Starting phenix.real_space_refine on Tue Mar 26 00:56:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rfi_24443/03_2024/7rfi_24443_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rfi_24443/03_2024/7rfi_24443.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rfi_24443/03_2024/7rfi_24443.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rfi_24443/03_2024/7rfi_24443.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rfi_24443/03_2024/7rfi_24443_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rfi_24443/03_2024/7rfi_24443_trim_updated.pdb" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.217 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 72 5.49 5 S 160 5.16 5 C 16504 2.51 5 N 4536 2.21 5 O 5224 1.98 5 H 25698 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 34": "OD1" <-> "OD2" Residue "A GLU 48": "OE1" <-> "OE2" Residue "A ASP 50": "OD1" <-> "OD2" Residue "A ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A 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 GLU 196": "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 255": "OD1" <-> "OD2" Residue "A ASP 256": "OD1" <-> "OD2" Residue "A TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 352": "OE1" <-> "OE2" Residue "A ARG 355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 399": "OE1" <-> "OE2" Residue "A PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 404": "OD1" <-> "OD2" Residue "A ARG 407": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 474": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 491": "OE1" <-> "OE2" Residue "A PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU -19": "OE1" <-> "OE2" 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 34": "OD1" <-> "OD2" 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 GLU 196": "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 255": "OD1" <-> "OD2" Residue "B ASP 256": "OD1" <-> "OD2" Residue "B TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 352": "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 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 PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 491": "OE1" <-> "OE2" Residue "B GLU 500": "OE1" <-> "OE2" 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 GLU 15": "OE1" <-> "OE2" Residue "C PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 34": "OD1" <-> "OD2" Residue "C GLU 48": "OE1" <-> "OE2" Residue "C ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 103": "OE1" <-> "OE2" Residue "C ARG 105": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 196": "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 GLU 254": "OE1" <-> "OE2" 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 352": "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 ARG 407": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ASP 418": "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 PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 491": "OE1" <-> "OE2" Residue "C GLU 500": "OE1" <-> "OE2" Residue "C PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 3": "OD1" <-> "OD2" 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 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 114": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 253": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 254": "OE1" <-> "OE2" Residue "D ASP 255": "OD1" <-> "OD2" Residue "D ASP 256": "OD1" <-> "OD2" Residue "D TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 352": "OE1" <-> "OE2" Residue "D ARG 355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D 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 PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 491": "OE1" <-> "OE2" Residue "D GLU 500": "OE1" <-> "OE2" 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 GLU 15": "OE1" <-> "OE2" Residue "E PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 77": "OD1" <-> "OD2" Residue "E PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 103": "OE1" <-> "OE2" Residue "E ARG 105": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 196": "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 255": "OD1" <-> "OD2" 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 352": "OE1" <-> "OE2" Residue "E ARG 355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" 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 ARG 474": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 491": "OE1" <-> "OE2" Residue "E GLU 500": "OE1" <-> "OE2" Residue "E PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU -19": "OE1" <-> "OE2" 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 34": "OD1" <-> "OD2" Residue "F GLU 48": "OE1" <-> "OE2" Residue "F ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ASP 77": "OD1" <-> "OD2" 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 GLU 196": "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 255": "OD1" <-> "OD2" Residue "F ASP 256": "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 352": "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 ARG 474": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 491": "OE1" <-> "OE2" Residue "F GLU 500": "OE1" <-> "OE2" 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 PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 34": "OD1" <-> "OD2" Residue "G GLU 48": "OE1" <-> "OE2" Residue "G ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ASP 77": "OD1" <-> "OD2" Residue "G PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 103": "OE1" <-> "OE2" Residue "G ARG 105": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ARG 253": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ASP 255": "OD1" <-> "OD2" Residue "G ASP 256": "OD1" <-> "OD2" Residue "G TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 352": "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 ARG 407": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ASP 418": "OD1" <-> "OD2" Residue "G ASP 470": "OD1" <-> "OD2" Residue "G ARG 474": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 491": "OE1" <-> "OE2" Residue "G GLU 500": "OE1" <-> "OE2" Residue "G PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 3": "OD1" <-> "OD2" 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 34": "OD1" <-> "OD2" Residue "H GLU 48": "OE1" <-> "OE2" Residue "H ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" 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 GLU 196": "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 255": "OD1" <-> "OD2" Residue "H ASP 256": "OD1" <-> "OD2" Residue "H TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 352": "OE1" <-> "OE2" Residue "H ARG 355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ARG 407": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ASP 418": "OD1" <-> "OD2" Residue "H ARG 474": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 491": "OE1" <-> "OE2" Residue "H GLU 500": "OE1" <-> "OE2" Residue "H PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 52194 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 6393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 6393 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 13, 'TRANS': 408} Chain breaks: 4 Chain: "B" Number of atoms: 6393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 6393 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 13, 'TRANS': 408} Chain breaks: 4 Chain: "C" Number of atoms: 6393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 6393 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 13, 'TRANS': 408} Chain breaks: 4 Chain: "D" Number of atoms: 6393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 6393 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 13, 'TRANS': 408} Chain breaks: 4 Chain: "E" Number of atoms: 6393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 6393 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 13, 'TRANS': 408} Chain breaks: 4 Chain: "F" Number of atoms: 6394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 6394 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 13, 'TRANS': 408} Chain breaks: 4 Chain: "G" Number of atoms: 6394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 6394 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 13, 'TRANS': 408} Chain breaks: 4 Chain: "H" Number of atoms: 6393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 6393 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 13, 'TRANS': 408} Chain breaks: 4 Chain: "A" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 131 Unusual residues: {'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "B" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 131 Unusual residues: {'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "C" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 131 Unusual residues: {'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "D" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 131 Unusual residues: {'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "E" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 131 Unusual residues: {'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "F" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 131 Unusual residues: {'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "G" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 131 Unusual residues: {'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "H" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 131 Unusual residues: {'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Time building chain proxies: 21.12, per 1000 atoms: 0.40 Number of scatterers: 52194 At special positions: 0 Unit cell: (137.409, 137.409, 120.549, 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 160 16.00 P 72 15.00 O 5224 8.00 N 4536 7.00 C 16504 6.00 H 25698 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: 43.55 Conformation dependent library (CDL) restraints added in 5.5 seconds 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6032 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 144 helices and 32 sheets defined 39.0% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.06 Creating SS restraints... Processing helix chain 'A' and resid -17 through -8 Processing helix chain 'A' and resid 2 through 7 removed outlier: 3.521A pdb=" N SER A 7 " --> pdb=" O ASP A 3 " (cutoff:3.500A) Processing helix chain 'A' and resid 20 through 25 Processing helix chain 'A' and resid 32 through 34 No H-bonds generated for 'chain 'A' and resid 32 through 34' Processing helix chain 'A' and resid 46 through 48 No H-bonds generated for 'chain 'A' and resid 46 through 48' Processing helix chain 'A' and resid 76 through 84 Processing helix chain 'A' and resid 97 through 110 Processing helix chain 'A' and resid 194 through 197 Processing helix chain 'A' and resid 224 through 232 Processing helix chain 'A' and resid 254 through 266 removed outlier: 3.622A 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: 3.752A pdb=" N ASN A 312 " --> pdb=" O ALA A 308 " (cutoff:3.500A) removed outlier: 3.534A 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: 4.451A pdb=" N ARG A 356 " --> pdb=" O GLU A 352 " (cutoff:3.500A) removed outlier: 4.342A 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 501 Processing helix chain 'B' and resid -17 through -8 Processing helix chain 'B' and resid 2 through 7 Processing helix chain 'B' and resid 20 through 25 Processing helix chain 'B' and resid 32 through 34 No H-bonds generated for 'chain 'B' and resid 32 through 34' Processing helix chain 'B' and resid 46 through 48 No H-bonds generated for 'chain 'B' and resid 46 through 48' Processing helix chain 'B' and resid 76 through 84 Processing helix chain 'B' and resid 97 through 110 Processing helix chain 'B' and resid 194 through 197 Processing helix chain 'B' and resid 224 through 232 Processing helix chain 'B' and resid 254 through 266 removed outlier: 3.508A pdb=" N LEU B 260 " --> pdb=" O LYS B 257 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU B 263 " --> pdb=" O LEU B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 293 Processing helix chain 'B' and resid 307 through 316 removed outlier: 3.747A pdb=" N ASN B 312 " --> pdb=" O ALA B 308 " (cutoff:3.500A) removed outlier: 3.539A 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: 4.515A pdb=" N ARG B 356 " --> pdb=" O GLU B 352 " (cutoff:3.500A) removed outlier: 4.334A 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 484 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 7 Processing helix chain 'C' and resid 20 through 25 Processing helix chain 'C' and resid 32 through 34 No H-bonds generated for 'chain 'C' and resid 32 through 34' Processing helix chain 'C' and resid 46 through 48 No H-bonds generated for 'chain 'C' and resid 46 through 48' Processing helix chain 'C' and resid 76 through 85 Processing helix chain 'C' and resid 97 through 110 Processing helix chain 'C' and resid 194 through 197 Processing helix chain 'C' and resid 224 through 232 Processing helix chain 'C' and resid 254 through 266 removed outlier: 3.669A pdb=" N LEU C 260 " --> pdb=" O LYS C 257 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU C 263 " --> pdb=" O LEU C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 293 Processing helix chain 'C' and resid 307 through 316 removed outlier: 3.738A pdb=" N ASN C 312 " --> pdb=" O ALA C 308 " (cutoff:3.500A) removed outlier: 3.526A 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: 4.355A pdb=" N ARG C 356 " --> pdb=" O GLU C 352 " (cutoff:3.500A) removed outlier: 4.352A 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 484 Processing helix chain 'C' and resid 495 through 501 Processing helix chain 'D' and resid -17 through -8 Processing helix chain 'D' and resid 2 through 7 Processing helix chain 'D' and resid 20 through 25 Processing helix chain 'D' and resid 32 through 34 No H-bonds generated for 'chain 'D' and resid 32 through 34' Processing helix chain 'D' and resid 46 through 48 No H-bonds generated for 'chain 'D' and resid 46 through 48' Processing helix chain 'D' and resid 76 through 85 Processing helix chain 'D' and resid 97 through 110 Processing helix chain 'D' and resid 194 through 197 Processing helix chain 'D' and resid 224 through 232 Processing helix chain 'D' and resid 254 through 266 removed outlier: 3.601A pdb=" N LEU D 260 " --> pdb=" O LYS D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 293 Processing helix chain 'D' and resid 307 through 316 removed outlier: 3.757A pdb=" N ASN D 312 " --> pdb=" O ALA D 308 " (cutoff:3.500A) removed outlier: 3.552A 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: 4.171A 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 484 Processing helix chain 'D' and resid 495 through 501 Processing helix chain 'E' and resid -17 through -8 Processing helix chain 'E' and resid 2 through 7 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 85 Processing helix chain 'E' and resid 97 through 109 Processing helix chain 'E' and resid 194 through 197 Processing helix chain 'E' and resid 224 through 232 Processing helix chain 'E' and resid 254 through 266 removed outlier: 3.639A pdb=" N TYR E 258 " --> pdb=" O ASP E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 293 Processing helix chain 'E' and resid 307 through 316 removed outlier: 3.747A pdb=" N ASN E 312 " --> pdb=" O ALA E 308 " (cutoff:3.500A) removed outlier: 3.516A 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: 4.350A pdb=" N ARG E 356 " --> pdb=" O GLU E 352 " (cutoff:3.500A) removed outlier: 4.351A 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 484 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 7 removed outlier: 3.538A pdb=" N SER F 7 " --> pdb=" O ASP F 3 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 25 Processing helix chain 'F' and resid 32 through 34 No H-bonds generated for 'chain 'F' and resid 32 through 34' Processing helix chain 'F' and resid 46 through 48 No H-bonds generated for 'chain 'F' and resid 46 through 48' Processing helix chain 'F' and resid 76 through 85 Processing helix chain 'F' and resid 97 through 109 Processing helix chain 'F' and resid 194 through 197 Processing helix chain 'F' and resid 224 through 232 Processing helix chain 'F' and resid 254 through 266 removed outlier: 3.783A pdb=" N TYR F 258 " --> pdb=" O ASP F 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 293 Processing helix chain 'F' and resid 307 through 316 removed outlier: 3.732A pdb=" N ASN F 312 " --> pdb=" O ALA F 308 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU F 313 " --> pdb=" O GLN F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 337 Processing helix chain 'F' and resid 343 through 357 removed outlier: 4.528A pdb=" N ARG F 356 " --> pdb=" O GLU F 352 " (cutoff:3.500A) removed outlier: 4.350A 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 484 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 7 removed outlier: 3.566A pdb=" N SER G 7 " --> pdb=" O ASP G 3 " (cutoff:3.500A) 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 85 Processing helix chain 'G' and resid 97 through 109 Processing helix chain 'G' and resid 194 through 197 Processing helix chain 'G' and resid 224 through 232 Processing helix chain 'G' and resid 254 through 266 removed outlier: 3.637A pdb=" N TYR G 258 " --> pdb=" O ASP G 255 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU G 260 " --> pdb=" O LYS G 257 " (cutoff:3.500A) Processing helix chain 'G' and resid 281 through 293 Processing helix chain 'G' and resid 307 through 316 removed outlier: 3.766A pdb=" N ASN G 312 " --> pdb=" O ALA G 308 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU G 313 " --> pdb=" O GLN G 309 " (cutoff:3.500A) Processing helix chain 'G' and resid 333 through 337 Processing helix chain 'G' and resid 343 through 357 removed outlier: 4.524A pdb=" N ARG G 356 " --> pdb=" O GLU G 352 " (cutoff:3.500A) removed outlier: 4.390A 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 484 Processing helix chain 'G' and resid 495 through 501 Processing helix chain 'H' and resid -17 through -8 Processing helix chain 'H' and resid 2 through 7 Processing helix chain 'H' and resid 20 through 25 Processing helix chain 'H' and resid 32 through 34 No H-bonds generated for 'chain 'H' and resid 32 through 34' Processing helix chain 'H' and resid 46 through 48 No H-bonds generated for 'chain 'H' and resid 46 through 48' Processing helix chain 'H' and resid 76 through 85 Processing helix chain 'H' and resid 97 through 110 Processing helix chain 'H' and resid 194 through 197 Processing helix chain 'H' and resid 224 through 232 Processing helix chain 'H' and resid 254 through 266 removed outlier: 3.791A pdb=" N TYR H 258 " --> pdb=" O ASP H 255 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU H 260 " --> pdb=" O LYS H 257 " (cutoff:3.500A) Processing helix chain 'H' and resid 281 through 293 Processing helix chain 'H' and resid 307 through 316 removed outlier: 3.748A pdb=" N ASN H 312 " --> pdb=" O ALA H 308 " (cutoff:3.500A) removed outlier: 3.542A 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: 4.350A pdb=" N ARG H 356 " --> pdb=" O GLU H 352 " (cutoff:3.500A) removed outlier: 4.360A 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 484 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: 6.431A pdb=" N VAL A 384 " --> pdb=" O ILE A 66 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 247 through 249 removed outlier: 6.633A pdb=" N VAL A 270 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLN A 298 " --> pdb=" O ILE A 271 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 408 through 411 Processing sheet with id= E, first strand: chain 'B' and resid 35 through 37 Processing sheet with id= F, first strand: chain 'B' and resid 65 through 67 removed outlier: 6.460A pdb=" N VAL B 384 " --> pdb=" O ILE B 66 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 247 through 249 removed outlier: 6.635A pdb=" N VAL B 270 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N GLN B 298 " --> pdb=" O ILE B 271 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'B' and resid 408 through 411 Processing sheet with id= I, first strand: chain 'C' and resid 35 through 37 Processing sheet with id= J, first strand: chain 'C' and resid 65 through 67 removed outlier: 6.461A pdb=" N VAL C 384 " --> pdb=" O ILE C 66 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 247 through 249 removed outlier: 6.637A pdb=" N VAL C 270 " --> pdb=" O ALA C 248 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N GLN C 298 " --> pdb=" O ILE C 271 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'C' and resid 408 through 411 Processing sheet with id= M, first strand: chain 'D' and resid 35 through 37 Processing sheet with id= N, first strand: chain 'D' and resid 65 through 67 removed outlier: 6.333A pdb=" N VAL D 384 " --> pdb=" O ILE D 66 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 247 through 249 removed outlier: 6.639A pdb=" N VAL D 270 " --> pdb=" O ALA D 248 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N GLN D 298 " --> pdb=" O ILE D 271 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'D' and resid 408 through 411 Processing sheet with id= Q, first strand: chain 'E' and resid 35 through 37 Processing sheet with id= R, first strand: chain 'E' and resid 65 through 67 removed outlier: 6.445A pdb=" N VAL E 384 " --> pdb=" O ILE E 66 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 247 through 249 removed outlier: 6.649A pdb=" N VAL E 270 " --> pdb=" O ALA E 248 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N GLN E 298 " --> pdb=" O ILE E 271 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'E' and resid 408 through 411 Processing sheet with id= U, first strand: chain 'F' and resid 35 through 37 Processing sheet with id= V, first strand: chain 'F' and resid 65 through 67 removed outlier: 6.470A pdb=" N VAL F 384 " --> pdb=" O ILE F 66 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'F' and resid 247 through 250 removed outlier: 6.639A pdb=" N VAL F 270 " --> pdb=" O ALA F 248 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N VAL F 250 " --> pdb=" O VAL F 270 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N VAL F 272 " --> pdb=" O VAL F 250 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N GLN F 298 " --> pdb=" O ILE F 271 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N LEU F 273 " --> pdb=" O GLN F 298 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ILE F 300 " --> pdb=" O LEU F 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'F' and resid 408 through 411 Processing sheet with id= Y, first strand: chain 'G' and resid 35 through 37 Processing sheet with id= Z, first strand: chain 'G' and resid 65 through 67 removed outlier: 6.450A pdb=" N VAL G 384 " --> pdb=" O ILE G 66 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'G' and resid 247 through 249 removed outlier: 6.636A pdb=" N VAL G 270 " --> pdb=" O ALA G 248 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N GLN G 298 " --> pdb=" O ILE G 271 " (cutoff:3.500A) No H-bonds generated for sheet with id= AA Processing sheet with id= AB, first strand: chain 'G' and resid 408 through 411 Processing sheet with id= AC, first strand: chain 'H' and resid 35 through 37 Processing sheet with id= AD, first strand: chain 'H' and resid 65 through 67 removed outlier: 6.459A pdb=" N VAL H 384 " --> pdb=" O ILE H 66 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'H' and resid 247 through 249 removed outlier: 6.623A pdb=" N VAL H 270 " --> pdb=" O ALA H 248 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N GLN H 298 " --> pdb=" O ILE H 271 " (cutoff:3.500A) No H-bonds generated for sheet with id= AE Processing sheet with id= AF, first strand: chain 'H' and resid 408 through 411 804 hydrogen bonds defined for protein. 2136 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: 18.02 Time building geometry restraints manager: 44.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.94 - 1.12: 25650 1.12 - 1.29: 4388 1.29 - 1.47: 9901 1.47 - 1.65: 12451 1.65 - 1.82: 276 Bond restraints: 52666 Sorted by residual: bond pdb=" C3' GTP C 602 " pdb=" C4' GTP C 602 " ideal model delta sigma weight residual 1.524 1.297 0.227 2.00e-02 2.50e+03 1.29e+02 bond pdb=" C3' GTP H 602 " pdb=" C4' GTP H 602 " ideal model delta sigma weight residual 1.524 1.299 0.225 2.00e-02 2.50e+03 1.27e+02 bond pdb=" C3' GTP D 602 " pdb=" C4' GTP D 602 " ideal model delta sigma weight residual 1.524 1.299 0.225 2.00e-02 2.50e+03 1.27e+02 bond pdb=" C4' GTP H 602 " pdb=" O4' GTP H 602 " ideal model delta sigma weight residual 1.410 1.613 -0.203 2.00e-02 2.50e+03 1.03e+02 bond pdb=" C4' GTP D 602 " pdb=" O4' GTP D 602 " ideal model delta sigma weight residual 1.410 1.613 -0.203 2.00e-02 2.50e+03 1.03e+02 ... (remaining 52661 not shown) Histogram of bond angle deviations from ideal: 93.46 - 101.81: 188 101.81 - 110.17: 48556 110.17 - 118.52: 23313 118.52 - 126.87: 22479 126.87 - 135.23: 356 Bond angle restraints: 94892 Sorted by residual: angle pdb=" O3A GTP G 602 " pdb=" PB GTP G 602 " pdb=" O3B GTP G 602 " ideal model delta sigma weight residual 102.60 121.60 -19.00 3.00e+00 1.11e-01 4.01e+01 angle pdb=" O3A GTP E 602 " pdb=" PB GTP E 602 " pdb=" O3B GTP E 602 " ideal model delta sigma weight residual 102.60 121.56 -18.96 3.00e+00 1.11e-01 4.00e+01 angle pdb=" O3A GTP B 602 " pdb=" PB GTP B 602 " pdb=" O3B GTP B 602 " ideal model delta sigma weight residual 102.60 121.17 -18.57 3.00e+00 1.11e-01 3.83e+01 angle pdb=" CA HIS H 504 " pdb=" CB HIS H 504 " pdb=" CG HIS H 504 " ideal model delta sigma weight residual 113.80 119.93 -6.13 1.00e+00 1.00e+00 3.76e+01 angle pdb=" OE1 GLN H 100 " pdb=" CD GLN H 100 " pdb=" NE2 GLN H 100 " ideal model delta sigma weight residual 122.60 116.57 6.03 1.00e+00 1.00e+00 3.64e+01 ... (remaining 94887 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 23547 35.98 - 71.97: 1199 71.97 - 107.95: 88 107.95 - 143.93: 36 143.93 - 179.92: 20 Dihedral angle restraints: 24890 sinusoidal: 14024 harmonic: 10866 Sorted by residual: dihedral pdb=" C8 GTP E 602 " pdb=" C1' GTP E 602 " pdb=" N9 GTP E 602 " pdb=" O4' GTP E 602 " ideal model delta sinusoidal sigma weight residual 104.59 -75.32 179.92 1 2.00e+01 2.50e-03 4.80e+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 -73.64 178.23 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O5' GTP B 602 " pdb=" O3A GTP B 602 " pdb=" PA GTP B 602 " pdb=" PB GTP B 602 " ideal model delta sinusoidal sigma weight residual -85.88 91.32 -177.19 1 2.00e+01 2.50e-03 4.80e+01 ... (remaining 24887 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.161: 3840 0.161 - 0.321: 259 0.321 - 0.482: 23 0.482 - 0.642: 14 0.642 - 0.803: 16 Chirality restraints: 4152 Sorted by residual: chirality pdb=" CG LEU C -8 " pdb=" CB LEU C -8 " pdb=" CD1 LEU C -8 " pdb=" CD2 LEU C -8 " both_signs ideal model delta sigma weight residual False -2.59 -1.79 -0.80 2.00e-01 2.50e+01 1.61e+01 chirality pdb=" CG LEU D -8 " pdb=" CB LEU D -8 " pdb=" CD1 LEU D -8 " pdb=" CD2 LEU D -8 " both_signs ideal model delta sigma weight residual False -2.59 -1.81 -0.78 2.00e-01 2.50e+01 1.51e+01 chirality pdb=" CG LEU F -8 " pdb=" CB LEU F -8 " pdb=" CD1 LEU F -8 " pdb=" CD2 LEU F -8 " both_signs ideal model delta sigma weight residual False -2.59 -1.82 -0.77 2.00e-01 2.50e+01 1.48e+01 ... (remaining 4149 not shown) Planarity restraints: 7760 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' GTP F 602 " 0.231 2.00e-02 2.50e+03 9.80e-02 2.88e+02 pdb=" C2 GTP F 602 " -0.043 2.00e-02 2.50e+03 pdb=" C4 GTP F 602 " -0.096 2.00e-02 2.50e+03 pdb=" C5 GTP F 602 " -0.072 2.00e-02 2.50e+03 pdb=" C6 GTP F 602 " 0.015 2.00e-02 2.50e+03 pdb=" C8 GTP F 602 " -0.058 2.00e-02 2.50e+03 pdb=" N1 GTP F 602 " 0.021 2.00e-02 2.50e+03 pdb=" N2 GTP F 602 " 0.012 2.00e-02 2.50e+03 pdb=" N3 GTP F 602 " -0.085 2.00e-02 2.50e+03 pdb=" N7 GTP F 602 " -0.069 2.00e-02 2.50e+03 pdb=" N9 GTP F 602 " -0.027 2.00e-02 2.50e+03 pdb=" O6 GTP F 602 " 0.169 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 283 " 0.110 2.00e-02 2.50e+03 9.97e-02 1.49e+02 pdb=" CD GLN B 283 " -0.059 2.00e-02 2.50e+03 pdb=" OE1 GLN B 283 " -0.049 2.00e-02 2.50e+03 pdb=" NE2 GLN B 283 " -0.101 2.00e-02 2.50e+03 pdb="HE21 GLN B 283 " -0.066 2.00e-02 2.50e+03 pdb="HE22 GLN B 283 " 0.165 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' GTP A 602 " -0.157 2.00e-02 2.50e+03 6.79e-02 1.38e+02 pdb=" C2 GTP A 602 " 0.011 2.00e-02 2.50e+03 pdb=" C4 GTP A 602 " 0.042 2.00e-02 2.50e+03 pdb=" C5 GTP A 602 " 0.025 2.00e-02 2.50e+03 pdb=" C6 GTP A 602 " -0.030 2.00e-02 2.50e+03 pdb=" C8 GTP A 602 " 0.076 2.00e-02 2.50e+03 pdb=" N1 GTP A 602 " -0.068 2.00e-02 2.50e+03 pdb=" N2 GTP A 602 " 0.054 2.00e-02 2.50e+03 pdb=" N3 GTP A 602 " 0.059 2.00e-02 2.50e+03 pdb=" N7 GTP A 602 " 0.066 2.00e-02 2.50e+03 pdb=" N9 GTP A 602 " 0.000 2.00e-02 2.50e+03 pdb=" O6 GTP A 602 " -0.078 2.00e-02 2.50e+03 ... (remaining 7757 not shown) Histogram of nonbonded interaction distances: 1.39 - 2.03: 1640 2.03 - 2.67: 67883 2.67 - 3.32: 160975 3.32 - 3.96: 219537 3.96 - 4.60: 325503 Nonbonded interactions: 775538 Sorted by model distance: nonbonded pdb=" HB3 LYS D 228 " pdb=" HE2 LYS D 228 " model vdw 1.388 2.440 nonbonded pdb=" HB3 LYS G 195 " pdb=" HE3 LYS G 195 " model vdw 1.506 2.440 nonbonded pdb=" HB3 LYS H 228 " pdb=" HE3 LYS H 228 " model vdw 1.512 2.440 nonbonded pdb=" HB3 LYS A 228 " pdb=" HE3 LYS A 228 " model vdw 1.518 2.440 nonbonded pdb=" HB3 LYS E 228 " pdb=" HE3 LYS E 228 " model vdw 1.523 2.440 ... (remaining 775533 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' and (resid -21 or (resid -20 and (name N or name CA or name C or name \ O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name \ H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name HE2)) or r \ esid -19 through 516 or resid 601 through 604)) selection = (chain 'G' and (resid -21 or (resid -20 and (name N or name CA or name C or name \ O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name \ H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name HE2)) or r \ esid -19 through 516 or resid 601 through 604)) 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: 5.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.760 Extract box with map and model: 15.840 Check model and map are aligned: 0.800 Set scattering table: 0.490 Process input model: 157.470 Find NCS groups from input model: 2.420 Set up NCS constraints: 0.330 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:10.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 193.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 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 : 0.014 0.227 26968 Z= 0.943 Angle : 1.868 19.005 36592 Z= 1.150 Chirality : 0.105 0.803 4152 Planarity : 0.013 0.123 4528 Dihedral : 19.322 179.917 10184 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.39 % Allowed : 3.97 % Favored : 95.63 % Rotamer: Outliers : 1.61 % Allowed : 7.90 % Favored : 90.49 % Cbeta Deviations : 0.27 % 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: -1.71 (0.12), residues: 3296 helix: -1.03 (0.12), residues: 1352 sheet: -0.95 (0.30), residues: 264 loop : -1.15 (0.13), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.020 0.004 HIS F 504 PHE 0.078 0.011 PHE C 44 TYR 0.120 0.019 TYR E 4 ARG 0.009 0.001 ARG B 480 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 683 residues out of total 2672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 640 time to evaluate : 3.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 450 LYS cc_start: 0.8117 (mtmm) cc_final: 0.7813 (mtmm) REVERT: B 75 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7808 (mt-10) REVERT: B 109 LYS cc_start: 0.8236 (mmmm) cc_final: 0.8013 (mmtm) REVERT: B 231 ARG cc_start: 0.7314 (ttp-170) cc_final: 0.7086 (ttp-170) REVERT: B 325 MET cc_start: 0.8995 (ttt) cc_final: 0.8716 (ttt) REVERT: B 335 GLU cc_start: 0.7119 (mm-30) cc_final: 0.6704 (mm-30) REVERT: B 410 LYS cc_start: 0.7604 (ptmt) cc_final: 0.7383 (ptmt) REVERT: C 75 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7788 (mt-10) REVERT: C 399 GLU cc_start: 0.7420 (mm-30) cc_final: 0.7204 (mm-30) REVERT: C 450 LYS cc_start: 0.8058 (mtmm) cc_final: 0.7836 (mtmt) REVERT: D 325 MET cc_start: 0.8957 (ttt) cc_final: 0.8630 (ttm) REVERT: D 450 LYS cc_start: 0.8091 (mtmm) cc_final: 0.7830 (mtmm) REVERT: E 265 GLN cc_start: 0.7897 (mt0) cc_final: 0.7665 (mt0) REVERT: E 325 MET cc_start: 0.8977 (ttt) cc_final: 0.8604 (ttt) REVERT: F 75 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7822 (mt-10) REVERT: F 335 GLU cc_start: 0.7084 (mm-30) cc_final: 0.6818 (mm-30) REVERT: F 410 LYS cc_start: 0.7605 (ptmt) cc_final: 0.7339 (ptmt) REVERT: F 450 LYS cc_start: 0.8115 (mtmm) cc_final: 0.7682 (mttt) REVERT: G 75 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7846 (mt-10) REVERT: G 325 MET cc_start: 0.8887 (ttt) cc_final: 0.8606 (ttt) REVERT: G 399 GLU cc_start: 0.7344 (mm-30) cc_final: 0.7129 (mm-30) REVERT: G 410 LYS cc_start: 0.7546 (ptmt) cc_final: 0.7255 (ptmt) REVERT: G 450 LYS cc_start: 0.8064 (mtmm) cc_final: 0.7797 (mtmt) REVERT: H 450 LYS cc_start: 0.8094 (mtmm) cc_final: 0.7837 (mtmt) outliers start: 43 outliers final: 20 residues processed: 670 average time/residue: 2.9664 time to fit residues: 2312.3244 Evaluate side-chains 557 residues out of total 2672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 537 time to evaluate : 3.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 485 SER Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 228 LYS Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain E residue 196 GLU Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 485 SER Chi-restraints excluded: chain F residue 10 THR Chi-restraints excluded: chain F residue 198 ASN Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain G residue 198 ASN Chi-restraints excluded: chain H residue 227 LEU Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 485 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 283 optimal weight: 0.8980 chunk 254 optimal weight: 0.7980 chunk 141 optimal weight: 0.6980 chunk 86 optimal weight: 0.7980 chunk 171 optimal weight: 1.9990 chunk 136 optimal weight: 0.8980 chunk 263 optimal weight: 0.7980 chunk 101 optimal weight: 0.9990 chunk 160 optimal weight: 0.9990 chunk 196 optimal weight: 0.6980 chunk 305 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN A 100 GLN A 230 ASN A 312 ASN A 498 GLN B 33 ASN B 100 GLN B 312 ASN B 498 GLN C 100 GLN C 230 ASN C 312 ASN D 100 GLN D 230 ASN D 303 ASN D 312 ASN E 33 ASN E 100 GLN E 265 GLN E 283 GLN E 312 ASN E 498 GLN F 100 GLN ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 312 ASN G 100 GLN ** G 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 312 ASN G 498 GLN H 33 ASN H 100 GLN H 230 ASN H 312 ASN H 498 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 26968 Z= 0.195 Angle : 0.596 7.621 36592 Z= 0.296 Chirality : 0.043 0.161 4152 Planarity : 0.004 0.048 4528 Dihedral : 18.593 179.997 4397 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.65 % Allowed : 12.61 % Favored : 85.74 % 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: -0.48 (0.14), residues: 3296 helix: 0.42 (0.14), residues: 1352 sheet: -0.13 (0.29), residues: 336 loop : -0.96 (0.14), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS G 92 PHE 0.015 0.002 PHE E 357 TYR 0.013 0.002 TYR D 353 ARG 0.004 0.000 ARG A 407 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 2672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 559 time to evaluate : 3.707 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: A 325 MET cc_start: 0.8756 (ttt) cc_final: 0.8535 (ttt) REVERT: A 335 GLU cc_start: 0.7205 (mm-30) cc_final: 0.6813 (mm-30) REVERT: A 450 LYS cc_start: 0.8116 (mtmm) cc_final: 0.7779 (mttt) REVERT: B 109 LYS cc_start: 0.8190 (mmmm) cc_final: 0.7923 (mmtm) REVERT: B 325 MET cc_start: 0.8786 (ttt) cc_final: 0.8442 (ttt) REVERT: B 335 GLU cc_start: 0.7267 (mm-30) cc_final: 0.7004 (mm-30) REVERT: B 410 LYS cc_start: 0.7519 (ptmt) cc_final: 0.7259 (ptmt) REVERT: B 450 LYS cc_start: 0.7965 (mtmt) cc_final: 0.7692 (mttt) REVERT: C 241 GLN cc_start: 0.7746 (mt0) cc_final: 0.7532 (mt0) REVERT: C 450 LYS cc_start: 0.7985 (mtmm) cc_final: 0.7553 (mttt) REVERT: D 241 GLN cc_start: 0.7764 (mt0) cc_final: 0.7537 (mt0) REVERT: D 325 MET cc_start: 0.8788 (ttt) cc_final: 0.8449 (ttt) REVERT: D 450 LYS cc_start: 0.8054 (mtmm) cc_final: 0.7757 (mttt) REVERT: E 241 GLN cc_start: 0.7455 (mt0) cc_final: 0.7121 (mt0) REVERT: E 265 GLN cc_start: 0.7707 (mt0) cc_final: 0.7464 (mt0) REVERT: E 325 MET cc_start: 0.8765 (ttt) cc_final: 0.8409 (ttt) REVERT: F 325 MET cc_start: 0.8798 (ttt) cc_final: 0.8574 (ttt) REVERT: F 335 GLU cc_start: 0.7200 (mm-30) cc_final: 0.6849 (mm-30) REVERT: F 410 LYS cc_start: 0.7606 (ptmt) cc_final: 0.7352 (ptmt) REVERT: F 450 LYS cc_start: 0.8044 (mtmm) cc_final: 0.7702 (mttt) REVERT: F 498 GLN cc_start: 0.8675 (mt0) cc_final: 0.8469 (mt0) REVERT: G 325 MET cc_start: 0.8711 (ttt) cc_final: 0.8365 (ttt) REVERT: G 410 LYS cc_start: 0.7549 (ptmt) cc_final: 0.7246 (ptmt) REVERT: G 450 LYS cc_start: 0.7959 (mtmm) cc_final: 0.7675 (mttt) REVERT: H 450 LYS cc_start: 0.8054 (mtmm) cc_final: 0.7793 (mttt) outliers start: 44 outliers final: 29 residues processed: 592 average time/residue: 3.0918 time to fit residues: 2130.8828 Evaluate side-chains 541 residues out of total 2672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 512 time to evaluate : 3.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -8 LEU Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain B residue -8 LEU Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain C residue -8 LEU Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain D residue -8 LEU Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain E residue -8 LEU Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain F residue -8 LEU Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 389 LEU Chi-restraints excluded: chain G residue -8 LEU Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 198 ASN Chi-restraints excluded: chain H residue -8 LEU Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 389 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 169 optimal weight: 5.9990 chunk 94 optimal weight: 0.9990 chunk 253 optimal weight: 5.9990 chunk 207 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 305 optimal weight: 0.9990 chunk 330 optimal weight: 0.2980 chunk 272 optimal weight: 1.9990 chunk 303 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 245 optimal weight: 5.9990 overall best weight: 1.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 498 GLN B 441 GLN B 498 GLN C 33 ASN ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 441 GLN D 33 ASN D 283 GLN E 283 GLN E 498 GLN F 33 ASN G 33 ASN ** G 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 498 GLN H 498 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 26968 Z= 0.238 Angle : 0.578 6.814 36592 Z= 0.287 Chirality : 0.044 0.163 4152 Planarity : 0.004 0.052 4528 Dihedral : 16.947 178.693 4373 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.02 % Allowed : 14.60 % Favored : 83.38 % 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 (0.14), residues: 3296 helix: 0.70 (0.14), residues: 1352 sheet: -0.21 (0.31), residues: 296 loop : -0.79 (0.14), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS H 372 PHE 0.015 0.002 PHE E 357 TYR 0.012 0.002 TYR G 282 ARG 0.003 0.000 ARG B 259 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 2672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 524 time to evaluate : 3.969 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: A 325 MET cc_start: 0.8687 (ttt) cc_final: 0.8398 (ttt) REVERT: A 450 LYS cc_start: 0.8095 (mtmm) cc_final: 0.7735 (mtmm) REVERT: B 277 GLN cc_start: 0.8966 (OUTLIER) cc_final: 0.7438 (tm-30) REVERT: B 325 MET cc_start: 0.8714 (ttt) cc_final: 0.8464 (ttt) REVERT: B 410 LYS cc_start: 0.7568 (ptmt) cc_final: 0.7340 (ptmt) REVERT: C 450 LYS cc_start: 0.8019 (mtmm) cc_final: 0.7693 (mtmm) REVERT: D 325 MET cc_start: 0.8668 (ttt) cc_final: 0.8428 (ttt) REVERT: D 450 LYS cc_start: 0.8011 (mtmm) cc_final: 0.7738 (mtmm) REVERT: E 325 MET cc_start: 0.8689 (ttt) cc_final: 0.8442 (ttt) REVERT: F 325 MET cc_start: 0.8714 (ttt) cc_final: 0.8432 (ttt) REVERT: F 410 LYS cc_start: 0.7629 (ptmt) cc_final: 0.7348 (ptmt) REVERT: F 450 LYS cc_start: 0.8064 (mtmm) cc_final: 0.7738 (mtmm) REVERT: G 410 LYS cc_start: 0.7545 (ptmt) cc_final: 0.7210 (ptmt) REVERT: G 450 LYS cc_start: 0.7970 (mtmm) cc_final: 0.7704 (mtmm) REVERT: H 450 LYS cc_start: 0.8033 (mtmm) cc_final: 0.7761 (mtmm) outliers start: 54 outliers final: 24 residues processed: 561 average time/residue: 3.0192 time to fit residues: 1956.4761 Evaluate side-chains 541 residues out of total 2672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 516 time to evaluate : 3.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -8 LEU Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain B residue -8 LEU Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain C residue -8 LEU Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain D residue -8 LEU Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain E residue -8 LEU Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain F residue -8 LEU Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain G residue -8 LEU Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain H residue -8 LEU Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 389 LEU Chi-restraints excluded: chain H residue 446 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 302 optimal weight: 1.9990 chunk 229 optimal weight: 1.9990 chunk 158 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 145 optimal weight: 2.9990 chunk 205 optimal weight: 1.9990 chunk 306 optimal weight: 1.9990 chunk 324 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 chunk 290 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 498 GLN ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 GLN ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 241 GLN E 265 GLN ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 498 GLN ** F 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 441 GLN F 507 HIS ** G 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 498 GLN H 498 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 26968 Z= 0.355 Angle : 0.616 7.102 36592 Z= 0.308 Chirality : 0.046 0.150 4152 Planarity : 0.005 0.052 4528 Dihedral : 16.887 179.794 4370 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.43 % Allowed : 14.22 % Favored : 83.35 % 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: -0.44 (0.14), residues: 3296 helix: 0.51 (0.14), residues: 1352 sheet: -0.39 (0.29), residues: 296 loop : -0.92 (0.14), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS C 466 PHE 0.017 0.002 PHE B 357 TYR 0.013 0.002 TYR G 282 ARG 0.004 0.000 ARG C 259 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 2672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 522 time to evaluate : 3.244 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 94 ASN cc_start: 0.8885 (t0) cc_final: 0.8667 (t0) REVERT: A 325 MET cc_start: 0.8672 (ttt) cc_final: 0.8448 (ttt) REVERT: A 450 LYS cc_start: 0.8044 (mtmm) cc_final: 0.7613 (mtmm) REVERT: B 109 LYS cc_start: 0.8251 (mmmm) cc_final: 0.7911 (mmtm) REVERT: B 325 MET cc_start: 0.8633 (ttt) cc_final: 0.8428 (ttt) REVERT: B 410 LYS cc_start: 0.7509 (ptmt) cc_final: 0.7215 (ptmt) REVERT: C 94 ASN cc_start: 0.8886 (t0) cc_final: 0.8664 (t0) REVERT: C 450 LYS cc_start: 0.7967 (mtmm) cc_final: 0.7554 (mtmm) REVERT: D 21 GLN cc_start: 0.8118 (OUTLIER) cc_final: 0.7524 (tm-30) REVERT: D 450 LYS cc_start: 0.7959 (mtmm) cc_final: 0.7677 (mtmm) REVERT: E 325 MET cc_start: 0.8624 (ttt) cc_final: 0.8403 (ttt) REVERT: F 325 MET cc_start: 0.8686 (ttt) cc_final: 0.8473 (ttt) REVERT: F 410 LYS cc_start: 0.7593 (ptmt) cc_final: 0.7298 (ptmt) REVERT: F 450 LYS cc_start: 0.8003 (mtmm) cc_final: 0.7614 (mtmt) REVERT: G 21 GLN cc_start: 0.8109 (OUTLIER) cc_final: 0.7511 (tm-30) REVERT: G 277 GLN cc_start: 0.9072 (OUTLIER) cc_final: 0.7235 (tm-30) REVERT: G 450 LYS cc_start: 0.7938 (mtmm) cc_final: 0.7601 (mtmm) REVERT: H 450 LYS cc_start: 0.7994 (mtmm) cc_final: 0.7569 (mtmt) outliers start: 65 outliers final: 30 residues processed: 562 average time/residue: 2.7432 time to fit residues: 1790.3847 Evaluate side-chains 552 residues out of total 2672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 519 time to evaluate : 3.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -8 LEU Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain B residue -8 LEU Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain C residue -8 LEU Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain D residue -8 LEU Chi-restraints excluded: chain D residue 21 GLN Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain E residue -8 LEU Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain F residue -8 LEU Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 389 LEU Chi-restraints excluded: chain G residue -8 LEU Chi-restraints excluded: chain G residue 21 GLN Chi-restraints excluded: chain G residue 75 GLU Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain H residue -8 LEU Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 333 THR Chi-restraints excluded: chain H residue 446 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 270 optimal weight: 0.9980 chunk 184 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 241 optimal weight: 2.9990 chunk 134 optimal weight: 0.9990 chunk 277 optimal weight: 3.9990 chunk 224 optimal weight: 7.9990 chunk 0 optimal weight: 4.9990 chunk 165 optimal weight: 0.6980 chunk 291 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 GLN ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 498 GLN ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 GLN ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 GLN E 230 ASN E 265 GLN ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 498 GLN ** F 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 498 GLN H 498 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 26968 Z= 0.211 Angle : 0.549 7.166 36592 Z= 0.269 Chirality : 0.043 0.147 4152 Planarity : 0.004 0.052 4528 Dihedral : 16.223 178.874 4370 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.57 % Allowed : 15.72 % Favored : 82.71 % 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: -0.17 (0.14), residues: 3296 helix: 0.79 (0.14), residues: 1352 sheet: -0.36 (0.29), residues: 296 loop : -0.78 (0.14), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS G 466 PHE 0.010 0.001 PHE G 357 TYR 0.011 0.001 TYR H 353 ARG 0.002 0.000 ARG D 259 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 2672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 522 time to evaluate : 3.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 325 MET cc_start: 0.8652 (ttt) cc_final: 0.8362 (ttt) REVERT: A 450 LYS cc_start: 0.8047 (mtmm) cc_final: 0.7610 (mtmm) REVERT: B 21 GLN cc_start: 0.8049 (OUTLIER) cc_final: 0.7475 (tm-30) REVERT: B 277 GLN cc_start: 0.8998 (OUTLIER) cc_final: 0.7370 (tm-30) REVERT: B 410 LYS cc_start: 0.7479 (ptmt) cc_final: 0.7183 (ptmt) REVERT: C 21 GLN cc_start: 0.8088 (OUTLIER) cc_final: 0.7475 (tm-30) REVERT: C 450 LYS cc_start: 0.7939 (mtmm) cc_final: 0.7528 (mtmm) REVERT: D 21 GLN cc_start: 0.8075 (OUTLIER) cc_final: 0.7453 (tm-30) REVERT: D 450 LYS cc_start: 0.7925 (mtmm) cc_final: 0.7652 (mtmm) REVERT: E 325 MET cc_start: 0.8574 (ttt) cc_final: 0.8341 (ttt) REVERT: F 325 MET cc_start: 0.8682 (ttt) cc_final: 0.8399 (ttt) REVERT: F 410 LYS cc_start: 0.7579 (ptmt) cc_final: 0.7285 (ptmt) REVERT: F 450 LYS cc_start: 0.7967 (mtmm) cc_final: 0.7714 (mtmm) REVERT: G 21 GLN cc_start: 0.8070 (OUTLIER) cc_final: 0.7452 (tm-30) REVERT: G 441 GLN cc_start: 0.8204 (mt0) cc_final: 0.7921 (mt0) REVERT: G 450 LYS cc_start: 0.7898 (mtmm) cc_final: 0.7422 (mtmm) REVERT: H 450 LYS cc_start: 0.7940 (mtmm) cc_final: 0.7466 (mtmm) outliers start: 42 outliers final: 18 residues processed: 551 average time/residue: 2.5884 time to fit residues: 1652.3046 Evaluate side-chains 542 residues out of total 2672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 519 time to evaluate : 2.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -8 LEU Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain B residue -8 LEU Chi-restraints excluded: chain B residue 21 GLN Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain C residue -8 LEU Chi-restraints excluded: chain C residue 21 GLN Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain D residue -8 LEU Chi-restraints excluded: chain D residue 21 GLN Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain E residue -8 LEU Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain F residue -8 LEU Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain G residue -8 LEU Chi-restraints excluded: chain G residue 21 GLN Chi-restraints excluded: chain G residue 446 SER Chi-restraints excluded: chain H residue -8 LEU Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 446 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 109 optimal weight: 3.9990 chunk 292 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 190 optimal weight: 1.9990 chunk 80 optimal weight: 0.5980 chunk 325 optimal weight: 3.9990 chunk 269 optimal weight: 3.9990 chunk 150 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 170 optimal weight: 1.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 GLN ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 498 GLN ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 GLN ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 GLN E 265 GLN ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 498 GLN ** F 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 441 GLN ** G 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 498 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 26968 Z= 0.315 Angle : 0.589 7.116 36592 Z= 0.292 Chirality : 0.045 0.146 4152 Planarity : 0.004 0.051 4528 Dihedral : 16.182 178.495 4370 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.06 % Allowed : 15.42 % Favored : 82.52 % 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: -0.34 (0.14), residues: 3296 helix: 0.62 (0.14), residues: 1352 sheet: -0.43 (0.28), residues: 296 loop : -0.85 (0.14), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS G 466 PHE 0.014 0.002 PHE A 357 TYR 0.012 0.002 TYR H 353 ARG 0.003 0.000 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 2672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 526 time to evaluate : 3.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 325 MET cc_start: 0.8671 (ttt) cc_final: 0.8438 (ttt) REVERT: A 450 LYS cc_start: 0.8043 (mtmm) cc_final: 0.7687 (mtmm) REVERT: B 21 GLN cc_start: 0.8082 (OUTLIER) cc_final: 0.7510 (tm-30) REVERT: B 410 LYS cc_start: 0.7499 (ptmt) cc_final: 0.7162 (ptmt) REVERT: C 21 GLN cc_start: 0.8135 (OUTLIER) cc_final: 0.7510 (tm-30) REVERT: C 450 LYS cc_start: 0.7898 (mtmm) cc_final: 0.7443 (mtmm) REVERT: D 21 GLN cc_start: 0.8114 (OUTLIER) cc_final: 0.7514 (tm-30) REVERT: D 441 GLN cc_start: 0.8169 (mt0) cc_final: 0.7922 (mt0) REVERT: D 450 LYS cc_start: 0.7897 (mtmm) cc_final: 0.7540 (mtmm) REVERT: E 325 MET cc_start: 0.8614 (ttt) cc_final: 0.8411 (ttt) REVERT: E 450 LYS cc_start: 0.8171 (ptpp) cc_final: 0.7951 (ptpp) REVERT: F 325 MET cc_start: 0.8696 (ttt) cc_final: 0.8474 (ttt) REVERT: F 410 LYS cc_start: 0.7601 (ptmt) cc_final: 0.7289 (ptmt) REVERT: F 450 LYS cc_start: 0.7950 (mtmm) cc_final: 0.7661 (mtmm) REVERT: G 21 GLN cc_start: 0.8107 (OUTLIER) cc_final: 0.7517 (tm-30) REVERT: G 450 LYS cc_start: 0.7867 (mtmm) cc_final: 0.7495 (mtmm) REVERT: H 450 LYS cc_start: 0.7891 (mtmm) cc_final: 0.7515 (mtmm) outliers start: 55 outliers final: 36 residues processed: 563 average time/residue: 2.4193 time to fit residues: 1573.5093 Evaluate side-chains 563 residues out of total 2672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 523 time to evaluate : 2.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -8 LEU Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain B residue -8 LEU Chi-restraints excluded: chain B residue 21 GLN Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain C residue -8 LEU Chi-restraints excluded: chain C residue 21 GLN Chi-restraints excluded: chain C residue 242 LYS Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 339 CYS Chi-restraints excluded: chain D residue -8 LEU Chi-restraints excluded: chain D residue 21 GLN Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 242 LYS Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain E residue -8 LEU Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain F residue -8 LEU Chi-restraints excluded: chain F residue 274 ASP Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 339 CYS Chi-restraints excluded: chain G residue -8 LEU Chi-restraints excluded: chain G residue 21 GLN Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 339 CYS Chi-restraints excluded: chain G residue 446 SER Chi-restraints excluded: chain H residue -8 LEU Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 339 CYS Chi-restraints excluded: chain H residue 446 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 313 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 185 optimal weight: 2.9990 chunk 237 optimal weight: 1.9990 chunk 183 optimal weight: 0.5980 chunk 273 optimal weight: 1.9990 chunk 181 optimal weight: 0.6980 chunk 323 optimal weight: 1.9990 chunk 202 optimal weight: 3.9990 chunk 197 optimal weight: 0.8980 chunk 149 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 GLN ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 498 GLN ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 GLN ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 441 GLN B 498 GLN ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 441 GLN E 265 GLN ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 498 GLN ** F 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 265 GLN ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 265 GLN ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 265 GLN H 498 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 26968 Z= 0.228 Angle : 0.550 7.133 36592 Z= 0.270 Chirality : 0.043 0.148 4152 Planarity : 0.004 0.051 4528 Dihedral : 15.888 176.965 4370 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.87 % Allowed : 15.87 % Favored : 82.26 % 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: -0.13 (0.14), residues: 3296 helix: 0.81 (0.14), residues: 1352 sheet: -0.60 (0.28), residues: 312 loop : -0.70 (0.14), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 466 PHE 0.010 0.001 PHE A 357 TYR 0.011 0.001 TYR H 353 ARG 0.002 0.000 ARG D 253 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 2672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 523 time to evaluate : 2.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 325 MET cc_start: 0.8643 (ttt) cc_final: 0.8372 (ttt) REVERT: A 450 LYS cc_start: 0.8020 (mtmm) cc_final: 0.7546 (mtmm) REVERT: B 21 GLN cc_start: 0.8067 (OUTLIER) cc_final: 0.7468 (tm-30) REVERT: B 277 GLN cc_start: 0.9007 (OUTLIER) cc_final: 0.7374 (tm-30) REVERT: B 410 LYS cc_start: 0.7488 (ptmt) cc_final: 0.7149 (ptmt) REVERT: C 21 GLN cc_start: 0.8105 (OUTLIER) cc_final: 0.7491 (tm-30) REVERT: C 450 LYS cc_start: 0.7896 (mtmm) cc_final: 0.7459 (mtmm) REVERT: D 21 GLN cc_start: 0.8088 (OUTLIER) cc_final: 0.7460 (tm-30) REVERT: D 441 GLN cc_start: 0.8147 (mt0) cc_final: 0.7899 (mt0) REVERT: D 450 LYS cc_start: 0.7908 (mtmm) cc_final: 0.7620 (mtmm) REVERT: E 325 MET cc_start: 0.8579 (ttt) cc_final: 0.8354 (ttt) REVERT: F 325 MET cc_start: 0.8665 (ttt) cc_final: 0.8406 (ttt) REVERT: F 410 LYS cc_start: 0.7572 (ptmt) cc_final: 0.7269 (ptmt) REVERT: F 450 LYS cc_start: 0.7941 (mtmm) cc_final: 0.7602 (mtmm) REVERT: G 21 GLN cc_start: 0.8078 (OUTLIER) cc_final: 0.7454 (tm-30) REVERT: G 450 LYS cc_start: 0.7883 (mtmm) cc_final: 0.7517 (mtmm) REVERT: H 450 LYS cc_start: 0.7876 (mtmm) cc_final: 0.7513 (mtmm) outliers start: 50 outliers final: 31 residues processed: 559 average time/residue: 2.2876 time to fit residues: 1479.4696 Evaluate side-chains 558 residues out of total 2672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 522 time to evaluate : 2.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -8 LEU Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 339 CYS Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain B residue -8 LEU Chi-restraints excluded: chain B residue 21 GLN Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain C residue -8 LEU Chi-restraints excluded: chain C residue 21 GLN Chi-restraints excluded: chain C residue 242 LYS Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 339 CYS Chi-restraints excluded: chain D residue -8 LEU Chi-restraints excluded: chain D residue 21 GLN Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain E residue -8 LEU Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain F residue -8 LEU Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 339 CYS Chi-restraints excluded: chain G residue -8 LEU Chi-restraints excluded: chain G residue 21 GLN Chi-restraints excluded: chain G residue 339 CYS Chi-restraints excluded: chain G residue 446 SER Chi-restraints excluded: chain G residue 495 MET Chi-restraints excluded: chain H residue -8 LEU Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 339 CYS Chi-restraints excluded: chain H residue 446 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 200 optimal weight: 0.9980 chunk 129 optimal weight: 1.9990 chunk 193 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 205 optimal weight: 1.9990 chunk 220 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 254 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 GLN ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 441 GLN A 498 GLN ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 GLN ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 GLN C 265 GLN ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 265 GLN ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 498 GLN ** F 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 265 GLN ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 265 GLN ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 265 GLN H 498 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 26968 Z= 0.291 Angle : 0.576 7.087 36592 Z= 0.285 Chirality : 0.044 0.145 4152 Planarity : 0.004 0.051 4528 Dihedral : 15.932 176.576 4370 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.02 % Allowed : 15.64 % 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: -0.24 (0.14), residues: 3296 helix: 0.66 (0.14), residues: 1352 sheet: -0.65 (0.27), residues: 312 loop : -0.70 (0.14), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS H 466 PHE 0.013 0.002 PHE H 357 TYR 0.012 0.002 TYR F 258 ARG 0.003 0.000 ARG D 253 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 2672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 521 time to evaluate : 2.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 325 MET cc_start: 0.8653 (ttt) cc_final: 0.8412 (ttt) REVERT: A 450 LYS cc_start: 0.7995 (mtmm) cc_final: 0.7627 (mtmm) REVERT: B 21 GLN cc_start: 0.8083 (OUTLIER) cc_final: 0.7513 (tm-30) REVERT: B 410 LYS cc_start: 0.7489 (ptmt) cc_final: 0.7140 (ptmt) REVERT: C 21 GLN cc_start: 0.8136 (OUTLIER) cc_final: 0.7515 (tm-30) REVERT: C 450 LYS cc_start: 0.7890 (mtmm) cc_final: 0.7430 (mtmm) REVERT: D 21 GLN cc_start: 0.8113 (OUTLIER) cc_final: 0.7514 (tm-30) REVERT: D 450 LYS cc_start: 0.7894 (mtmm) cc_final: 0.7540 (mtmm) REVERT: E 325 MET cc_start: 0.8615 (ttt) cc_final: 0.8407 (ttt) REVERT: F 325 MET cc_start: 0.8692 (ttt) cc_final: 0.8467 (ttt) REVERT: F 410 LYS cc_start: 0.7567 (ptmt) cc_final: 0.7230 (ptmt) REVERT: F 450 LYS cc_start: 0.7880 (mtmm) cc_final: 0.7534 (mtmm) REVERT: G 21 GLN cc_start: 0.8104 (OUTLIER) cc_final: 0.7512 (tm-30) REVERT: G 277 GLN cc_start: 0.9018 (OUTLIER) cc_final: 0.7456 (tm-30) REVERT: G 450 LYS cc_start: 0.7863 (mtmm) cc_final: 0.7487 (mtmm) REVERT: H 450 LYS cc_start: 0.7859 (mtmm) cc_final: 0.7480 (mtmm) outliers start: 54 outliers final: 39 residues processed: 562 average time/residue: 2.1344 time to fit residues: 1383.8907 Evaluate side-chains 561 residues out of total 2672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 517 time to evaluate : 2.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -8 LEU Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 339 CYS Chi-restraints excluded: chain A residue 441 GLN Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain B residue -8 LEU Chi-restraints excluded: chain B residue 21 GLN Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain C residue -8 LEU Chi-restraints excluded: chain C residue 21 GLN Chi-restraints excluded: chain C residue 242 LYS Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 339 CYS Chi-restraints excluded: chain D residue -8 LEU Chi-restraints excluded: chain D residue 21 GLN Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 242 LYS Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain E residue -8 LEU Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain F residue -8 LEU Chi-restraints excluded: chain F residue 274 ASP Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 339 CYS Chi-restraints excluded: chain G residue -8 LEU Chi-restraints excluded: chain G residue 21 GLN Chi-restraints excluded: chain G residue 75 GLU Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 339 CYS Chi-restraints excluded: chain G residue 446 SER Chi-restraints excluded: chain H residue -8 LEU Chi-restraints excluded: chain H residue 75 GLU Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 339 CYS Chi-restraints excluded: chain H residue 446 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 294 optimal weight: 4.9990 chunk 310 optimal weight: 1.9990 chunk 283 optimal weight: 3.9990 chunk 301 optimal weight: 0.7980 chunk 181 optimal weight: 0.9990 chunk 131 optimal weight: 1.9990 chunk 236 optimal weight: 1.9990 chunk 92 optimal weight: 0.6980 chunk 272 optimal weight: 0.8980 chunk 285 optimal weight: 2.9990 chunk 300 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 GLN ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 498 GLN B 265 GLN ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 GLN C 265 GLN ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 441 GLN E 265 GLN ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 441 GLN E 498 GLN ** F 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 265 GLN ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 265 GLN ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 265 GLN H 441 GLN H 498 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 26968 Z= 0.210 Angle : 0.541 7.013 36592 Z= 0.265 Chirality : 0.043 0.147 4152 Planarity : 0.004 0.050 4528 Dihedral : 15.624 176.876 4370 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.42 % Allowed : 16.21 % Favored : 82.37 % 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: -0.05 (0.14), residues: 3296 helix: 0.86 (0.15), residues: 1352 sheet: -0.62 (0.27), residues: 312 loop : -0.62 (0.14), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 466 PHE 0.009 0.001 PHE A 357 TYR 0.011 0.001 TYR H 353 ARG 0.002 0.000 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 2672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 517 time to evaluate : 2.651 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 325 MET cc_start: 0.8623 (ttt) cc_final: 0.8343 (ttt) REVERT: A 450 LYS cc_start: 0.8011 (mtmm) cc_final: 0.7536 (mtmm) REVERT: B 21 GLN cc_start: 0.8057 (OUTLIER) cc_final: 0.7453 (tm-30) REVERT: B 231 ARG cc_start: 0.7490 (ttp-170) cc_final: 0.7268 (ttp-170) REVERT: B 277 GLN cc_start: 0.8997 (OUTLIER) cc_final: 0.7365 (tm-30) REVERT: C 1 MET cc_start: 0.6709 (tpp) cc_final: 0.6182 (tpt) REVERT: C 21 GLN cc_start: 0.8100 (OUTLIER) cc_final: 0.7485 (tm-30) REVERT: C 450 LYS cc_start: 0.7886 (mtmm) cc_final: 0.7426 (mtmm) REVERT: D 21 GLN cc_start: 0.8087 (OUTLIER) cc_final: 0.7456 (tm-30) REVERT: D 450 LYS cc_start: 0.7902 (mtmm) cc_final: 0.7596 (mtmm) REVERT: E 325 MET cc_start: 0.8569 (ttt) cc_final: 0.8339 (ttt) REVERT: F 325 MET cc_start: 0.8660 (ttt) cc_final: 0.8396 (ttt) REVERT: F 410 LYS cc_start: 0.7563 (ptmt) cc_final: 0.7230 (ptmt) REVERT: F 450 LYS cc_start: 0.7859 (mtmm) cc_final: 0.7383 (mtmm) REVERT: G 21 GLN cc_start: 0.8079 (OUTLIER) cc_final: 0.7453 (tm-30) REVERT: G 277 GLN cc_start: 0.8993 (OUTLIER) cc_final: 0.7505 (tm-30) REVERT: G 450 LYS cc_start: 0.7870 (mtmm) cc_final: 0.7507 (mtmm) REVERT: H 450 LYS cc_start: 0.7862 (mtmm) cc_final: 0.7490 (mtmm) outliers start: 38 outliers final: 25 residues processed: 544 average time/residue: 2.2311 time to fit residues: 1399.8612 Evaluate side-chains 548 residues out of total 2672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 517 time to evaluate : 2.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -8 LEU Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain B residue -8 LEU Chi-restraints excluded: chain B residue 21 GLN Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain C residue -8 LEU Chi-restraints excluded: chain C residue 21 GLN Chi-restraints excluded: chain C residue 242 LYS Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain D residue -8 LEU Chi-restraints excluded: chain D residue 21 GLN Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 242 LYS Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain E residue -8 LEU Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain F residue -8 LEU Chi-restraints excluded: chain F residue 274 ASP Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain G residue -8 LEU Chi-restraints excluded: chain G residue 21 GLN Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 446 SER Chi-restraints excluded: chain H residue -8 LEU Chi-restraints excluded: chain H residue 75 GLU Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 446 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 198 optimal weight: 2.9990 chunk 319 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 chunk 151 optimal weight: 3.9990 chunk 221 optimal weight: 0.2980 chunk 334 optimal weight: 0.9990 chunk 308 optimal weight: 0.0770 chunk 266 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 chunk 205 optimal weight: 1.9990 chunk 163 optimal weight: 2.9990 overall best weight: 1.0744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 GLN ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 GLN ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 441 GLN B 498 GLN C 265 GLN ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 441 GLN E 265 GLN ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 441 GLN E 498 GLN ** F 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 265 GLN ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 441 GLN ** G 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 265 GLN ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 303 ASN H 265 GLN H 441 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.3329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 26968 Z= 0.210 Angle : 0.538 7.145 36592 Z= 0.262 Chirality : 0.043 0.146 4152 Planarity : 0.004 0.050 4528 Dihedral : 15.399 177.772 4370 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.68 % Allowed : 16.17 % Favored : 82.15 % 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: -0.01 (0.14), residues: 3296 helix: 0.88 (0.15), residues: 1352 sheet: -0.42 (0.28), residues: 296 loop : -0.62 (0.14), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS H 466 PHE 0.009 0.001 PHE E 357 TYR 0.011 0.001 TYR G 258 ARG 0.002 0.000 ARG D 253 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 2672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 516 time to evaluate : 2.517 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 325 MET cc_start: 0.8632 (ttt) cc_final: 0.8350 (ttt) REVERT: A 450 LYS cc_start: 0.7967 (mtmm) cc_final: 0.7490 (mtmm) REVERT: B 21 GLN cc_start: 0.8059 (OUTLIER) cc_final: 0.7467 (tm-30) REVERT: B 231 ARG cc_start: 0.7499 (ttp-170) cc_final: 0.7265 (ttp-170) REVERT: B 277 GLN cc_start: 0.8984 (OUTLIER) cc_final: 0.7358 (tm-30) REVERT: C 21 GLN cc_start: 0.8093 (OUTLIER) cc_final: 0.7467 (tm-30) REVERT: C 450 LYS cc_start: 0.7886 (mtmm) cc_final: 0.7436 (mtmm) REVERT: D 450 LYS cc_start: 0.7859 (mtmm) cc_final: 0.7538 (mtmm) REVERT: E 325 MET cc_start: 0.8556 (ttt) cc_final: 0.8355 (ttt) REVERT: F 325 MET cc_start: 0.8669 (ttt) cc_final: 0.8399 (ttt) REVERT: F 410 LYS cc_start: 0.7566 (ptmt) cc_final: 0.7193 (ptmt) REVERT: F 450 LYS cc_start: 0.7879 (mtmm) cc_final: 0.7416 (mtmm) REVERT: G 277 GLN cc_start: 0.8978 (OUTLIER) cc_final: 0.7489 (tm-30) REVERT: G 450 LYS cc_start: 0.7869 (mtmm) cc_final: 0.7510 (mtmm) REVERT: H 450 LYS cc_start: 0.7857 (mtmm) cc_final: 0.7368 (mtmm) outliers start: 45 outliers final: 30 residues processed: 551 average time/residue: 2.1523 time to fit residues: 1365.8624 Evaluate side-chains 550 residues out of total 2672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 516 time to evaluate : 2.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -8 LEU Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 339 CYS Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain B residue -8 LEU Chi-restraints excluded: chain B residue 21 GLN Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 441 GLN Chi-restraints excluded: chain C residue -8 LEU Chi-restraints excluded: chain C residue 21 GLN Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 339 CYS Chi-restraints excluded: chain D residue -8 LEU Chi-restraints excluded: chain D residue 242 LYS Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain E residue -8 LEU Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain F residue -8 LEU Chi-restraints excluded: chain F residue 274 ASP Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 339 CYS Chi-restraints excluded: chain G residue -8 LEU Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 446 SER Chi-restraints excluded: chain H residue -8 LEU Chi-restraints excluded: chain H residue 75 GLU Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 339 CYS Chi-restraints excluded: chain H residue 441 GLN Chi-restraints excluded: chain H residue 446 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 211 optimal weight: 0.9990 chunk 283 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 245 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 74 optimal weight: 0.0670 chunk 266 optimal weight: 7.9990 chunk 111 optimal weight: 1.9990 chunk 274 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 overall best weight: 1.1724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 GLN ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 441 GLN B 265 GLN ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 GLN C 265 GLN ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 441 GLN E 265 GLN ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 441 GLN E 498 GLN ** F 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 265 GLN ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 441 GLN ** G 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 265 GLN ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 441 GLN H 265 GLN ** H 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.138170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.106174 restraints weight = 78248.785| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 1.56 r_work: 0.2993 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 26968 Z= 0.235 Angle : 0.770 59.183 36592 Z= 0.439 Chirality : 0.043 0.264 4152 Planarity : 0.004 0.054 4528 Dihedral : 15.401 177.777 4370 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.38 % Allowed : 16.32 % Favored : 82.30 % Cbeta Deviations : 0.07 % 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: -0.00 (0.14), residues: 3296 helix: 0.88 (0.15), residues: 1352 sheet: -0.42 (0.28), residues: 296 loop : -0.61 (0.14), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS H 466 PHE 0.009 0.001 PHE A 357 TYR 0.011 0.001 TYR H 353 ARG 0.002 0.000 ARG B 355 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22152.27 seconds wall clock time: 380 minutes 46.06 seconds (22846.06 seconds total)