " --> pdb=" O LYS A 208 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 247 through 250 removed outlier: 6.674A pdb=" N VAL A 270 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N VAL A 250 " --> pdb=" O VAL A 270 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N VAL A 272 " --> pdb=" O VAL A 250 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLN A 298 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N LEU A 273 " --> pdb=" O GLN A 298 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ILE A 300 " --> pdb=" O LEU A 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 408 through 411 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: 6.429A pdb=" N VAL B 384 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY B 320 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ASN B 303 " --> pdb=" O ARG B 322 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 187 through 189 removed outlier: 8.139A pdb=" N ALA B 188 " --> pdb=" O LYS B 208 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 409 through 411 Processing sheet with id= K, first strand: chain 'B' and resid 142 through 145 Processing sheet with id= L, first strand: chain 'C' and resid 35 through 37 Processing sheet with id= M, first strand: chain 'C' and resid 65 through 67 removed outlier: 6.435A pdb=" N VAL C 384 " --> pdb=" O ILE C 66 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 187 through 189 removed outlier: 8.117A pdb=" N ALA C 188 " --> pdb=" O LYS C 208 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 247 through 249 removed outlier: 6.645A pdb=" N VAL C 270 " --> pdb=" O ALA C 248 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N GLN C 298 " --> pdb=" O ILE C 271 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'C' and resid 142 through 145 Processing sheet with id= Q, first strand: chain 'D' and resid 35 through 37 Processing sheet with id= R, first strand: chain 'D' and resid 65 through 67 removed outlier: 6.456A pdb=" N VAL D 384 " --> pdb=" O ILE D 66 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 187 through 189 removed outlier: 8.176A pdb=" N ALA D 188 " --> pdb=" O LYS D 208 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 247 through 249 removed outlier: 6.707A pdb=" N VAL D 270 " --> pdb=" O ALA D 248 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N GLN D 298 " --> pdb=" O ILE D 271 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'D' and resid 409 through 411 removed outlier: 3.828A pdb=" N TYR D 411 " --> pdb=" O GLY D 445 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 142 through 145 Processing sheet with id= W, first strand: chain 'E' and resid 35 through 37 Processing sheet with id= X, first strand: chain 'E' and resid 65 through 67 removed outlier: 6.399A pdb=" N VAL E 384 " --> pdb=" O ILE E 66 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 187 through 189 removed outlier: 8.091A pdb=" N ALA E 188 " --> pdb=" O LYS E 208 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 247 through 250 removed outlier: 6.711A pdb=" N VAL E 270 " --> pdb=" O ALA E 248 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N VAL E 250 " --> pdb=" O VAL E 270 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N VAL E 272 " --> pdb=" O VAL E 250 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLN E 298 " --> pdb=" O ILE E 271 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N LEU E 273 " --> pdb=" O GLN E 298 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE E 300 " --> pdb=" O LEU E 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= Z Processing sheet with id= AA, first strand: chain 'E' and resid 409 through 411 Processing sheet with id= AB, first strand: chain 'E' and resid 142 through 145 Processing sheet with id= AC, first strand: chain 'F' and resid 35 through 37 Processing sheet with id= AD, first strand: chain 'F' and resid 65 through 67 removed outlier: 6.425A pdb=" N VAL F 384 " --> pdb=" O ILE F 66 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'F' and resid 187 through 189 removed outlier: 8.158A pdb=" N ALA F 188 " --> pdb=" O LYS F 208 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'F' and resid 247 through 249 removed outlier: 6.664A pdb=" N VAL F 270 " --> pdb=" O ALA F 248 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N GLN F 298 " --> pdb=" O ILE F 271 " (cutoff:3.500A) No H-bonds generated for sheet with id= AF Processing sheet with id= AG, first strand: chain 'F' and resid 408 through 411 removed outlier: 3.744A pdb=" N TYR F 411 " --> pdb=" O GLY F 445 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'F' and resid 142 through 145 Processing sheet with id= AI, first strand: chain 'G' and resid 35 through 37 Processing sheet with id= AJ, first strand: chain 'G' and resid 65 through 67 removed outlier: 6.479A pdb=" N VAL G 384 " --> pdb=" O ILE G 66 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'G' and resid 187 through 189 removed outlier: 8.160A pdb=" N ALA G 188 " --> pdb=" O LYS G 208 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'G' and resid 247 through 250 removed outlier: 6.624A pdb=" N VAL G 270 " --> pdb=" O ALA G 248 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N VAL G 250 " --> pdb=" O VAL G 270 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N VAL G 272 " --> pdb=" O VAL G 250 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N GLN G 298 " --> pdb=" O ILE G 271 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N LEU G 273 " --> pdb=" O GLN G 298 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE G 300 " --> pdb=" O LEU G 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= AL Processing sheet with id= AM, first strand: chain 'G' and resid 409 through 411 removed outlier: 3.762A pdb=" N TYR G 411 " --> pdb=" O GLY G 445 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'G' and resid 142 through 145 Processing sheet with id= AO, first strand: chain 'H' and resid 35 through 37 Processing sheet with id= AP, first strand: chain 'H' and resid 65 through 67 removed outlier: 6.488A pdb=" N VAL H 384 " --> pdb=" O ILE H 66 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'H' and resid 187 through 189 removed outlier: 8.135A pdb=" N ALA H 188 " --> pdb=" O LYS H 208 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'H' and resid 247 through 249 removed outlier: 6.648A pdb=" N VAL H 270 " --> pdb=" O ALA H 248 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N GLN H 298 " --> pdb=" O ILE H 271 " (cutoff:3.500A) No H-bonds generated for sheet with id= AR Processing sheet with id= AS, first strand: chain 'H' and resid 408 through 411 removed outlier: 3.825A pdb=" N TYR H 411 " --> pdb=" O GLY H 445 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'H' and resid 141 through 145 946 hydrogen bonds defined for protein. 2559 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: 23.46 Time building geometry restraints manager: 44.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.70 - 0.93: 2 0.93 - 1.16: 31782 1.16 - 1.39: 11329 1.39 - 1.62: 21551 1.62 - 1.85: 344 Bond restraints: 65008 Sorted by residual: bond pdb=" CZ PHE C 511 " pdb=" HZ PHE C 511 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" NH2 ARG F 322 " pdb="HH21 ARG F 322 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N LEU G 227 " pdb=" H LEU G 227 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" NE2 GLN D 454 " pdb="HE21 GLN D 454 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" NH1 ARG E 105 " pdb="HH12 ARG E 105 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 ... (remaining 65003 not shown) Histogram of bond angle deviations from ideal: 91.08 - 99.86: 134 99.86 - 108.65: 28241 108.65 - 117.43: 56720 117.43 - 126.22: 31462 126.22 - 135.00: 907 Bond angle restraints: 117464 Sorted by residual: angle pdb=" PB ATP B 603 " pdb=" O3B ATP B 603 " pdb=" PG ATP B 603 " ideal model delta sigma weight residual 139.87 121.76 18.11 1.00e+00 1.00e+00 3.28e+02 angle pdb=" PB ATP G 603 " pdb=" O3B ATP G 603 " pdb=" PG ATP G 603 " ideal model delta sigma weight residual 139.87 122.27 17.60 1.00e+00 1.00e+00 3.10e+02 angle pdb=" PB ATP C 603 " pdb=" O3B ATP C 603 " pdb=" PG ATP C 603 " ideal model delta sigma weight residual 139.87 122.66 17.21 1.00e+00 1.00e+00 2.96e+02 angle pdb=" PB ATP D 603 " pdb=" O3B ATP D 603 " pdb=" PG ATP D 603 " ideal model delta sigma weight residual 139.87 122.72 17.15 1.00e+00 1.00e+00 2.94e+02 angle pdb=" PB ATP H 603 " pdb=" O3B ATP H 603 " pdb=" PG ATP H 603 " ideal model delta sigma weight residual 139.87 123.83 16.04 1.00e+00 1.00e+00 2.57e+02 ... (remaining 117459 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.00: 28886 35.00 - 70.00: 1713 70.00 - 105.00: 94 105.00 - 140.00: 34 140.00 - 175.00: 25 Dihedral angle restraints: 30752 sinusoidal: 17520 harmonic: 13232 Sorted by residual: dihedral pdb=" O5' GTP D 602 " pdb=" O3A GTP D 602 " pdb=" PA GTP D 602 " pdb=" PB GTP D 602 " ideal model delta sinusoidal sigma weight residual 274.12 99.13 175.00 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O5' GTP G 602 " pdb=" O3A GTP G 602 " pdb=" PA GTP G 602 " pdb=" PB GTP G 602 " ideal model delta sinusoidal sigma weight residual 274.12 99.20 174.92 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C8 GTP G 602 " pdb=" C1' GTP G 602 " pdb=" N9 GTP G 602 " pdb=" O4' GTP G 602 " ideal model delta sinusoidal sigma weight residual 104.59 -68.23 172.82 1 2.00e+01 2.50e-03 4.78e+01 ... (remaining 30749 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 4024 0.112 - 0.224: 999 0.224 - 0.336: 138 0.336 - 0.449: 22 0.449 - 0.561: 9 Chirality restraints: 5192 Sorted by residual: chirality pdb=" CA THR F 515 " pdb=" N THR F 515 " pdb=" C THR F 515 " pdb=" CB THR F 515 " both_signs ideal model delta sigma weight residual False 2.53 1.97 0.56 2.00e-01 2.50e+01 7.86e+00 chirality pdb=" CA PHE G 401 " pdb=" N PHE G 401 " pdb=" C PHE G 401 " pdb=" CB PHE G 401 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.42e+00 chirality pdb=" CA PHE D 401 " pdb=" N PHE D 401 " pdb=" C PHE D 401 " pdb=" CB PHE D 401 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 6.05e+00 ... (remaining 5189 not shown) Planarity restraints: 9544 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' IMP D 604 " 0.150 2.00e-02 2.50e+03 8.60e-02 1.85e+02 pdb=" C2 IMP D 604 " -0.097 2.00e-02 2.50e+03 pdb=" C4 IMP D 604 " -0.023 2.00e-02 2.50e+03 pdb=" C5 IMP D 604 " 0.009 2.00e-02 2.50e+03 pdb=" C6 IMP D 604 " 0.125 2.00e-02 2.50e+03 pdb=" C8 IMP D 604 " -0.080 2.00e-02 2.50e+03 pdb=" N1 IMP D 604 " 0.078 2.00e-02 2.50e+03 pdb=" N3 IMP D 604 " -0.092 2.00e-02 2.50e+03 pdb=" N7 IMP D 604 " -0.070 2.00e-02 2.50e+03 pdb=" N9 IMP D 604 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' IMP H 604 " 0.138 2.00e-02 2.50e+03 8.29e-02 1.72e+02 pdb=" C2 IMP H 604 " -0.097 2.00e-02 2.50e+03 pdb=" C4 IMP H 604 " -0.019 2.00e-02 2.50e+03 pdb=" C5 IMP H 604 " 0.004 2.00e-02 2.50e+03 pdb=" C6 IMP H 604 " 0.123 2.00e-02 2.50e+03 pdb=" C8 IMP H 604 " -0.069 2.00e-02 2.50e+03 pdb=" N1 IMP H 604 " 0.079 2.00e-02 2.50e+03 pdb=" N3 IMP H 604 " -0.089 2.00e-02 2.50e+03 pdb=" N7 IMP H 604 " -0.077 2.00e-02 2.50e+03 pdb=" N9 IMP H 604 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' IMP C 604 " -0.135 2.00e-02 2.50e+03 8.19e-02 1.67e+02 pdb=" C2 IMP C 604 " 0.097 2.00e-02 2.50e+03 pdb=" C4 IMP C 604 " 0.012 2.00e-02 2.50e+03 pdb=" C5 IMP C 604 " -0.007 2.00e-02 2.50e+03 pdb=" C6 IMP C 604 " -0.117 2.00e-02 2.50e+03 pdb=" C8 IMP C 604 " 0.072 2.00e-02 2.50e+03 pdb=" N1 IMP C 604 " -0.080 2.00e-02 2.50e+03 pdb=" N3 IMP C 604 " 0.091 2.00e-02 2.50e+03 pdb=" N7 IMP C 604 " 0.075 2.00e-02 2.50e+03 pdb=" N9 IMP C 604 " -0.008 2.00e-02 2.50e+03 ... (remaining 9541 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.05: 2312 2.05 - 2.69: 87997 2.69 - 3.33: 198640 3.33 - 3.96: 265418 3.96 - 4.60: 396526 Nonbonded interactions: 950893 Sorted by model distance: nonbonded pdb=" HB2 MET B 1 " pdb=" HE3 MET B 1 " model vdw 1.417 2.440 nonbonded pdb=" H SER B 122 " pdb=" HD2 HIS B 125 " model vdw 1.433 2.100 nonbonded pdb=" HA3 GLY F 156 " pdb=" HE2 MET F 179 " model vdw 1.454 2.440 nonbonded pdb=" H SER F 122 " pdb=" HD2 HIS F 125 " model vdw 1.463 2.100 nonbonded pdb=" H SER E 140 " pdb=" HG SER E 140 " model vdw 1.466 2.100 ... (remaining 950888 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: 2.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.710 Extract box with map and model: 14.160 Check model and map are aligned: 0.690 Set scattering table: 0.430 Process input model: 162.690 Find NCS groups from input model: 3.060 Set up NCS constraints: 0.350 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 195.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 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 0.102 33168 Z= 0.842 Angle : 2.006 19.516 45072 Z= 1.278 Chirality : 0.100 0.561 5192 Planarity : 0.014 0.128 5560 Dihedral : 19.225 174.998 12728 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.60 % Favored : 93.08 % Rotamer: Outliers : 3.19 % Allowed : 7.91 % Favored : 88.90 % Cbeta Deviations : 0.43 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.12), residues: 4104 helix: -1.04 (0.11), residues: 1528 sheet: -0.51 (0.25), residues: 392 loop : -1.16 (0.12), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.021 0.004 HIS C 504 PHE 0.083 0.014 PHE B 44 TYR 0.118 0.020 TYR B 348 ARG 0.009 0.001 ARG C 480 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 921 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 814 time to evaluate : 3.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLU cc_start: 0.7758 (mm-30) cc_final: 0.7403 (mm-30) REVERT: A 106 LYS cc_start: 0.8611 (mtpt) cc_final: 0.8408 (mtpm) REVERT: A 131 LEU cc_start: 0.8074 (mp) cc_final: 0.7725 (mm) REVERT: A 228 LYS cc_start: 0.8358 (mtmt) cc_final: 0.8069 (mtmt) REVERT: A 315 ASP cc_start: 0.7540 (m-30) cc_final: 0.7220 (m-30) REVERT: A 337 MET cc_start: 0.7482 (mmm) cc_final: 0.6906 (mmp) REVERT: A 454 GLN cc_start: 0.7929 (mt0) cc_final: 0.7718 (mt0) REVERT: A 509 TYR cc_start: 0.6917 (OUTLIER) cc_final: 0.6444 (t80) REVERT: B 103 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7526 (mm-30) REVERT: B 106 LYS cc_start: 0.8532 (mtpt) cc_final: 0.8232 (mtpm) REVERT: B 131 LEU cc_start: 0.7873 (mp) cc_final: 0.7531 (mm) REVERT: B 179 MET cc_start: 0.8017 (ptt) cc_final: 0.7654 (ptm) REVERT: B 195 LYS cc_start: 0.7763 (ttpp) cc_final: 0.7507 (ttmm) REVERT: B 228 LYS cc_start: 0.8323 (mtmt) cc_final: 0.8088 (mtmt) REVERT: B 281 VAL cc_start: 0.9096 (p) cc_final: 0.8776 (m) REVERT: B 454 GLN cc_start: 0.8003 (mt0) cc_final: 0.7800 (mt0) REVERT: B 509 TYR cc_start: 0.7073 (OUTLIER) cc_final: 0.6391 (t80) REVERT: C 103 GLU cc_start: 0.7753 (mm-30) cc_final: 0.7429 (mm-30) REVERT: C 106 LYS cc_start: 0.8553 (mtpt) cc_final: 0.8350 (mtpm) REVERT: C 129 ASP cc_start: 0.7643 (m-30) cc_final: 0.7166 (m-30) REVERT: C 131 LEU cc_start: 0.7890 (mp) cc_final: 0.7554 (mm) REVERT: C 196 GLU cc_start: 0.7405 (mt-10) cc_final: 0.6961 (mt-10) REVERT: C 228 LYS cc_start: 0.8326 (mtmt) cc_final: 0.8077 (mtmt) REVERT: C 281 VAL cc_start: 0.9177 (p) cc_final: 0.8839 (m) REVERT: C 368 GLN cc_start: 0.8104 (mt0) cc_final: 0.7894 (mt0) REVERT: C 410 LYS cc_start: 0.7066 (tttt) cc_final: 0.6863 (ttmm) REVERT: C 509 TYR cc_start: 0.6924 (OUTLIER) cc_final: 0.6404 (t80) REVERT: D 103 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7443 (mm-30) REVERT: D 105 ARG cc_start: 0.7751 (ttm110) cc_final: 0.7500 (ttm110) REVERT: D 106 LYS cc_start: 0.8581 (mtpt) cc_final: 0.8352 (mtpm) REVERT: D 131 LEU cc_start: 0.8017 (mp) cc_final: 0.7747 (mm) REVERT: D 195 LYS cc_start: 0.7861 (ttpp) cc_final: 0.7593 (ttmm) REVERT: D 228 LYS cc_start: 0.8346 (mtmt) cc_final: 0.8088 (mtmt) REVERT: D 281 VAL cc_start: 0.9155 (p) cc_final: 0.8813 (m) REVERT: D 315 ASP cc_start: 0.7550 (m-30) cc_final: 0.7240 (m-30) REVERT: D 368 GLN cc_start: 0.8066 (mt0) cc_final: 0.7865 (mt0) REVERT: D 509 TYR cc_start: 0.6881 (OUTLIER) cc_final: 0.5853 (t80) REVERT: D 515 THR cc_start: 0.7494 (OUTLIER) cc_final: 0.7272 (t) REVERT: E 71 ASP cc_start: 0.8082 (p0) cc_final: 0.7842 (p0) REVERT: E 103 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7411 (mm-30) REVERT: E 106 LYS cc_start: 0.8493 (mtpt) cc_final: 0.8287 (mtpm) REVERT: E 129 ASP cc_start: 0.7599 (m-30) cc_final: 0.7346 (m-30) REVERT: E 131 LEU cc_start: 0.8114 (mp) cc_final: 0.7751 (mm) REVERT: E 195 LYS cc_start: 0.7782 (ttpp) cc_final: 0.7557 (ttmm) REVERT: E 335 GLU cc_start: 0.7010 (mp0) cc_final: 0.6806 (mp0) REVERT: E 410 LYS cc_start: 0.6967 (ttpt) cc_final: 0.6709 (ttpp) REVERT: E 474 ARG cc_start: 0.7296 (mtp85) cc_final: 0.6990 (mtt90) REVERT: E 509 TYR cc_start: 0.6983 (OUTLIER) cc_final: 0.6143 (t80) REVERT: E 515 THR cc_start: 0.7373 (OUTLIER) cc_final: 0.7138 (t) REVERT: F 103 GLU cc_start: 0.7761 (mm-30) cc_final: 0.7432 (mm-30) REVERT: F 105 ARG cc_start: 0.7681 (ttm110) cc_final: 0.7440 (ttm110) REVERT: F 106 LYS cc_start: 0.8502 (mtpt) cc_final: 0.8281 (mtpm) REVERT: F 131 LEU cc_start: 0.7772 (mp) cc_final: 0.7442 (mm) REVERT: F 195 LYS cc_start: 0.7777 (ttpp) cc_final: 0.7501 (ttmm) REVERT: F 228 LYS cc_start: 0.8360 (mtmt) cc_final: 0.8118 (mtmt) REVERT: F 281 VAL cc_start: 0.9199 (p) cc_final: 0.8855 (m) REVERT: F 368 GLN cc_start: 0.8003 (mt0) cc_final: 0.7789 (mt0) REVERT: F 474 ARG cc_start: 0.7533 (ttm-80) cc_final: 0.7208 (ttt90) REVERT: F 509 TYR cc_start: 0.6991 (OUTLIER) cc_final: 0.6361 (t80) REVERT: G 70 MET cc_start: 0.9012 (mtm) cc_final: 0.8797 (mtp) REVERT: G 103 GLU cc_start: 0.7720 (mm-30) cc_final: 0.7382 (mm-30) REVERT: G 106 LYS cc_start: 0.8553 (mtpt) cc_final: 0.8301 (mtpp) REVERT: G 131 LEU cc_start: 0.8077 (mp) cc_final: 0.7800 (mm) REVERT: G 195 LYS cc_start: 0.7948 (ttpp) cc_final: 0.7673 (ttmm) REVERT: G 196 GLU cc_start: 0.7318 (mt-10) cc_final: 0.6979 (mt-10) REVERT: G 243 GLN cc_start: 0.8909 (mt0) cc_final: 0.8392 (mt0) REVERT: G 322 ARG cc_start: 0.9077 (OUTLIER) cc_final: 0.7325 (ttm170) REVERT: G 410 LYS cc_start: 0.7054 (tttt) cc_final: 0.6836 (ttpp) REVERT: G 509 TYR cc_start: 0.6972 (OUTLIER) cc_final: 0.6162 (t80) REVERT: G 515 THR cc_start: 0.7159 (OUTLIER) cc_final: 0.6834 (t) REVERT: H 103 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7485 (mm-30) REVERT: H 106 LYS cc_start: 0.8573 (mtpt) cc_final: 0.8349 (mtpm) REVERT: H 160 SER cc_start: 0.8435 (t) cc_final: 0.8184 (m) REVERT: H 195 LYS cc_start: 0.7956 (ttpp) cc_final: 0.7670 (ttmm) REVERT: H 281 VAL cc_start: 0.9102 (p) cc_final: 0.8821 (m) REVERT: H 337 MET cc_start: 0.7412 (mmm) cc_final: 0.7211 (mpp) REVERT: H 368 GLN cc_start: 0.8130 (mt0) cc_final: 0.7909 (mt0) REVERT: H 509 TYR cc_start: 0.6836 (OUTLIER) cc_final: 0.5910 (t80) REVERT: H 515 THR cc_start: 0.7285 (OUTLIER) cc_final: 0.7018 (t) outliers start: 107 outliers final: 54 residues processed: 897 average time/residue: 2.3100 time to fit residues: 2507.6133 Evaluate side-chains 727 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 660 time to evaluate : 3.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 117 ASP Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 509 TYR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 117 ASP Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 509 TYR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 322 ARG Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 509 TYR Chi-restraints excluded: chain C residue 512 LEU Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 117 ASP Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 322 ARG Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 509 TYR Chi-restraints excluded: chain D residue 511 PHE Chi-restraints excluded: chain D residue 515 THR Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 117 ASP Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 214 ASP Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain E residue 457 VAL Chi-restraints excluded: chain E residue 509 TYR Chi-restraints excluded: chain E residue 515 THR Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 117 ASP Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 225 THR Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 322 ARG Chi-restraints excluded: chain F residue 335 GLU Chi-restraints excluded: chain F residue 457 VAL Chi-restraints excluded: chain F residue 509 TYR Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 117 ASP Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 322 ARG Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 509 TYR Chi-restraints excluded: chain G residue 515 THR Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 322 ARG Chi-restraints excluded: chain H residue 333 THR Chi-restraints excluded: chain H residue 420 MET Chi-restraints excluded: chain H residue 457 VAL Chi-restraints excluded: chain H residue 509 TYR Chi-restraints excluded: chain H residue 511 PHE Chi-restraints excluded: chain H residue 515 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 344 optimal weight: 0.7980 chunk 309 optimal weight: 0.9980 chunk 171 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 chunk 208 optimal weight: 0.9990 chunk 165 optimal weight: 0.8980 chunk 319 optimal weight: 1.9990 chunk 123 optimal weight: 0.9980 chunk 194 optimal weight: 0.9990 chunk 238 optimal weight: 0.9990 chunk 370 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 303 ASN A 312 ASN B 94 ASN B 125 HIS B 312 ASN C -20 HIS C 94 ASN C 100 GLN C 125 HIS ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 ASN C 312 ASN D -20 HIS D 94 ASN D 100 GLN D 125 HIS D 303 ASN D 312 ASN E -20 HIS E 94 ASN E 100 GLN E 198 ASN ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 303 ASN E 312 ASN F -20 HIS F 100 GLN ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 303 ASN F 312 ASN F 507 HIS G -20 HIS G 94 ASN G 198 ASN G 312 ASN G 454 GLN H 100 GLN H 283 GLN H 303 ASN H 312 ASN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 33168 Z= 0.204 Angle : 0.657 7.300 45072 Z= 0.338 Chirality : 0.045 0.184 5192 Planarity : 0.005 0.071 5560 Dihedral : 19.693 175.050 5561 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 3.40 % Allowed : 14.26 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.12), residues: 4104 helix: 0.32 (0.13), residues: 1544 sheet: -1.35 (0.32), residues: 264 loop : -1.04 (0.12), residues: 2296 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS G 92 PHE 0.018 0.002 PHE H 24 TYR 0.015 0.001 TYR A 509 ARG 0.009 0.001 ARG D 203 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 793 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 679 time to evaluate : 3.776 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 103 GLU cc_start: 0.7630 (mm-30) cc_final: 0.7296 (mm-30) REVERT: A 106 LYS cc_start: 0.8476 (mtpt) cc_final: 0.8228 (ttmm) REVERT: A 179 MET cc_start: 0.8082 (ptm) cc_final: 0.7502 (ptm) REVERT: A 195 LYS cc_start: 0.7826 (OUTLIER) cc_final: 0.7502 (ttmm) REVERT: A 228 LYS cc_start: 0.8325 (mtmt) cc_final: 0.8012 (mtmt) REVERT: A 277 GLN cc_start: 0.8930 (OUTLIER) cc_final: 0.7298 (tm-30) REVERT: A 296 HIS cc_start: 0.7655 (OUTLIER) cc_final: 0.7200 (p-80) REVERT: A 322 ARG cc_start: 0.8771 (OUTLIER) cc_final: 0.7104 (ttm170) REVERT: A 509 TYR cc_start: 0.6813 (OUTLIER) cc_final: 0.6506 (t80) REVERT: B 58 LYS cc_start: 0.8339 (mttt) cc_final: 0.8083 (mttp) REVERT: B 75 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7260 (mt-10) REVERT: B 103 GLU cc_start: 0.7726 (mm-30) cc_final: 0.7390 (mm-30) REVERT: B 106 LYS cc_start: 0.8490 (mtpt) cc_final: 0.8270 (ttmm) REVERT: B 228 LYS cc_start: 0.8295 (mtmt) cc_final: 0.8017 (mtmt) REVERT: B 277 GLN cc_start: 0.8953 (OUTLIER) cc_final: 0.7481 (tm-30) REVERT: B 281 VAL cc_start: 0.8872 (p) cc_final: 0.8606 (m) REVERT: B 474 ARG cc_start: 0.7819 (ptm160) cc_final: 0.7619 (ptp-110) REVERT: B 509 TYR cc_start: 0.6876 (OUTLIER) cc_final: 0.6332 (t80) REVERT: C 75 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7243 (mt-10) REVERT: C 103 GLU cc_start: 0.7723 (mm-30) cc_final: 0.7342 (mm-30) REVERT: C 106 LYS cc_start: 0.8484 (mtpt) cc_final: 0.8237 (ttmm) REVERT: C 129 ASP cc_start: 0.7634 (m-30) cc_final: 0.7144 (m-30) REVERT: C 131 LEU cc_start: 0.7709 (mp) cc_final: 0.7381 (mm) REVERT: C 196 GLU cc_start: 0.7106 (mt-10) cc_final: 0.6798 (mt-10) REVERT: C 277 GLN cc_start: 0.8764 (OUTLIER) cc_final: 0.7299 (tm-30) REVERT: C 281 VAL cc_start: 0.8953 (p) cc_final: 0.8689 (m) REVERT: C 322 ARG cc_start: 0.8996 (OUTLIER) cc_final: 0.7426 (ttm170) REVERT: C 337 MET cc_start: 0.7485 (mmm) cc_final: 0.7261 (mmm) REVERT: C 368 GLN cc_start: 0.8229 (mt0) cc_final: 0.8003 (mt0) REVERT: C 410 LYS cc_start: 0.6964 (tttt) cc_final: 0.6693 (ttpp) REVERT: C 509 TYR cc_start: 0.6758 (OUTLIER) cc_final: 0.6335 (t80) REVERT: D 75 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7259 (mt-10) REVERT: D 103 GLU cc_start: 0.7719 (mm-30) cc_final: 0.7328 (mm-30) REVERT: D 105 ARG cc_start: 0.7666 (ttm110) cc_final: 0.7404 (ttm110) REVERT: D 106 LYS cc_start: 0.8507 (mtpt) cc_final: 0.8256 (ttmm) REVERT: D 131 LEU cc_start: 0.7707 (mp) cc_final: 0.7418 (mm) REVERT: D 228 LYS cc_start: 0.8315 (mtmt) cc_final: 0.7963 (mtpt) REVERT: D 281 VAL cc_start: 0.8890 (p) cc_final: 0.8661 (m) REVERT: D 322 ARG cc_start: 0.8988 (OUTLIER) cc_final: 0.7387 (ttm170) REVERT: D 368 GLN cc_start: 0.8203 (mt0) cc_final: 0.7970 (mt0) REVERT: D 509 TYR cc_start: 0.6758 (OUTLIER) cc_final: 0.5879 (t80) REVERT: E 58 LYS cc_start: 0.8323 (mttt) cc_final: 0.8055 (mttp) REVERT: E 103 GLU cc_start: 0.7655 (mm-30) cc_final: 0.7366 (mm-30) REVERT: E 131 LEU cc_start: 0.7771 (mp) cc_final: 0.7423 (mm) REVERT: E 277 GLN cc_start: 0.8921 (OUTLIER) cc_final: 0.7393 (tm-30) REVERT: E 322 ARG cc_start: 0.8879 (OUTLIER) cc_final: 0.7165 (ttm170) REVERT: E 335 GLU cc_start: 0.7007 (mp0) cc_final: 0.6781 (mp0) REVERT: E 410 LYS cc_start: 0.6708 (ttpt) cc_final: 0.6446 (ttpp) REVERT: E 474 ARG cc_start: 0.7356 (mtp85) cc_final: 0.6976 (mtt90) REVERT: E 509 TYR cc_start: 0.6854 (OUTLIER) cc_final: 0.6130 (t80) REVERT: F 1 MET cc_start: 0.6974 (mpp) cc_final: 0.6681 (mpt) REVERT: F 58 LYS cc_start: 0.8337 (OUTLIER) cc_final: 0.8098 (mttp) REVERT: F 75 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7294 (mt-10) REVERT: F 103 GLU cc_start: 0.7727 (mm-30) cc_final: 0.7358 (mm-30) REVERT: F 106 LYS cc_start: 0.8470 (mtpt) cc_final: 0.8253 (ttmm) REVERT: F 228 LYS cc_start: 0.8361 (mtmt) cc_final: 0.7532 (mtpt) REVERT: F 232 ASP cc_start: 0.7766 (m-30) cc_final: 0.7331 (m-30) REVERT: F 277 GLN cc_start: 0.8685 (OUTLIER) cc_final: 0.7277 (tm-30) REVERT: F 281 VAL cc_start: 0.8918 (p) cc_final: 0.8651 (m) REVERT: F 322 ARG cc_start: 0.8900 (OUTLIER) cc_final: 0.7367 (ttm170) REVERT: F 368 GLN cc_start: 0.8193 (mt0) cc_final: 0.7964 (mt0) REVERT: F 474 ARG cc_start: 0.7580 (ttm-80) cc_final: 0.7284 (ttt90) REVERT: F 509 TYR cc_start: 0.6829 (OUTLIER) cc_final: 0.6412 (t80) REVERT: G 58 LYS cc_start: 0.8356 (OUTLIER) cc_final: 0.8109 (mttp) REVERT: G 103 GLU cc_start: 0.7631 (mm-30) cc_final: 0.7329 (mm-30) REVERT: G 131 LEU cc_start: 0.7900 (mp) cc_final: 0.7616 (mm) REVERT: G 134 LYS cc_start: 0.7331 (OUTLIER) cc_final: 0.6695 (tptt) REVERT: G 196 GLU cc_start: 0.7170 (mt-10) cc_final: 0.6747 (mt-10) REVERT: G 232 ASP cc_start: 0.7809 (m-30) cc_final: 0.7352 (m-30) REVERT: G 322 ARG cc_start: 0.8931 (OUTLIER) cc_final: 0.7174 (ttm170) REVERT: G 410 LYS cc_start: 0.6820 (tttt) cc_final: 0.6619 (ttpp) REVERT: G 509 TYR cc_start: 0.6834 (OUTLIER) cc_final: 0.6250 (t80) REVERT: H 103 GLU cc_start: 0.7666 (mm-30) cc_final: 0.7358 (mm-30) REVERT: H 106 LYS cc_start: 0.8479 (mtpt) cc_final: 0.8269 (ttmm) REVERT: H 131 LEU cc_start: 0.7843 (mp) cc_final: 0.7504 (mm) REVERT: H 277 GLN cc_start: 0.8957 (OUTLIER) cc_final: 0.7298 (tm-30) REVERT: H 281 VAL cc_start: 0.8875 (p) cc_final: 0.8655 (m) REVERT: H 322 ARG cc_start: 0.8951 (OUTLIER) cc_final: 0.7375 (ttm170) REVERT: H 337 MET cc_start: 0.7426 (mmm) cc_final: 0.7194 (mpp) REVERT: H 509 TYR cc_start: 0.6733 (OUTLIER) cc_final: 0.5950 (t80) REVERT: H 515 THR cc_start: 0.7100 (OUTLIER) cc_final: 0.6860 (t) outliers start: 114 outliers final: 46 residues processed: 765 average time/residue: 2.4793 time to fit residues: 2295.4302 Evaluate side-chains 701 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 624 time to evaluate : 3.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain A residue 322 ARG Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 509 TYR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 509 TYR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 322 ARG Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 509 TYR Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 150 MET Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 322 ARG Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 509 TYR Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 162 ASP Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 322 ARG Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain E residue 509 TYR Chi-restraints excluded: chain F residue 58 LYS Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 225 THR Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 322 ARG Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 509 TYR Chi-restraints excluded: chain G residue 58 LYS Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 134 LYS Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 322 ARG Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 509 TYR Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 322 ARG Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 333 THR Chi-restraints excluded: chain H residue 420 MET Chi-restraints excluded: chain H residue 470 ASP Chi-restraints excluded: chain H residue 509 TYR Chi-restraints excluded: chain H residue 515 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 205 optimal weight: 6.9990 chunk 114 optimal weight: 2.9990 chunk 308 optimal weight: 3.9990 chunk 252 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 371 optimal weight: 2.9990 chunk 400 optimal weight: 5.9990 chunk 330 optimal weight: 0.9980 chunk 368 optimal weight: 0.9990 chunk 126 optimal weight: 1.9990 chunk 297 optimal weight: 4.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 198 ASN ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 454 GLN ** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 198 ASN ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 441 GLN C 454 GLN D 94 ASN D 198 ASN F 441 GLN G 94 ASN G 303 ASN G 454 GLN H 198 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 33168 Z= 0.290 Angle : 0.617 7.417 45072 Z= 0.312 Chirality : 0.045 0.165 5192 Planarity : 0.006 0.086 5560 Dihedral : 17.947 171.392 5522 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 3.28 % Allowed : 16.02 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.13), residues: 4104 helix: 0.80 (0.14), residues: 1520 sheet: -1.02 (0.29), residues: 320 loop : -0.86 (0.13), residues: 2264 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS H 372 PHE 0.020 0.002 PHE F 24 TYR 0.015 0.001 TYR H 509 ARG 0.011 0.001 ARG C 203 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 755 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 645 time to evaluate : 3.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7419 (mt-10) REVERT: A 103 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7349 (mm-30) REVERT: A 106 LYS cc_start: 0.8624 (mtpt) cc_final: 0.8345 (ttmm) REVERT: A 195 LYS cc_start: 0.7835 (ttpp) cc_final: 0.7538 (ttmm) REVERT: A 228 LYS cc_start: 0.8294 (mtmt) cc_final: 0.7764 (mtmt) REVERT: A 232 ASP cc_start: 0.7795 (m-30) cc_final: 0.7450 (m-30) REVERT: A 262 LEU cc_start: 0.8186 (mp) cc_final: 0.7891 (mp) REVERT: A 277 GLN cc_start: 0.9019 (OUTLIER) cc_final: 0.7677 (tm-30) REVERT: A 296 HIS cc_start: 0.7763 (OUTLIER) cc_final: 0.7308 (p-80) REVERT: A 322 ARG cc_start: 0.8825 (OUTLIER) cc_final: 0.7177 (ttm170) REVERT: A 509 TYR cc_start: 0.6898 (OUTLIER) cc_final: 0.6454 (t80) REVERT: B -18 THR cc_start: 0.8303 (m) cc_final: 0.8085 (p) REVERT: B 58 LYS cc_start: 0.8317 (mttt) cc_final: 0.8076 (mttp) REVERT: B 75 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7375 (mt-10) REVERT: B 103 GLU cc_start: 0.7792 (mm-30) cc_final: 0.7482 (mm-30) REVERT: B 106 LYS cc_start: 0.8592 (mtpt) cc_final: 0.8316 (ttmm) REVERT: B 131 LEU cc_start: 0.7772 (mp) cc_final: 0.7406 (mm) REVERT: B 217 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7645 (mm-30) REVERT: B 228 LYS cc_start: 0.8265 (mtmt) cc_final: 0.7631 (mtmt) REVERT: B 232 ASP cc_start: 0.7861 (m-30) cc_final: 0.7493 (m-30) REVERT: B 277 GLN cc_start: 0.8994 (OUTLIER) cc_final: 0.7805 (tm-30) REVERT: B 281 VAL cc_start: 0.8925 (p) cc_final: 0.8719 (m) REVERT: B 509 TYR cc_start: 0.6828 (OUTLIER) cc_final: 0.6379 (t80) REVERT: C 75 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7339 (mt-10) REVERT: C 103 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7434 (mm-30) REVERT: C 106 LYS cc_start: 0.8600 (mtpt) cc_final: 0.8299 (ttmm) REVERT: C 129 ASP cc_start: 0.7604 (m-30) cc_final: 0.7106 (m-30) REVERT: C 131 LEU cc_start: 0.7746 (mp) cc_final: 0.7394 (mm) REVERT: C 196 GLU cc_start: 0.7150 (mt-10) cc_final: 0.6741 (mt-10) REVERT: C 228 LYS cc_start: 0.8236 (mtmt) cc_final: 0.7797 (mtmt) REVERT: C 232 ASP cc_start: 0.7861 (m-30) cc_final: 0.7565 (m-30) REVERT: C 277 GLN cc_start: 0.8854 (OUTLIER) cc_final: 0.7487 (tm-30) REVERT: C 322 ARG cc_start: 0.9025 (OUTLIER) cc_final: 0.7410 (ttm170) REVERT: C 368 GLN cc_start: 0.8202 (mt0) cc_final: 0.7950 (mt0) REVERT: C 410 LYS cc_start: 0.7033 (tttt) cc_final: 0.6745 (ttpp) REVERT: C 509 TYR cc_start: 0.6832 (OUTLIER) cc_final: 0.6435 (t80) REVERT: D 75 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7384 (mt-10) REVERT: D 103 GLU cc_start: 0.7766 (mm-30) cc_final: 0.7371 (mm-30) REVERT: D 106 LYS cc_start: 0.8598 (mtpt) cc_final: 0.8324 (ttmm) REVERT: D 131 LEU cc_start: 0.7734 (mp) cc_final: 0.7419 (mm) REVERT: D 228 LYS cc_start: 0.8283 (mtmt) cc_final: 0.7953 (mtpt) REVERT: D 262 LEU cc_start: 0.8195 (mp) cc_final: 0.7849 (mp) REVERT: D 296 HIS cc_start: 0.7683 (OUTLIER) cc_final: 0.7336 (p-80) REVERT: D 322 ARG cc_start: 0.9055 (OUTLIER) cc_final: 0.7440 (ttm170) REVERT: D 410 LYS cc_start: 0.6894 (ttmp) cc_final: 0.6445 (ttpp) REVERT: D 509 TYR cc_start: 0.6768 (OUTLIER) cc_final: 0.5834 (t80) REVERT: E 58 LYS cc_start: 0.8304 (mttt) cc_final: 0.8053 (mttp) REVERT: E 75 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7354 (mt-10) REVERT: E 103 GLU cc_start: 0.7660 (mm-30) cc_final: 0.7396 (mm-30) REVERT: E 129 ASP cc_start: 0.7844 (m-30) cc_final: 0.7442 (m-30) REVERT: E 131 LEU cc_start: 0.7772 (mp) cc_final: 0.7425 (mm) REVERT: E 150 MET cc_start: 0.7599 (pmm) cc_final: 0.7192 (pmm) REVERT: E 262 LEU cc_start: 0.8127 (mp) cc_final: 0.7801 (mp) REVERT: E 277 GLN cc_start: 0.8991 (OUTLIER) cc_final: 0.7623 (tm-30) REVERT: E 322 ARG cc_start: 0.8959 (OUTLIER) cc_final: 0.7311 (ttm170) REVERT: E 335 GLU cc_start: 0.7331 (mp0) cc_final: 0.7002 (mp0) REVERT: E 474 ARG cc_start: 0.7329 (mtp85) cc_final: 0.7117 (mtt90) REVERT: E 509 TYR cc_start: 0.6795 (OUTLIER) cc_final: 0.6259 (t80) REVERT: F 58 LYS cc_start: 0.8360 (mptt) cc_final: 0.8140 (mttp) REVERT: F 65 LEU cc_start: 0.8958 (mt) cc_final: 0.8753 (mm) REVERT: F 75 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7355 (mt-10) REVERT: F 103 GLU cc_start: 0.7808 (mm-30) cc_final: 0.7461 (mm-30) REVERT: F 106 LYS cc_start: 0.8582 (mtpt) cc_final: 0.8317 (ttmm) REVERT: F 131 LEU cc_start: 0.7799 (mp) cc_final: 0.7433 (mm) REVERT: F 228 LYS cc_start: 0.8317 (mtmt) cc_final: 0.7501 (mtmt) REVERT: F 232 ASP cc_start: 0.7785 (m-30) cc_final: 0.7400 (m-30) REVERT: F 262 LEU cc_start: 0.8184 (mp) cc_final: 0.7842 (mp) REVERT: F 277 GLN cc_start: 0.8800 (OUTLIER) cc_final: 0.7420 (tm-30) REVERT: F 281 VAL cc_start: 0.8954 (p) cc_final: 0.8747 (m) REVERT: F 322 ARG cc_start: 0.8885 (OUTLIER) cc_final: 0.7325 (ttm170) REVERT: F 333 THR cc_start: 0.8099 (OUTLIER) cc_final: 0.7850 (t) REVERT: F 368 GLN cc_start: 0.8208 (mt0) cc_final: 0.7987 (mt0) REVERT: F 474 ARG cc_start: 0.7592 (ttm-80) cc_final: 0.7334 (ttt90) REVERT: F 509 TYR cc_start: 0.6802 (OUTLIER) cc_final: 0.6392 (t80) REVERT: G 58 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.8132 (mttm) REVERT: G 75 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7443 (mt-10) REVERT: G 103 GLU cc_start: 0.7650 (mm-30) cc_final: 0.7370 (mm-30) REVERT: G 131 LEU cc_start: 0.7800 (mp) cc_final: 0.7481 (mm) REVERT: G 196 GLU cc_start: 0.7187 (mt-10) cc_final: 0.6732 (mt-10) REVERT: G 262 LEU cc_start: 0.8137 (mp) cc_final: 0.7808 (mp) REVERT: G 296 HIS cc_start: 0.7715 (OUTLIER) cc_final: 0.7367 (p-80) REVERT: G 322 ARG cc_start: 0.9045 (OUTLIER) cc_final: 0.7264 (ttm170) REVERT: G 410 LYS cc_start: 0.6899 (tttt) cc_final: 0.6653 (ttpp) REVERT: G 509 TYR cc_start: 0.6793 (OUTLIER) cc_final: 0.6230 (t80) REVERT: H 75 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7364 (mt-10) REVERT: H 103 GLU cc_start: 0.7780 (mm-30) cc_final: 0.7457 (mm-30) REVERT: H 106 LYS cc_start: 0.8595 (mtpt) cc_final: 0.8333 (ttmm) REVERT: H 131 LEU cc_start: 0.7859 (mp) cc_final: 0.7502 (mm) REVERT: H 232 ASP cc_start: 0.7786 (m-30) cc_final: 0.7451 (m-30) REVERT: H 262 LEU cc_start: 0.8132 (mp) cc_final: 0.7810 (mp) REVERT: H 277 GLN cc_start: 0.9014 (OUTLIER) cc_final: 0.7684 (tm-30) REVERT: H 281 VAL cc_start: 0.8940 (p) cc_final: 0.8727 (m) REVERT: H 322 ARG cc_start: 0.8985 (OUTLIER) cc_final: 0.7406 (ttm170) REVERT: H 509 TYR cc_start: 0.6723 (OUTLIER) cc_final: 0.5982 (t80) outliers start: 110 outliers final: 41 residues processed: 728 average time/residue: 2.6316 time to fit residues: 2293.9310 Evaluate side-chains 697 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 621 time to evaluate : 3.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain A residue 322 ARG Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 509 TYR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 509 TYR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 322 ARG Chi-restraints excluded: chain C residue 474 ARG Chi-restraints excluded: chain C residue 509 TYR Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 296 HIS Chi-restraints excluded: chain D residue 322 ARG Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 474 ARG Chi-restraints excluded: chain D residue 509 TYR Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 275 SER Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 322 ARG Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain E residue 509 TYR Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 322 ARG Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 509 TYR Chi-restraints excluded: chain G residue 58 LYS Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 75 GLU Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 296 HIS Chi-restraints excluded: chain G residue 322 ARG Chi-restraints excluded: chain G residue 509 TYR Chi-restraints excluded: chain G residue 510 THR Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 75 GLU Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 162 ASP Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 322 ARG Chi-restraints excluded: chain H residue 333 THR Chi-restraints excluded: chain H residue 420 MET Chi-restraints excluded: chain H residue 509 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 366 optimal weight: 0.7980 chunk 279 optimal weight: 1.9990 chunk 192 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 177 optimal weight: 2.9990 chunk 249 optimal weight: 4.9990 chunk 372 optimal weight: 7.9990 chunk 394 optimal weight: 0.8980 chunk 194 optimal weight: 4.9990 chunk 353 optimal weight: 2.9990 chunk 106 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 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 198 ASN ** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 198 ASN ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 507 HIS ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 303 ASN F 198 ASN ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G -20 HIS ** G 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 198 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 33168 Z= 0.252 Angle : 0.584 7.453 45072 Z= 0.291 Chirality : 0.043 0.155 5192 Planarity : 0.006 0.089 5560 Dihedral : 17.009 169.764 5516 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 2.95 % Allowed : 16.65 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.13), residues: 4104 helix: 0.95 (0.14), residues: 1528 sheet: -1.11 (0.29), residues: 320 loop : -0.80 (0.13), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 466 PHE 0.015 0.001 PHE H 24 TYR 0.012 0.001 TYR A 509 ARG 0.009 0.001 ARG D 203 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 741 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 642 time to evaluate : 3.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLU cc_start: 0.7761 (mm-30) cc_final: 0.7388 (mm-30) REVERT: A 106 LYS cc_start: 0.8626 (mtpt) cc_final: 0.8342 (ttmm) REVERT: A 131 LEU cc_start: 0.7940 (mt) cc_final: 0.7688 (mm) REVERT: A 150 MET cc_start: 0.7606 (pmm) cc_final: 0.7188 (pmm) REVERT: A 195 LYS cc_start: 0.7831 (ttpp) cc_final: 0.7470 (ttmm) REVERT: A 199 GLU cc_start: 0.7241 (mt-10) cc_final: 0.7027 (mm-30) REVERT: A 228 LYS cc_start: 0.8288 (mtmt) cc_final: 0.8031 (mtmt) REVERT: A 262 LEU cc_start: 0.8209 (mp) cc_final: 0.7910 (mp) REVERT: A 277 GLN cc_start: 0.8992 (OUTLIER) cc_final: 0.7753 (tm-30) REVERT: A 322 ARG cc_start: 0.8835 (OUTLIER) cc_final: 0.7238 (ttm170) REVERT: A 509 TYR cc_start: 0.6904 (OUTLIER) cc_final: 0.6562 (t80) REVERT: B 58 LYS cc_start: 0.8347 (mttt) cc_final: 0.8120 (mttp) REVERT: B 75 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.7392 (mt-10) REVERT: B 103 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7455 (mm-30) REVERT: B 106 LYS cc_start: 0.8612 (mtpt) cc_final: 0.8323 (ttmm) REVERT: B 131 LEU cc_start: 0.7774 (mp) cc_final: 0.7395 (mm) REVERT: B 228 LYS cc_start: 0.8298 (mtmt) cc_final: 0.8037 (mtmt) REVERT: B 277 GLN cc_start: 0.8970 (OUTLIER) cc_final: 0.7882 (tm-30) REVERT: B 509 TYR cc_start: 0.6811 (OUTLIER) cc_final: 0.6337 (t80) REVERT: C 103 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7404 (mm-30) REVERT: C 106 LYS cc_start: 0.8595 (mtpt) cc_final: 0.8293 (ttmm) REVERT: C 129 ASP cc_start: 0.7611 (m-30) cc_final: 0.7114 (m-30) REVERT: C 131 LEU cc_start: 0.7772 (mp) cc_final: 0.7416 (mm) REVERT: C 196 GLU cc_start: 0.7226 (mt-10) cc_final: 0.6792 (mt-10) REVERT: C 228 LYS cc_start: 0.8217 (mtmt) cc_final: 0.7800 (mtmt) REVERT: C 232 ASP cc_start: 0.7857 (m-30) cc_final: 0.7559 (m-30) REVERT: C 262 LEU cc_start: 0.8182 (mp) cc_final: 0.7883 (mp) REVERT: C 277 GLN cc_start: 0.8921 (OUTLIER) cc_final: 0.7778 (tm-30) REVERT: C 322 ARG cc_start: 0.9016 (OUTLIER) cc_final: 0.7402 (ttm170) REVERT: C 410 LYS cc_start: 0.7093 (tttt) cc_final: 0.6800 (ttpp) REVERT: C 509 TYR cc_start: 0.6768 (OUTLIER) cc_final: 0.6478 (t80) REVERT: D 103 GLU cc_start: 0.7784 (mm-30) cc_final: 0.7407 (mm-30) REVERT: D 106 LYS cc_start: 0.8639 (mtpt) cc_final: 0.8362 (ttmm) REVERT: D 131 LEU cc_start: 0.7748 (mp) cc_final: 0.7491 (mm) REVERT: D 228 LYS cc_start: 0.8309 (mtmt) cc_final: 0.7997 (mtmt) REVERT: D 262 LEU cc_start: 0.8225 (mp) cc_final: 0.7883 (mp) REVERT: D 277 GLN cc_start: 0.8874 (OUTLIER) cc_final: 0.7212 (tm-30) REVERT: D 296 HIS cc_start: 0.7675 (OUTLIER) cc_final: 0.7351 (p-80) REVERT: D 322 ARG cc_start: 0.9053 (OUTLIER) cc_final: 0.7502 (ttm170) REVERT: D 410 LYS cc_start: 0.6962 (ttmp) cc_final: 0.6505 (ttpp) REVERT: D 509 TYR cc_start: 0.6645 (OUTLIER) cc_final: 0.5748 (t80) REVERT: E 75 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7397 (mt-10) REVERT: E 103 GLU cc_start: 0.7677 (mm-30) cc_final: 0.7396 (mm-30) REVERT: E 129 ASP cc_start: 0.7836 (m-30) cc_final: 0.7422 (m-30) REVERT: E 131 LEU cc_start: 0.7806 (mp) cc_final: 0.7460 (mm) REVERT: E 228 LYS cc_start: 0.8186 (mtpt) cc_final: 0.7832 (mtpt) REVERT: E 232 ASP cc_start: 0.7915 (m-30) cc_final: 0.7598 (m-30) REVERT: E 262 LEU cc_start: 0.8161 (mp) cc_final: 0.7858 (mp) REVERT: E 277 GLN cc_start: 0.8963 (OUTLIER) cc_final: 0.7798 (tm-30) REVERT: E 322 ARG cc_start: 0.8946 (OUTLIER) cc_final: 0.7370 (ttm170) REVERT: E 474 ARG cc_start: 0.7327 (mtp85) cc_final: 0.6920 (mtt90) REVERT: E 509 TYR cc_start: 0.6705 (OUTLIER) cc_final: 0.6211 (t80) REVERT: F 75 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7409 (mt-10) REVERT: F 103 GLU cc_start: 0.7796 (mm-30) cc_final: 0.7438 (mm-30) REVERT: F 106 LYS cc_start: 0.8593 (mtpt) cc_final: 0.8306 (ttmm) REVERT: F 131 LEU cc_start: 0.7762 (mp) cc_final: 0.7420 (mm) REVERT: F 228 LYS cc_start: 0.8313 (mtmt) cc_final: 0.7479 (mtmt) REVERT: F 232 ASP cc_start: 0.7830 (m-30) cc_final: 0.7452 (m-30) REVERT: F 262 LEU cc_start: 0.8202 (mp) cc_final: 0.7876 (mp) REVERT: F 277 GLN cc_start: 0.8916 (OUTLIER) cc_final: 0.7705 (tm-30) REVERT: F 322 ARG cc_start: 0.8909 (OUTLIER) cc_final: 0.7353 (ttm170) REVERT: F 368 GLN cc_start: 0.8193 (mt0) cc_final: 0.7984 (mt0) REVERT: F 474 ARG cc_start: 0.7609 (ttm-80) cc_final: 0.7324 (ttt90) REVERT: F 509 TYR cc_start: 0.6750 (OUTLIER) cc_final: 0.6361 (t80) REVERT: G 103 GLU cc_start: 0.7656 (mm-30) cc_final: 0.7381 (mm-30) REVERT: G 131 LEU cc_start: 0.7874 (mp) cc_final: 0.7585 (mm) REVERT: G 150 MET cc_start: 0.7402 (pmm) cc_final: 0.7153 (pmm) REVERT: G 196 GLU cc_start: 0.7176 (mt-10) cc_final: 0.6755 (mt-10) REVERT: G 296 HIS cc_start: 0.7737 (OUTLIER) cc_final: 0.7353 (p-80) REVERT: G 322 ARG cc_start: 0.8966 (OUTLIER) cc_final: 0.7363 (ttm170) REVERT: G 336 VAL cc_start: 0.8669 (t) cc_final: 0.8385 (t) REVERT: G 509 TYR cc_start: 0.6765 (OUTLIER) cc_final: 0.6242 (t80) REVERT: H 75 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.7393 (mt-10) REVERT: H 103 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7423 (mm-30) REVERT: H 106 LYS cc_start: 0.8606 (mtpt) cc_final: 0.8328 (ttmm) REVERT: H 131 LEU cc_start: 0.7929 (mp) cc_final: 0.7597 (mm) REVERT: H 262 LEU cc_start: 0.8170 (mp) cc_final: 0.7812 (mp) REVERT: H 277 GLN cc_start: 0.8972 (OUTLIER) cc_final: 0.7576 (tm-30) REVERT: H 322 ARG cc_start: 0.8994 (OUTLIER) cc_final: 0.7454 (ttm170) REVERT: H 509 TYR cc_start: 0.6716 (OUTLIER) cc_final: 0.6041 (t80) outliers start: 99 outliers final: 43 residues processed: 718 average time/residue: 2.5723 time to fit residues: 2199.1539 Evaluate side-chains 694 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 623 time to evaluate : 3.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 322 ARG Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 509 TYR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 509 TYR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 322 ARG Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 509 TYR Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 296 HIS Chi-restraints excluded: chain D residue 322 ARG Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 509 TYR Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 162 ASP Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 322 ARG Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain E residue 455 LYS Chi-restraints excluded: chain E residue 509 TYR Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 322 ARG Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 509 TYR Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 296 HIS Chi-restraints excluded: chain G residue 322 ARG Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 509 TYR Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 75 GLU Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 162 ASP Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 322 ARG Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 333 THR Chi-restraints excluded: chain H residue 420 MET Chi-restraints excluded: chain H residue 509 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 328 optimal weight: 2.9990 chunk 223 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 293 optimal weight: 2.9990 chunk 162 optimal weight: 0.6980 chunk 336 optimal weight: 2.9990 chunk 272 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 201 optimal weight: 1.9990 chunk 353 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 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 100 GLN A 198 ASN B 100 GLN B 137 HIS B 198 ASN ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 507 HIS ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 198 ASN ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 198 ASN ** G 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 198 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.3445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 33168 Z= 0.256 Angle : 0.576 7.808 45072 Z= 0.287 Chirality : 0.044 0.172 5192 Planarity : 0.006 0.090 5560 Dihedral : 16.413 164.330 5515 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 2.77 % Allowed : 17.06 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.13), residues: 4104 helix: 0.96 (0.14), residues: 1528 sheet: -1.08 (0.29), residues: 320 loop : -0.73 (0.13), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS G -20 PHE 0.014 0.001 PHE E 24 TYR 0.012 0.001 TYR C 509 ARG 0.011 0.001 ARG F 203 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 736 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 643 time to evaluate : 3.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLU cc_start: 0.7831 (mm-30) cc_final: 0.7444 (mm-30) REVERT: A 106 LYS cc_start: 0.8645 (mtpt) cc_final: 0.8340 (ttmm) REVERT: A 131 LEU cc_start: 0.7926 (mt) cc_final: 0.7665 (mm) REVERT: A 150 MET cc_start: 0.7595 (pmm) cc_final: 0.7242 (pmm) REVERT: A 195 LYS cc_start: 0.7850 (ttpp) cc_final: 0.7501 (ttmm) REVERT: A 228 LYS cc_start: 0.8294 (mtmt) cc_final: 0.8041 (mtmt) REVERT: A 277 GLN cc_start: 0.8994 (OUTLIER) cc_final: 0.7821 (tm-30) REVERT: A 296 HIS cc_start: 0.7789 (OUTLIER) cc_final: 0.7346 (p-80) REVERT: A 322 ARG cc_start: 0.8875 (OUTLIER) cc_final: 0.7264 (ttm170) REVERT: A 509 TYR cc_start: 0.6897 (OUTLIER) cc_final: 0.6576 (t80) REVERT: B 58 LYS cc_start: 0.8349 (mttt) cc_final: 0.8124 (mttp) REVERT: B 103 GLU cc_start: 0.7814 (mm-30) cc_final: 0.7466 (mm-30) REVERT: B 106 LYS cc_start: 0.8634 (mtpt) cc_final: 0.8337 (ttmm) REVERT: B 131 LEU cc_start: 0.7789 (mp) cc_final: 0.7399 (mm) REVERT: B 150 MET cc_start: 0.7553 (mmm) cc_final: 0.7336 (mmm) REVERT: B 196 GLU cc_start: 0.7113 (mt-10) cc_final: 0.6808 (mt-10) REVERT: B 228 LYS cc_start: 0.8293 (mtmt) cc_final: 0.7669 (mtmt) REVERT: B 232 ASP cc_start: 0.7849 (m-30) cc_final: 0.7507 (m-30) REVERT: B 277 GLN cc_start: 0.8971 (OUTLIER) cc_final: 0.7966 (tm-30) REVERT: B 441 GLN cc_start: 0.8020 (mt0) cc_final: 0.7741 (mt0) REVERT: B 509 TYR cc_start: 0.6754 (OUTLIER) cc_final: 0.6315 (t80) REVERT: C 75 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.7331 (mt-10) REVERT: C 103 GLU cc_start: 0.7799 (mm-30) cc_final: 0.7414 (mm-30) REVERT: C 106 LYS cc_start: 0.8626 (mtpt) cc_final: 0.8319 (ttmm) REVERT: C 129 ASP cc_start: 0.7617 (m-30) cc_final: 0.7114 (m-30) REVERT: C 131 LEU cc_start: 0.7807 (mp) cc_final: 0.7454 (mm) REVERT: C 196 GLU cc_start: 0.7230 (mt-10) cc_final: 0.6816 (mt-10) REVERT: C 228 LYS cc_start: 0.8209 (mtmt) cc_final: 0.7799 (mtmt) REVERT: C 232 ASP cc_start: 0.7875 (m-30) cc_final: 0.7599 (m-30) REVERT: C 277 GLN cc_start: 0.8961 (OUTLIER) cc_final: 0.7856 (tm-30) REVERT: C 322 ARG cc_start: 0.9032 (OUTLIER) cc_final: 0.7483 (ttm170) REVERT: C 410 LYS cc_start: 0.7081 (tttt) cc_final: 0.6760 (ttpp) REVERT: C 509 TYR cc_start: 0.6771 (OUTLIER) cc_final: 0.6502 (t80) REVERT: D 103 GLU cc_start: 0.7792 (mm-30) cc_final: 0.7427 (mm-30) REVERT: D 106 LYS cc_start: 0.8640 (mtpt) cc_final: 0.8351 (ttmm) REVERT: D 131 LEU cc_start: 0.7828 (mp) cc_final: 0.7533 (mm) REVERT: D 228 LYS cc_start: 0.8308 (mtmt) cc_final: 0.7997 (mtmt) REVERT: D 277 GLN cc_start: 0.8886 (OUTLIER) cc_final: 0.7256 (tm-30) REVERT: D 296 HIS cc_start: 0.7708 (OUTLIER) cc_final: 0.7379 (p-80) REVERT: D 322 ARG cc_start: 0.9056 (OUTLIER) cc_final: 0.7553 (ttm170) REVERT: D 410 LYS cc_start: 0.7012 (ttmp) cc_final: 0.6556 (ttpp) REVERT: E 103 GLU cc_start: 0.7694 (mm-30) cc_final: 0.7427 (mm-30) REVERT: E 129 ASP cc_start: 0.7840 (m-30) cc_final: 0.7407 (m-30) REVERT: E 131 LEU cc_start: 0.7821 (mp) cc_final: 0.7467 (mm) REVERT: E 228 LYS cc_start: 0.8188 (mtpt) cc_final: 0.7842 (mtpt) REVERT: E 232 ASP cc_start: 0.7858 (m-30) cc_final: 0.7555 (m-30) REVERT: E 277 GLN cc_start: 0.8967 (OUTLIER) cc_final: 0.7801 (tm-30) REVERT: E 322 ARG cc_start: 0.8960 (OUTLIER) cc_final: 0.7353 (ttm170) REVERT: E 474 ARG cc_start: 0.7310 (mtp85) cc_final: 0.6918 (mtt90) REVERT: E 509 TYR cc_start: 0.6663 (OUTLIER) cc_final: 0.6264 (t80) REVERT: F 103 GLU cc_start: 0.7807 (mm-30) cc_final: 0.7457 (mm-30) REVERT: F 106 LYS cc_start: 0.8590 (mtpt) cc_final: 0.8300 (ttmm) REVERT: F 131 LEU cc_start: 0.7786 (mp) cc_final: 0.7438 (mm) REVERT: F 228 LYS cc_start: 0.8330 (mtmt) cc_final: 0.8048 (mtmt) REVERT: F 277 GLN cc_start: 0.8960 (OUTLIER) cc_final: 0.7876 (tm-30) REVERT: F 322 ARG cc_start: 0.8906 (OUTLIER) cc_final: 0.7370 (ttm170) REVERT: F 333 THR cc_start: 0.8100 (OUTLIER) cc_final: 0.7865 (t) REVERT: F 474 ARG cc_start: 0.7618 (ttm-80) cc_final: 0.7321 (ttt90) REVERT: F 509 TYR cc_start: 0.6732 (OUTLIER) cc_final: 0.6366 (t80) REVERT: G 103 GLU cc_start: 0.7707 (mm-30) cc_final: 0.7445 (mm-30) REVERT: G 131 LEU cc_start: 0.7891 (mp) cc_final: 0.7560 (mm) REVERT: G 196 GLU cc_start: 0.7213 (mt-10) cc_final: 0.6812 (mt-10) REVERT: G 296 HIS cc_start: 0.7744 (OUTLIER) cc_final: 0.7400 (p-80) REVERT: G 322 ARG cc_start: 0.8996 (OUTLIER) cc_final: 0.7415 (ttm170) REVERT: G 336 VAL cc_start: 0.8662 (t) cc_final: 0.8400 (t) REVERT: G 455 LYS cc_start: 0.8382 (OUTLIER) cc_final: 0.8069 (tppt) REVERT: G 509 TYR cc_start: 0.6737 (OUTLIER) cc_final: 0.6294 (t80) REVERT: H 103 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7454 (mm-30) REVERT: H 106 LYS cc_start: 0.8611 (mtpt) cc_final: 0.8341 (ttmm) REVERT: H 131 LEU cc_start: 0.7915 (mp) cc_final: 0.7589 (mm) REVERT: H 160 SER cc_start: 0.8147 (m) cc_final: 0.7889 (p) REVERT: H 262 LEU cc_start: 0.8227 (mp) cc_final: 0.7915 (mp) REVERT: H 277 GLN cc_start: 0.8976 (OUTLIER) cc_final: 0.7681 (tm-30) REVERT: H 322 ARG cc_start: 0.8998 (OUTLIER) cc_final: 0.7483 (ttm170) REVERT: H 509 TYR cc_start: 0.6702 (OUTLIER) cc_final: 0.6122 (t80) outliers start: 93 outliers final: 49 residues processed: 716 average time/residue: 2.5664 time to fit residues: 2188.2512 Evaluate side-chains 701 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 625 time to evaluate : 3.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain A residue 322 ARG Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 509 TYR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 117 ASP Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 509 TYR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 322 ARG Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 509 TYR Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 296 HIS Chi-restraints excluded: chain D residue 322 ARG Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 162 ASP Chi-restraints excluded: chain E residue 275 SER Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 322 ARG Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain E residue 455 LYS Chi-restraints excluded: chain E residue 509 TYR Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 322 ARG Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 509 TYR Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 296 HIS Chi-restraints excluded: chain G residue 322 ARG Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain G residue 455 LYS Chi-restraints excluded: chain G residue 509 TYR Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 162 ASP Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 322 ARG Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 333 THR Chi-restraints excluded: chain H residue 420 MET Chi-restraints excluded: chain H residue 509 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 132 optimal weight: 2.9990 chunk 355 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 231 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 394 optimal weight: 0.4980 chunk 327 optimal weight: 0.9980 chunk 182 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 207 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 202 GLN ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 507 HIS ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 198 ASN ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 507 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.3586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 33168 Z= 0.221 Angle : 0.557 7.214 45072 Z= 0.276 Chirality : 0.043 0.173 5192 Planarity : 0.005 0.095 5560 Dihedral : 15.870 168.567 5513 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 2.80 % Allowed : 17.30 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.14), residues: 4104 helix: 1.07 (0.14), residues: 1528 sheet: -1.05 (0.30), residues: 320 loop : -0.65 (0.13), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS G -20 PHE 0.012 0.001 PHE E 24 TYR 0.011 0.001 TYR C 509 ARG 0.014 0.001 ARG F 203 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 737 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 643 time to evaluate : 3.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLU cc_start: 0.7824 (mm-30) cc_final: 0.7449 (mm-30) REVERT: A 106 LYS cc_start: 0.8630 (mtpt) cc_final: 0.8333 (ttmm) REVERT: A 131 LEU cc_start: 0.7931 (mt) cc_final: 0.7674 (mm) REVERT: A 150 MET cc_start: 0.7579 (pmm) cc_final: 0.7227 (pmm) REVERT: A 195 LYS cc_start: 0.7827 (ttpp) cc_final: 0.7485 (ttmm) REVERT: A 228 LYS cc_start: 0.8298 (mtmt) cc_final: 0.7688 (mtmt) REVERT: A 232 ASP cc_start: 0.7824 (m-30) cc_final: 0.7496 (m-30) REVERT: A 277 GLN cc_start: 0.8985 (OUTLIER) cc_final: 0.7881 (tm-30) REVERT: A 296 HIS cc_start: 0.7763 (OUTLIER) cc_final: 0.7327 (p-80) REVERT: A 322 ARG cc_start: 0.8840 (OUTLIER) cc_final: 0.7208 (ttm170) REVERT: A 509 TYR cc_start: 0.6859 (OUTLIER) cc_final: 0.6604 (t80) REVERT: B 103 GLU cc_start: 0.7829 (mm-30) cc_final: 0.7474 (mm-30) REVERT: B 106 LYS cc_start: 0.8634 (mtpt) cc_final: 0.8332 (ttmm) REVERT: B 131 LEU cc_start: 0.7782 (mp) cc_final: 0.7388 (mm) REVERT: B 196 GLU cc_start: 0.7111 (mt-10) cc_final: 0.6817 (mt-10) REVERT: B 228 LYS cc_start: 0.8270 (mtmt) cc_final: 0.7648 (mtmt) REVERT: B 232 ASP cc_start: 0.7856 (m-30) cc_final: 0.7509 (m-30) REVERT: B 277 GLN cc_start: 0.8951 (OUTLIER) cc_final: 0.7997 (tm-30) REVERT: B 441 GLN cc_start: 0.8009 (mt0) cc_final: 0.7739 (mt0) REVERT: B 455 LYS cc_start: 0.8343 (OUTLIER) cc_final: 0.8020 (tppt) REVERT: B 509 TYR cc_start: 0.6705 (OUTLIER) cc_final: 0.6275 (t80) REVERT: C 103 GLU cc_start: 0.7818 (mm-30) cc_final: 0.7447 (mm-30) REVERT: C 106 LYS cc_start: 0.8645 (mtpt) cc_final: 0.8340 (ttmm) REVERT: C 131 LEU cc_start: 0.7814 (mp) cc_final: 0.7454 (mm) REVERT: C 196 GLU cc_start: 0.7244 (mt-10) cc_final: 0.6836 (mt-10) REVERT: C 228 LYS cc_start: 0.8200 (mtmt) cc_final: 0.7800 (mtmt) REVERT: C 232 ASP cc_start: 0.7872 (m-30) cc_final: 0.7597 (m-30) REVERT: C 277 GLN cc_start: 0.8937 (OUTLIER) cc_final: 0.7893 (tm-30) REVERT: C 322 ARG cc_start: 0.8999 (OUTLIER) cc_final: 0.7469 (ttm170) REVERT: C 410 LYS cc_start: 0.7042 (tttt) cc_final: 0.6744 (ttpp) REVERT: C 509 TYR cc_start: 0.6728 (OUTLIER) cc_final: 0.6478 (t80) REVERT: D 103 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7458 (mm-30) REVERT: D 106 LYS cc_start: 0.8619 (mtpt) cc_final: 0.8334 (ttmm) REVERT: D 131 LEU cc_start: 0.7759 (mp) cc_final: 0.7514 (mm) REVERT: D 203 ARG cc_start: 0.7833 (mtm110) cc_final: 0.7549 (mtm110) REVERT: D 228 LYS cc_start: 0.8306 (mtmt) cc_final: 0.7991 (mtmt) REVERT: D 277 GLN cc_start: 0.8861 (OUTLIER) cc_final: 0.7301 (tm-30) REVERT: D 296 HIS cc_start: 0.7694 (OUTLIER) cc_final: 0.7357 (p-80) REVERT: D 322 ARG cc_start: 0.9039 (OUTLIER) cc_final: 0.7554 (ttm170) REVERT: D 410 LYS cc_start: 0.7002 (ttmp) cc_final: 0.6621 (ttpp) REVERT: E 103 GLU cc_start: 0.7698 (mm-30) cc_final: 0.7425 (mm-30) REVERT: E 131 LEU cc_start: 0.7835 (mp) cc_final: 0.7469 (mm) REVERT: E 160 SER cc_start: 0.8169 (m) cc_final: 0.7743 (p) REVERT: E 228 LYS cc_start: 0.8201 (mtpt) cc_final: 0.7832 (mtpt) REVERT: E 232 ASP cc_start: 0.7853 (m-30) cc_final: 0.7568 (m-30) REVERT: E 277 GLN cc_start: 0.8936 (OUTLIER) cc_final: 0.7812 (tm-30) REVERT: E 322 ARG cc_start: 0.8946 (OUTLIER) cc_final: 0.7319 (ttm170) REVERT: E 474 ARG cc_start: 0.7305 (mtp85) cc_final: 0.6912 (mtt90) REVERT: E 509 TYR cc_start: 0.6653 (OUTLIER) cc_final: 0.6243 (t80) REVERT: F 103 GLU cc_start: 0.7808 (mm-30) cc_final: 0.7458 (mm-30) REVERT: F 106 LYS cc_start: 0.8601 (mtpt) cc_final: 0.8318 (ttmm) REVERT: F 131 LEU cc_start: 0.7809 (mp) cc_final: 0.7463 (mm) REVERT: F 228 LYS cc_start: 0.8334 (mtmt) cc_final: 0.8047 (mtmt) REVERT: F 277 GLN cc_start: 0.8941 (OUTLIER) cc_final: 0.7907 (tm-30) REVERT: F 322 ARG cc_start: 0.8886 (OUTLIER) cc_final: 0.7355 (ttm170) REVERT: F 333 THR cc_start: 0.8119 (OUTLIER) cc_final: 0.7889 (t) REVERT: F 410 LYS cc_start: 0.7383 (ttmt) cc_final: 0.6968 (tttm) REVERT: F 474 ARG cc_start: 0.7615 (ttm-80) cc_final: 0.7313 (ttt90) REVERT: F 509 TYR cc_start: 0.6686 (OUTLIER) cc_final: 0.6388 (t80) REVERT: G 103 GLU cc_start: 0.7712 (mm-30) cc_final: 0.7447 (mm-30) REVERT: G 131 LEU cc_start: 0.7889 (mp) cc_final: 0.7610 (mm) REVERT: G 196 GLU cc_start: 0.7185 (mt-10) cc_final: 0.6797 (mt-10) REVERT: G 228 LYS cc_start: 0.8150 (mtmt) cc_final: 0.7801 (mtmt) REVERT: G 232 ASP cc_start: 0.7860 (m-30) cc_final: 0.7584 (m-30) REVERT: G 296 HIS cc_start: 0.7746 (OUTLIER) cc_final: 0.7404 (p-80) REVERT: G 322 ARG cc_start: 0.8970 (OUTLIER) cc_final: 0.7416 (ttm170) REVERT: G 336 VAL cc_start: 0.8664 (t) cc_final: 0.8400 (t) REVERT: G 455 LYS cc_start: 0.8375 (OUTLIER) cc_final: 0.8142 (tppt) REVERT: G 509 TYR cc_start: 0.6668 (OUTLIER) cc_final: 0.6249 (t80) REVERT: H 103 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7446 (mm-30) REVERT: H 106 LYS cc_start: 0.8613 (mtpt) cc_final: 0.8339 (ttmm) REVERT: H 131 LEU cc_start: 0.7915 (mp) cc_final: 0.7580 (mm) REVERT: H 160 SER cc_start: 0.8073 (m) cc_final: 0.7867 (p) REVERT: H 232 ASP cc_start: 0.7825 (m-30) cc_final: 0.7473 (m-30) REVERT: H 277 GLN cc_start: 0.8942 (OUTLIER) cc_final: 0.7685 (tm-30) REVERT: H 322 ARG cc_start: 0.8982 (OUTLIER) cc_final: 0.7482 (ttm170) REVERT: H 509 TYR cc_start: 0.6632 (OUTLIER) cc_final: 0.6078 (t80) outliers start: 94 outliers final: 51 residues processed: 721 average time/residue: 2.5887 time to fit residues: 2237.3370 Evaluate side-chains 708 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 630 time to evaluate : 3.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain A residue 322 ARG Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 509 TYR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 455 LYS Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 509 TYR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 322 ARG Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 509 TYR Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 296 HIS Chi-restraints excluded: chain D residue 322 ARG Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 162 ASP Chi-restraints excluded: chain E residue 275 SER Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 322 ARG Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain E residue 455 LYS Chi-restraints excluded: chain E residue 509 TYR Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 322 ARG Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 455 LYS Chi-restraints excluded: chain F residue 509 TYR Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 296 HIS Chi-restraints excluded: chain G residue 322 ARG Chi-restraints excluded: chain G residue 455 LYS Chi-restraints excluded: chain G residue 509 TYR Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 162 ASP Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 322 ARG Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 333 THR Chi-restraints excluded: chain H residue 420 MET Chi-restraints excluded: chain H residue 509 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 380 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 224 optimal weight: 2.9990 chunk 288 optimal weight: 2.9990 chunk 223 optimal weight: 2.9990 chunk 332 optimal weight: 1.9990 chunk 220 optimal weight: 3.9990 chunk 393 optimal weight: 2.9990 chunk 246 optimal weight: 4.9990 chunk 239 optimal weight: 2.9990 chunk 181 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 303 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.3639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 33168 Z= 0.405 Angle : 0.635 7.361 45072 Z= 0.320 Chirality : 0.046 0.173 5192 Planarity : 0.006 0.108 5560 Dihedral : 16.107 165.234 5513 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 3.37 % Allowed : 17.30 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.13), residues: 4104 helix: 0.66 (0.14), residues: 1528 sheet: -1.09 (0.30), residues: 320 loop : -0.78 (0.13), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS G -20 PHE 0.019 0.002 PHE B 24 TYR 0.012 0.001 TYR C 348 ARG 0.015 0.001 ARG C 203 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 759 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 646 time to evaluate : 3.634 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: A 103 GLU cc_start: 0.7865 (mm-30) cc_final: 0.7501 (mm-30) REVERT: A 131 LEU cc_start: 0.7949 (mt) cc_final: 0.7701 (mm) REVERT: A 150 MET cc_start: 0.7610 (pmm) cc_final: 0.7264 (pmm) REVERT: A 195 LYS cc_start: 0.7891 (ttpp) cc_final: 0.7509 (ttmm) REVERT: A 228 LYS cc_start: 0.8317 (mtmt) cc_final: 0.7734 (mtmt) REVERT: A 232 ASP cc_start: 0.7808 (m-30) cc_final: 0.7501 (m-30) REVERT: A 296 HIS cc_start: 0.7814 (OUTLIER) cc_final: 0.7357 (p-80) REVERT: A 322 ARG cc_start: 0.8946 (OUTLIER) cc_final: 0.7324 (ttm170) REVERT: B 103 GLU cc_start: 0.7850 (mm-30) cc_final: 0.7502 (mm-30) REVERT: B 106 LYS cc_start: 0.8671 (mtpt) cc_final: 0.8346 (ttmm) REVERT: B 131 LEU cc_start: 0.7881 (mp) cc_final: 0.7470 (mm) REVERT: B 196 GLU cc_start: 0.7147 (mt-10) cc_final: 0.6917 (mt-10) REVERT: B 228 LYS cc_start: 0.8288 (mtmt) cc_final: 0.7405 (mtmt) REVERT: B 232 ASP cc_start: 0.7830 (m-30) cc_final: 0.7422 (m-30) REVERT: B 455 LYS cc_start: 0.8374 (OUTLIER) cc_final: 0.8053 (tppt) REVERT: B 509 TYR cc_start: 0.6843 (OUTLIER) cc_final: 0.6434 (t80) REVERT: C 75 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.7402 (mt-10) REVERT: C 103 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7502 (mm-30) REVERT: C 131 LEU cc_start: 0.7832 (mp) cc_final: 0.7461 (mm) REVERT: C 196 GLU cc_start: 0.7254 (mt-10) cc_final: 0.6860 (mt-10) REVERT: C 228 LYS cc_start: 0.8209 (mtmt) cc_final: 0.7852 (mtmt) REVERT: C 232 ASP cc_start: 0.7839 (m-30) cc_final: 0.7533 (m-30) REVERT: C 410 LYS cc_start: 0.7062 (tttt) cc_final: 0.6784 (ttpp) REVERT: C 509 TYR cc_start: 0.6881 (OUTLIER) cc_final: 0.6460 (t80) REVERT: D 103 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7500 (mm-30) REVERT: D 131 LEU cc_start: 0.7855 (mp) cc_final: 0.7542 (mm) REVERT: D 203 ARG cc_start: 0.7823 (mtm110) cc_final: 0.7529 (mtm110) REVERT: D 228 LYS cc_start: 0.8297 (mtmt) cc_final: 0.7675 (mtmt) REVERT: D 232 ASP cc_start: 0.7839 (m-30) cc_final: 0.7525 (m-30) REVERT: D 277 GLN cc_start: 0.8919 (OUTLIER) cc_final: 0.7403 (tm-30) REVERT: D 296 HIS cc_start: 0.7761 (OUTLIER) cc_final: 0.7438 (p-80) REVERT: D 410 LYS cc_start: 0.7138 (ttmp) cc_final: 0.6753 (ttpp) REVERT: D 509 TYR cc_start: 0.6645 (OUTLIER) cc_final: 0.5702 (t80) REVERT: E 103 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7457 (mm-30) REVERT: E 131 LEU cc_start: 0.7943 (mp) cc_final: 0.7588 (mm) REVERT: E 160 SER cc_start: 0.8247 (m) cc_final: 0.7869 (p) REVERT: E 228 LYS cc_start: 0.8204 (mtpt) cc_final: 0.7804 (mtpt) REVERT: E 232 ASP cc_start: 0.7851 (m-30) cc_final: 0.7514 (m-30) REVERT: E 322 ARG cc_start: 0.9040 (OUTLIER) cc_final: 0.7440 (ttm170) REVERT: E 474 ARG cc_start: 0.7377 (mtp85) cc_final: 0.6964 (mtt90) REVERT: E 509 TYR cc_start: 0.6793 (OUTLIER) cc_final: 0.6475 (t80) REVERT: F 103 GLU cc_start: 0.7840 (mm-30) cc_final: 0.7502 (mm-30) REVERT: F 131 LEU cc_start: 0.7845 (mp) cc_final: 0.7487 (mm) REVERT: F 179 MET cc_start: 0.7969 (ptt) cc_final: 0.7754 (ptm) REVERT: F 228 LYS cc_start: 0.8337 (mtmt) cc_final: 0.7465 (mtmt) REVERT: F 232 ASP cc_start: 0.7835 (m-30) cc_final: 0.7431 (m-30) REVERT: F 333 THR cc_start: 0.8212 (OUTLIER) cc_final: 0.7975 (t) REVERT: F 349 LYS cc_start: 0.9123 (OUTLIER) cc_final: 0.8676 (mptp) REVERT: F 474 ARG cc_start: 0.7648 (ttm-80) cc_final: 0.7316 (ttt180) REVERT: F 509 TYR cc_start: 0.6827 (OUTLIER) cc_final: 0.6580 (t80) REVERT: G 103 GLU cc_start: 0.7767 (mm-30) cc_final: 0.7440 (mm-30) REVERT: G 131 LEU cc_start: 0.7963 (mp) cc_final: 0.7614 (mm) REVERT: G 196 GLU cc_start: 0.7290 (mt-10) cc_final: 0.6904 (mt-10) REVERT: G 228 LYS cc_start: 0.8132 (mtmt) cc_final: 0.7749 (mtmt) REVERT: G 232 ASP cc_start: 0.7819 (m-30) cc_final: 0.7510 (m-30) REVERT: G 296 HIS cc_start: 0.7825 (OUTLIER) cc_final: 0.7459 (p-80) REVERT: G 336 VAL cc_start: 0.8744 (t) cc_final: 0.8477 (t) REVERT: G 455 LYS cc_start: 0.8424 (OUTLIER) cc_final: 0.8210 (tppt) REVERT: G 509 TYR cc_start: 0.6794 (OUTLIER) cc_final: 0.6453 (t80) REVERT: H 103 GLU cc_start: 0.7839 (mm-30) cc_final: 0.7496 (mm-30) REVERT: H 131 LEU cc_start: 0.7955 (mp) cc_final: 0.7612 (mm) REVERT: H 232 ASP cc_start: 0.7793 (m-30) cc_final: 0.7456 (m-30) REVERT: H 509 TYR cc_start: 0.6791 (OUTLIER) cc_final: 0.6378 (t80) outliers start: 113 outliers final: 73 residues processed: 737 average time/residue: 2.5859 time to fit residues: 2285.0651 Evaluate side-chains 718 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 627 time to evaluate : 3.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain A residue 322 ARG Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 509 TYR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 455 LYS Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 509 TYR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 322 ARG Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 474 ARG Chi-restraints excluded: chain C residue 509 TYR Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 296 HIS Chi-restraints excluded: chain D residue 322 ARG Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 474 ARG Chi-restraints excluded: chain D residue 509 TYR Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 162 ASP Chi-restraints excluded: chain E residue 275 SER Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 303 ASN Chi-restraints excluded: chain E residue 322 ARG Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain E residue 455 LYS Chi-restraints excluded: chain E residue 509 TYR Chi-restraints excluded: chain E residue 511 PHE Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 322 ARG Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 349 LYS Chi-restraints excluded: chain F residue 455 LYS Chi-restraints excluded: chain F residue 509 TYR Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 296 HIS Chi-restraints excluded: chain G residue 322 ARG Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain G residue 455 LYS Chi-restraints excluded: chain G residue 509 TYR Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 303 ASN Chi-restraints excluded: chain H residue 322 ARG Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 333 THR Chi-restraints excluded: chain H residue 420 MET Chi-restraints excluded: chain H residue 509 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 243 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 234 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 76 optimal weight: 0.1980 chunk 250 optimal weight: 0.7980 chunk 267 optimal weight: 2.9990 chunk 194 optimal weight: 0.4980 chunk 36 optimal weight: 1.9990 chunk 309 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 507 HIS C 202 GLN ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 507 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.3761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 33168 Z= 0.179 Angle : 0.553 7.095 45072 Z= 0.273 Chirality : 0.043 0.149 5192 Planarity : 0.005 0.107 5560 Dihedral : 15.434 165.887 5512 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 2.45 % Allowed : 18.20 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.14), residues: 4104 helix: 1.00 (0.14), residues: 1536 sheet: -0.98 (0.30), residues: 320 loop : -0.64 (0.14), residues: 2248 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.001 HIS G -20 PHE 0.009 0.001 PHE E 24 TYR 0.012 0.001 TYR C 509 ARG 0.017 0.001 ARG F 203 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 727 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 645 time to evaluate : 3.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLU cc_start: 0.7749 (mm-30) cc_final: 0.7452 (mm-30) REVERT: A 131 LEU cc_start: 0.7940 (mt) cc_final: 0.7696 (mm) REVERT: A 150 MET cc_start: 0.7578 (pmm) cc_final: 0.7227 (pmm) REVERT: A 195 LYS cc_start: 0.7736 (ttpp) cc_final: 0.7415 (ttmm) REVERT: A 228 LYS cc_start: 0.8320 (mtmt) cc_final: 0.8021 (mtmt) REVERT: A 277 GLN cc_start: 0.8953 (OUTLIER) cc_final: 0.7846 (tm-30) REVERT: A 296 HIS cc_start: 0.7755 (OUTLIER) cc_final: 0.7338 (p-80) REVERT: A 322 ARG cc_start: 0.8845 (OUTLIER) cc_final: 0.7206 (ttm170) REVERT: B 103 GLU cc_start: 0.7834 (mm-30) cc_final: 0.7500 (mm-30) REVERT: B 106 LYS cc_start: 0.8608 (mtpt) cc_final: 0.8315 (ttmm) REVERT: B 131 LEU cc_start: 0.7801 (mp) cc_final: 0.7424 (mm) REVERT: B 196 GLU cc_start: 0.7100 (mt-10) cc_final: 0.6815 (mt-10) REVERT: B 203 ARG cc_start: 0.7754 (mtm110) cc_final: 0.7550 (mtm110) REVERT: B 228 LYS cc_start: 0.8276 (mtmt) cc_final: 0.7667 (mtmt) REVERT: B 232 ASP cc_start: 0.7865 (m-30) cc_final: 0.7539 (m-30) REVERT: B 277 GLN cc_start: 0.8941 (OUTLIER) cc_final: 0.8014 (tm-30) REVERT: B 455 LYS cc_start: 0.8343 (OUTLIER) cc_final: 0.8108 (tppt) REVERT: B 509 TYR cc_start: 0.6625 (OUTLIER) cc_final: 0.6227 (t80) REVERT: C 103 GLU cc_start: 0.7742 (mm-30) cc_final: 0.7492 (mm-30) REVERT: C 131 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7457 (mm) REVERT: C 196 GLU cc_start: 0.7238 (mt-10) cc_final: 0.6806 (mt-10) REVERT: C 228 LYS cc_start: 0.8214 (mtmt) cc_final: 0.7787 (mtmt) REVERT: C 232 ASP cc_start: 0.7881 (m-30) cc_final: 0.7601 (m-30) REVERT: C 277 GLN cc_start: 0.8935 (OUTLIER) cc_final: 0.7911 (tm-30) REVERT: C 322 ARG cc_start: 0.8997 (OUTLIER) cc_final: 0.7455 (ttm170) REVERT: C 410 LYS cc_start: 0.6934 (tttt) cc_final: 0.6690 (ttpp) REVERT: C 509 TYR cc_start: 0.6820 (OUTLIER) cc_final: 0.6519 (t80) REVERT: D 103 GLU cc_start: 0.7737 (mm-30) cc_final: 0.7469 (mm-30) REVERT: D 131 LEU cc_start: 0.7834 (mp) cc_final: 0.7573 (mm) REVERT: D 228 LYS cc_start: 0.8300 (mtmt) cc_final: 0.7647 (mtmt) REVERT: D 232 ASP cc_start: 0.7847 (m-30) cc_final: 0.7526 (m-30) REVERT: D 277 GLN cc_start: 0.8822 (OUTLIER) cc_final: 0.7284 (tm-30) REVERT: D 296 HIS cc_start: 0.7727 (OUTLIER) cc_final: 0.7392 (p-80) REVERT: D 410 LYS cc_start: 0.7041 (ttmp) cc_final: 0.6684 (ttpm) REVERT: E 103 GLU cc_start: 0.7707 (mm-30) cc_final: 0.7411 (mm-30) REVERT: E 131 LEU cc_start: 0.7929 (mp) cc_final: 0.7556 (mm) REVERT: E 160 SER cc_start: 0.8152 (m) cc_final: 0.7818 (p) REVERT: E 228 LYS cc_start: 0.8225 (mtpt) cc_final: 0.7830 (mtpt) REVERT: E 232 ASP cc_start: 0.7844 (m-30) cc_final: 0.7534 (m-30) REVERT: E 277 GLN cc_start: 0.8950 (OUTLIER) cc_final: 0.7811 (tm-30) REVERT: E 322 ARG cc_start: 0.8930 (OUTLIER) cc_final: 0.7328 (ttm170) REVERT: E 474 ARG cc_start: 0.7336 (mtp85) cc_final: 0.6951 (mtt90) REVERT: E 509 TYR cc_start: 0.6627 (OUTLIER) cc_final: 0.6225 (t80) REVERT: F 103 GLU cc_start: 0.7746 (mm-30) cc_final: 0.7511 (mm-30) REVERT: F 131 LEU cc_start: 0.7853 (mp) cc_final: 0.7517 (mm) REVERT: F 228 LYS cc_start: 0.8346 (mtmt) cc_final: 0.8054 (mtmt) REVERT: F 277 GLN cc_start: 0.8933 (OUTLIER) cc_final: 0.7932 (tm-30) REVERT: F 322 ARG cc_start: 0.8893 (OUTLIER) cc_final: 0.7320 (ttm170) REVERT: F 333 THR cc_start: 0.8132 (OUTLIER) cc_final: 0.7897 (t) REVERT: F 410 LYS cc_start: 0.7426 (ttmt) cc_final: 0.6982 (tttm) REVERT: F 474 ARG cc_start: 0.7622 (ttm-80) cc_final: 0.7305 (ttt90) REVERT: F 509 TYR cc_start: 0.6696 (OUTLIER) cc_final: 0.6394 (t80) REVERT: G 103 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7396 (mm-30) REVERT: G 131 LEU cc_start: 0.7921 (mp) cc_final: 0.7599 (mm) REVERT: G 196 GLU cc_start: 0.7205 (mt-10) cc_final: 0.6845 (mt-10) REVERT: G 203 ARG cc_start: 0.7814 (mtm110) cc_final: 0.7565 (mtm110) REVERT: G 296 HIS cc_start: 0.7769 (OUTLIER) cc_final: 0.7386 (p-80) REVERT: G 322 ARG cc_start: 0.8953 (OUTLIER) cc_final: 0.7422 (ttm170) REVERT: G 336 VAL cc_start: 0.8711 (t) cc_final: 0.8436 (t) REVERT: G 455 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.8126 (tppt) REVERT: G 509 TYR cc_start: 0.6652 (OUTLIER) cc_final: 0.6245 (t80) REVERT: H 103 GLU cc_start: 0.7727 (mm-30) cc_final: 0.7444 (mm-30) REVERT: H 131 LEU cc_start: 0.7931 (mp) cc_final: 0.7604 (mm) REVERT: H 217 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7547 (tt0) REVERT: H 232 ASP cc_start: 0.7817 (m-30) cc_final: 0.7473 (m-30) REVERT: H 277 GLN cc_start: 0.8923 (OUTLIER) cc_final: 0.7645 (tm-30) REVERT: H 509 TYR cc_start: 0.6655 (OUTLIER) cc_final: 0.6189 (t80) outliers start: 82 outliers final: 48 residues processed: 708 average time/residue: 2.6041 time to fit residues: 2208.6283 Evaluate side-chains 707 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 634 time to evaluate : 3.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain A residue 322 ARG Chi-restraints excluded: chain A residue 509 TYR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 455 LYS Chi-restraints excluded: chain B residue 509 TYR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 322 ARG Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 509 TYR Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 296 HIS Chi-restraints excluded: chain D residue 322 ARG Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 162 ASP Chi-restraints excluded: chain E residue 275 SER Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 322 ARG Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain E residue 455 LYS Chi-restraints excluded: chain E residue 509 TYR Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 322 ARG Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 455 LYS Chi-restraints excluded: chain F residue 509 TYR Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 296 HIS Chi-restraints excluded: chain G residue 322 ARG Chi-restraints excluded: chain G residue 455 LYS Chi-restraints excluded: chain G residue 509 TYR Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 322 ARG Chi-restraints excluded: chain H residue 333 THR Chi-restraints excluded: chain H residue 420 MET Chi-restraints excluded: chain H residue 509 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 357 optimal weight: 3.9990 chunk 376 optimal weight: 0.8980 chunk 343 optimal weight: 1.9990 chunk 366 optimal weight: 0.0030 chunk 220 optimal weight: 0.1980 chunk 159 optimal weight: 1.9990 chunk 287 optimal weight: 0.9990 chunk 112 optimal weight: 0.4980 chunk 331 optimal weight: 2.9990 chunk 346 optimal weight: 3.9990 chunk 365 optimal weight: 0.7980 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 507 HIS C 112 GLN ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 202 GLN ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 507 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.3886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 33168 Z= 0.144 Angle : 0.535 7.208 45072 Z= 0.261 Chirality : 0.042 0.149 5192 Planarity : 0.005 0.112 5560 Dihedral : 14.788 174.570 5512 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 1.97 % Allowed : 19.39 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.14), residues: 4104 helix: 1.30 (0.14), residues: 1552 sheet: -0.85 (0.31), residues: 320 loop : -0.48 (0.14), residues: 2232 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS G -20 PHE 0.006 0.001 PHE F 24 TYR 0.012 0.001 TYR A 509 ARG 0.017 0.001 ARG F 203 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 738 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 672 time to evaluate : 3.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLU cc_start: 0.7653 (mm-30) cc_final: 0.7360 (mm-30) REVERT: A 131 LEU cc_start: 0.7905 (mt) cc_final: 0.7680 (mm) REVERT: A 150 MET cc_start: 0.7568 (pmm) cc_final: 0.7219 (pmm) REVERT: A 195 LYS cc_start: 0.7747 (ttpp) cc_final: 0.7397 (ttmm) REVERT: A 228 LYS cc_start: 0.8311 (mtmt) cc_final: 0.7672 (mtmt) REVERT: A 232 ASP cc_start: 0.7843 (m-30) cc_final: 0.7538 (m-30) REVERT: A 277 GLN cc_start: 0.8887 (OUTLIER) cc_final: 0.7812 (tm-30) REVERT: A 296 HIS cc_start: 0.7719 (OUTLIER) cc_final: 0.7282 (p-80) REVERT: B 70 MET cc_start: 0.8814 (mtp) cc_final: 0.8605 (mtp) REVERT: B 103 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7448 (mm-30) REVERT: B 106 LYS cc_start: 0.8607 (mtpt) cc_final: 0.8296 (ttmm) REVERT: B 131 LEU cc_start: 0.7858 (mp) cc_final: 0.7479 (mm) REVERT: B 203 ARG cc_start: 0.7691 (mtm110) cc_final: 0.7441 (mtm110) REVERT: B 217 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.6955 (mm-30) REVERT: B 228 LYS cc_start: 0.8278 (mtmt) cc_final: 0.7678 (mtmt) REVERT: B 232 ASP cc_start: 0.7895 (m-30) cc_final: 0.7582 (m-30) REVERT: B 277 GLN cc_start: 0.8841 (OUTLIER) cc_final: 0.7945 (tm-30) REVERT: B 337 MET cc_start: 0.7339 (mpt) cc_final: 0.6807 (mpm) REVERT: B 455 LYS cc_start: 0.8327 (OUTLIER) cc_final: 0.8085 (tppt) REVERT: B 509 TYR cc_start: 0.6322 (OUTLIER) cc_final: 0.5841 (t80) REVERT: C 75 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7395 (mt-10) REVERT: C 103 GLU cc_start: 0.7685 (mm-30) cc_final: 0.7389 (mm-30) REVERT: C 131 LEU cc_start: 0.7809 (OUTLIER) cc_final: 0.7444 (mm) REVERT: C 196 GLU cc_start: 0.7206 (mt-10) cc_final: 0.6786 (mt-10) REVERT: C 228 LYS cc_start: 0.8196 (mtmt) cc_final: 0.7807 (mtmt) REVERT: C 232 ASP cc_start: 0.7895 (m-30) cc_final: 0.7649 (m-30) REVERT: C 277 GLN cc_start: 0.8867 (OUTLIER) cc_final: 0.7994 (tm-30) REVERT: C 322 ARG cc_start: 0.8901 (OUTLIER) cc_final: 0.7470 (ttm170) REVERT: C 410 LYS cc_start: 0.6893 (tttt) cc_final: 0.6650 (ttpp) REVERT: D 98 GLU cc_start: 0.7633 (mp0) cc_final: 0.7289 (mp0) REVERT: D 103 GLU cc_start: 0.7704 (mm-30) cc_final: 0.7415 (mm-30) REVERT: D 131 LEU cc_start: 0.7865 (mp) cc_final: 0.7561 (mm) REVERT: D 228 LYS cc_start: 0.8285 (mtmt) cc_final: 0.7987 (mtmt) REVERT: D 296 HIS cc_start: 0.7702 (OUTLIER) cc_final: 0.7329 (p-80) REVERT: D 322 ARG cc_start: 0.8939 (OUTLIER) cc_final: 0.7509 (ttm170) REVERT: D 337 MET cc_start: 0.7393 (mmm) cc_final: 0.6926 (mpm) REVERT: D 410 LYS cc_start: 0.6988 (ttmp) cc_final: 0.6632 (ttpm) REVERT: E 58 LYS cc_start: 0.8279 (mttt) cc_final: 0.8072 (mttm) REVERT: E 98 GLU cc_start: 0.7635 (mp0) cc_final: 0.7307 (mp0) REVERT: E 103 GLU cc_start: 0.7678 (mm-30) cc_final: 0.7386 (mm-30) REVERT: E 131 LEU cc_start: 0.7908 (mp) cc_final: 0.7546 (mm) REVERT: E 160 SER cc_start: 0.8146 (m) cc_final: 0.7844 (p) REVERT: E 228 LYS cc_start: 0.8217 (mtpt) cc_final: 0.7856 (mtpt) REVERT: E 232 ASP cc_start: 0.7827 (m-30) cc_final: 0.7555 (m-30) REVERT: E 277 GLN cc_start: 0.8878 (OUTLIER) cc_final: 0.7872 (tm-30) REVERT: E 322 ARG cc_start: 0.8842 (OUTLIER) cc_final: 0.7248 (ttm170) REVERT: E 474 ARG cc_start: 0.7315 (mtp85) cc_final: 0.6936 (mtt90) REVERT: E 509 TYR cc_start: 0.6440 (OUTLIER) cc_final: 0.6030 (t80) REVERT: F 103 GLU cc_start: 0.7677 (mm-30) cc_final: 0.7386 (mm-30) REVERT: F 131 LEU cc_start: 0.7856 (mp) cc_final: 0.7511 (mm) REVERT: F 228 LYS cc_start: 0.8337 (mtmt) cc_final: 0.7730 (mtmt) REVERT: F 232 ASP cc_start: 0.7854 (m-30) cc_final: 0.7561 (m-30) REVERT: F 277 GLN cc_start: 0.8845 (OUTLIER) cc_final: 0.7960 (tm-30) REVERT: F 322 ARG cc_start: 0.8809 (OUTLIER) cc_final: 0.7393 (ttm170) REVERT: F 410 LYS cc_start: 0.7409 (OUTLIER) cc_final: 0.7037 (tttt) REVERT: F 474 ARG cc_start: 0.7602 (ttm-80) cc_final: 0.7291 (ttt90) REVERT: F 509 TYR cc_start: 0.6630 (OUTLIER) cc_final: 0.6318 (t80) REVERT: G 103 GLU cc_start: 0.7695 (mm-30) cc_final: 0.7400 (mm-30) REVERT: G 131 LEU cc_start: 0.7899 (mp) cc_final: 0.7685 (mm) REVERT: G 196 GLU cc_start: 0.7171 (mt-10) cc_final: 0.6828 (mt-10) REVERT: G 203 ARG cc_start: 0.7790 (mtm110) cc_final: 0.7537 (mtm110) REVERT: G 228 LYS cc_start: 0.8121 (mtmt) cc_final: 0.7628 (mtmt) REVERT: G 232 ASP cc_start: 0.7879 (m-30) cc_final: 0.7621 (m-30) REVERT: G 272 VAL cc_start: 0.8710 (t) cc_final: 0.8267 (p) REVERT: G 296 HIS cc_start: 0.7752 (OUTLIER) cc_final: 0.7376 (p-80) REVERT: G 322 ARG cc_start: 0.8912 (OUTLIER) cc_final: 0.7347 (ttm170) REVERT: G 336 VAL cc_start: 0.8675 (t) cc_final: 0.8411 (t) REVERT: G 455 LYS cc_start: 0.8339 (OUTLIER) cc_final: 0.8110 (tppt) REVERT: H 70 MET cc_start: 0.8835 (mtp) cc_final: 0.8612 (mtp) REVERT: H 103 GLU cc_start: 0.7652 (mm-30) cc_final: 0.7370 (mm-30) REVERT: H 131 LEU cc_start: 0.7918 (mp) cc_final: 0.7579 (mm) REVERT: H 217 GLU cc_start: 0.7753 (mt-10) cc_final: 0.7506 (tt0) REVERT: H 232 ASP cc_start: 0.7813 (m-30) cc_final: 0.7513 (m-30) REVERT: H 277 GLN cc_start: 0.8848 (OUTLIER) cc_final: 0.7547 (tm-30) REVERT: H 322 ARG cc_start: 0.8928 (OUTLIER) cc_final: 0.7535 (ttm170) REVERT: H 337 MET cc_start: 0.7333 (mmm) cc_final: 0.6951 (mpm) REVERT: H 455 LYS cc_start: 0.8298 (OUTLIER) cc_final: 0.8060 (tppt) REVERT: H 509 TYR cc_start: 0.6458 (OUTLIER) cc_final: 0.6078 (t80) outliers start: 66 outliers final: 32 residues processed: 721 average time/residue: 2.5291 time to fit residues: 2189.3147 Evaluate side-chains 706 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 648 time to evaluate : 3.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 455 LYS Chi-restraints excluded: chain B residue 509 TYR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 322 ARG Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 296 HIS Chi-restraints excluded: chain D residue 322 ARG Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 322 ARG Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain E residue 455 LYS Chi-restraints excluded: chain E residue 509 TYR Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 322 ARG Chi-restraints excluded: chain F residue 410 LYS Chi-restraints excluded: chain F residue 509 TYR Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 296 HIS Chi-restraints excluded: chain G residue 322 ARG Chi-restraints excluded: chain G residue 455 LYS Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 322 ARG Chi-restraints excluded: chain H residue 333 THR Chi-restraints excluded: chain H residue 420 MET Chi-restraints excluded: chain H residue 455 LYS Chi-restraints excluded: chain H residue 509 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 240 optimal weight: 0.9990 chunk 387 optimal weight: 1.9990 chunk 236 optimal weight: 1.9990 chunk 183 optimal weight: 2.9990 chunk 269 optimal weight: 3.9990 chunk 406 optimal weight: 0.5980 chunk 374 optimal weight: 0.3980 chunk 323 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 250 optimal weight: 2.9990 chunk 198 optimal weight: 6.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 507 HIS ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G -20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 507 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.3912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 33168 Z= 0.217 Angle : 0.558 8.024 45072 Z= 0.274 Chirality : 0.043 0.150 5192 Planarity : 0.005 0.120 5560 Dihedral : 14.843 173.798 5500 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 1.85 % Allowed : 19.84 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.14), residues: 4104 helix: 1.28 (0.14), residues: 1528 sheet: -0.82 (0.31), residues: 320 loop : -0.47 (0.14), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.001 HIS G -20 PHE 0.012 0.001 PHE E 24 TYR 0.010 0.001 TYR C 509 ARG 0.021 0.001 ARG C 203 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 712 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 650 time to evaluate : 3.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLU cc_start: 0.7681 (mm-30) cc_final: 0.7371 (mm-30) REVERT: A 131 LEU cc_start: 0.7923 (mt) cc_final: 0.7716 (mm) REVERT: A 150 MET cc_start: 0.7555 (pmm) cc_final: 0.7208 (pmm) REVERT: A 195 LYS cc_start: 0.7757 (ttpp) cc_final: 0.7377 (ttmm) REVERT: A 228 LYS cc_start: 0.8315 (mtmt) cc_final: 0.7674 (mtmt) REVERT: A 232 ASP cc_start: 0.7859 (m-30) cc_final: 0.7532 (m-30) REVERT: A 277 GLN cc_start: 0.8932 (OUTLIER) cc_final: 0.7824 (tm-30) REVERT: A 296 HIS cc_start: 0.7740 (OUTLIER) cc_final: 0.7299 (p-80) REVERT: B 103 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7543 (mm-30) REVERT: B 106 LYS cc_start: 0.8620 (mtpt) cc_final: 0.8412 (mtpt) REVERT: B 131 LEU cc_start: 0.7880 (mp) cc_final: 0.7502 (mm) REVERT: B 203 ARG cc_start: 0.7690 (mtm110) cc_final: 0.7434 (mtm110) REVERT: B 228 LYS cc_start: 0.8285 (mtmt) cc_final: 0.7661 (mtmt) REVERT: B 232 ASP cc_start: 0.7910 (m-30) cc_final: 0.7571 (m-30) REVERT: B 277 GLN cc_start: 0.8899 (OUTLIER) cc_final: 0.7902 (tm-30) REVERT: B 455 LYS cc_start: 0.8332 (OUTLIER) cc_final: 0.8093 (tppt) REVERT: B 509 TYR cc_start: 0.6345 (OUTLIER) cc_final: 0.5864 (t80) REVERT: C 103 GLU cc_start: 0.7713 (mm-30) cc_final: 0.7407 (mm-30) REVERT: C 131 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.7456 (mm) REVERT: C 196 GLU cc_start: 0.7244 (mt-10) cc_final: 0.6804 (mt-10) REVERT: C 228 LYS cc_start: 0.8207 (mtmt) cc_final: 0.7789 (mtmt) REVERT: C 232 ASP cc_start: 0.7887 (m-30) cc_final: 0.7616 (m-30) REVERT: C 277 GLN cc_start: 0.8926 (OUTLIER) cc_final: 0.7931 (tm-30) REVERT: C 322 ARG cc_start: 0.8967 (OUTLIER) cc_final: 0.7526 (ttm170) REVERT: C 410 LYS cc_start: 0.6930 (tttt) cc_final: 0.6687 (ttpp) REVERT: C 509 TYR cc_start: 0.6634 (OUTLIER) cc_final: 0.6287 (t80) REVERT: D 103 GLU cc_start: 0.7706 (mm-30) cc_final: 0.7389 (mm-30) REVERT: D 131 LEU cc_start: 0.7873 (mp) cc_final: 0.7570 (mm) REVERT: D 228 LYS cc_start: 0.8271 (mtmt) cc_final: 0.8030 (mtmt) REVERT: D 296 HIS cc_start: 0.7727 (OUTLIER) cc_final: 0.7352 (p-80) REVERT: D 322 ARG cc_start: 0.8987 (OUTLIER) cc_final: 0.7578 (ttm170) REVERT: D 410 LYS cc_start: 0.7040 (ttmp) cc_final: 0.6678 (ttpp) REVERT: E 103 GLU cc_start: 0.7712 (mm-30) cc_final: 0.7417 (mm-30) REVERT: E 131 LEU cc_start: 0.7921 (mp) cc_final: 0.7557 (mm) REVERT: E 160 SER cc_start: 0.8186 (m) cc_final: 0.7891 (p) REVERT: E 228 LYS cc_start: 0.8198 (mtpt) cc_final: 0.7813 (mtpt) REVERT: E 232 ASP cc_start: 0.7828 (m-30) cc_final: 0.7529 (m-30) REVERT: E 277 GLN cc_start: 0.8921 (OUTLIER) cc_final: 0.7849 (tm-30) REVERT: E 322 ARG cc_start: 0.8928 (OUTLIER) cc_final: 0.7296 (ttm170) REVERT: E 337 MET cc_start: 0.7440 (mmm) cc_final: 0.6926 (mpm) REVERT: E 474 ARG cc_start: 0.7309 (mtp85) cc_final: 0.6903 (mtt90) REVERT: E 509 TYR cc_start: 0.6468 (OUTLIER) cc_final: 0.6039 (t80) REVERT: F 103 GLU cc_start: 0.7696 (mm-30) cc_final: 0.7388 (mm-30) REVERT: F 131 LEU cc_start: 0.7867 (mp) cc_final: 0.7519 (mm) REVERT: F 228 LYS cc_start: 0.8312 (mtmt) cc_final: 0.7738 (mtmt) REVERT: F 232 ASP cc_start: 0.7865 (m-30) cc_final: 0.7560 (m-30) REVERT: F 277 GLN cc_start: 0.8898 (OUTLIER) cc_final: 0.7911 (tm-30) REVERT: F 322 ARG cc_start: 0.8871 (OUTLIER) cc_final: 0.7406 (ttm170) REVERT: F 474 ARG cc_start: 0.7617 (ttm-80) cc_final: 0.7307 (ttt180) REVERT: F 509 TYR cc_start: 0.6640 (OUTLIER) cc_final: 0.6348 (t80) REVERT: G 103 GLU cc_start: 0.7734 (mm-30) cc_final: 0.7424 (mm-30) REVERT: G 131 LEU cc_start: 0.7935 (mp) cc_final: 0.7705 (mm) REVERT: G 196 GLU cc_start: 0.7218 (mt-10) cc_final: 0.6860 (mt-10) REVERT: G 203 ARG cc_start: 0.7792 (mtm110) cc_final: 0.7539 (mtm110) REVERT: G 232 ASP cc_start: 0.7884 (m-30) cc_final: 0.7606 (m-30) REVERT: G 272 VAL cc_start: 0.8714 (t) cc_final: 0.8282 (p) REVERT: G 296 HIS cc_start: 0.7767 (OUTLIER) cc_final: 0.7390 (p-80) REVERT: G 322 ARG cc_start: 0.8984 (OUTLIER) cc_final: 0.7451 (ttm170) REVERT: G 336 VAL cc_start: 0.8713 (t) cc_final: 0.8441 (t) REVERT: G 455 LYS cc_start: 0.8342 (OUTLIER) cc_final: 0.8110 (tppt) REVERT: H 103 GLU cc_start: 0.7684 (mm-30) cc_final: 0.7377 (mm-30) REVERT: H 131 LEU cc_start: 0.7924 (mp) cc_final: 0.7586 (mm) REVERT: H 217 GLU cc_start: 0.7763 (mt-10) cc_final: 0.7543 (tt0) REVERT: H 232 ASP cc_start: 0.7849 (m-30) cc_final: 0.7527 (m-30) REVERT: H 277 GLN cc_start: 0.8911 (OUTLIER) cc_final: 0.7624 (tm-30) REVERT: H 322 ARG cc_start: 0.8978 (OUTLIER) cc_final: 0.7597 (ttm170) REVERT: H 455 LYS cc_start: 0.8306 (OUTLIER) cc_final: 0.8070 (tppt) REVERT: H 509 TYR cc_start: 0.6477 (OUTLIER) cc_final: 0.6039 (t80) outliers start: 62 outliers final: 33 residues processed: 697 average time/residue: 2.6317 time to fit residues: 2195.2665 Evaluate side-chains 699 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 642 time to evaluate : 3.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 117 ASP Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 455 LYS Chi-restraints excluded: chain B residue 509 TYR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 322 ARG Chi-restraints excluded: chain C residue 509 TYR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 296 HIS Chi-restraints excluded: chain D residue 322 ARG Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 322 ARG Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain E residue 455 LYS Chi-restraints excluded: chain E residue 509 TYR Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 322 ARG Chi-restraints excluded: chain F residue 455 LYS Chi-restraints excluded: chain F residue 509 TYR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 296 HIS Chi-restraints excluded: chain G residue 322 ARG Chi-restraints excluded: chain G residue 455 LYS Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 322 ARG Chi-restraints excluded: chain H residue 333 THR Chi-restraints excluded: chain H residue 420 MET Chi-restraints excluded: chain H residue 455 LYS Chi-restraints excluded: chain H residue 509 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 257 optimal weight: 0.2980 chunk 344 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 298 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 324 optimal weight: 4.9990 chunk 135 optimal weight: 2.9990 chunk 332 optimal weight: 3.9990 chunk 41 optimal weight: 0.5980 chunk 59 optimal weight: 0.6980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 507 HIS ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G -20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 507 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.142577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.106403 restraints weight = 102288.388| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 1.70 r_work: 0.2818 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2686 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.3960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 33168 Z= 0.182 Angle : 0.549 7.883 45072 Z= 0.269 Chirality : 0.042 0.147 5192 Planarity : 0.005 0.122 5560 Dihedral : 14.670 173.135 5498 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 1.88 % Allowed : 19.96 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.14), residues: 4104 helix: 1.34 (0.14), residues: 1528 sheet: -0.79 (0.31), residues: 320 loop : -0.44 (0.14), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.001 HIS G -20 PHE 0.009 0.001 PHE F 24 TYR 0.011 0.001 TYR A 509 ARG 0.019 0.001 ARG F 203 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 28709.66 seconds wall clock time: 491 minutes 17.84 seconds (29477.84 seconds total)