Starting phenix.real_space_refine on Sun Feb 25 11:43:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rgl_24451/02_2024/7rgl_24451_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rgl_24451/02_2024/7rgl_24451.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rgl_24451/02_2024/7rgl_24451.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rgl_24451/02_2024/7rgl_24451.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rgl_24451/02_2024/7rgl_24451_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rgl_24451/02_2024/7rgl_24451_trim_updated.pdb" } resolution = 2.4 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= 0.239 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 24 5.49 5 S 168 5.16 5 C 16112 2.51 5 N 4328 2.21 5 O 4896 1.98 5 H 25408 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 47": "OD1" <-> "OD2" Residue "A GLU 48": "OE1" <-> "OE2" Residue "A GLU 75": "OE1" <-> "OE2" Residue "A PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 103": "OE1" <-> "OE2" Residue "A GLU 196": "OE1" <-> "OE2" Residue "A ASP 226": "OD1" <-> "OD2" Residue "A ARG 231": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 261": "OD1" <-> "OD2" Residue "A ASP 269": "OD1" <-> "OD2" Residue "A ASP 319": "OD1" <-> "OD2" Residue "A GLU 335": "OE1" <-> "OE2" Residue "A ARG 356": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 364": "OD1" <-> "OD2" Residue "A GLU 395": "OE1" <-> "OE2" Residue "A GLU 399": "OE1" <-> "OE2" Residue "A ASP 404": "OD1" <-> "OD2" Residue "A ARG 407": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 412": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 421": "OE1" <-> "OE2" Residue "A PHE 511": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 47": "OD1" <-> "OD2" Residue "B GLU 75": "OE1" <-> "OE2" Residue "B PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 103": "OE1" <-> "OE2" Residue "B GLU 111": "OE1" <-> "OE2" Residue "B ARG 231": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 261": "OD1" <-> "OD2" Residue "B ASP 269": "OD1" <-> "OD2" Residue "B ASP 319": "OD1" <-> "OD2" Residue "B ARG 356": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 364": "OD1" <-> "OD2" Residue "B GLU 395": "OE1" <-> "OE2" Residue "B GLU 399": "OE1" <-> "OE2" Residue "B ASP 404": "OD1" <-> "OD2" Residue "B ARG 407": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 412": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 421": "OE1" <-> "OE2" Residue "B PHE 511": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 47": "OD1" <-> "OD2" Residue "C GLU 48": "OE1" <-> "OE2" Residue "C GLU 75": "OE1" <-> "OE2" Residue "C PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 103": "OE1" <-> "OE2" Residue "C GLU 111": "OE1" <-> "OE2" Residue "C ASP 117": "OD1" <-> "OD2" Residue "C GLU 196": "OE1" <-> "OE2" Residue "C ASP 226": "OD1" <-> "OD2" Residue "C ARG 231": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 261": "OD1" <-> "OD2" Residue "C ASP 269": "OD1" <-> "OD2" Residue "C ASP 319": "OD1" <-> "OD2" Residue "C GLU 335": "OE1" <-> "OE2" Residue "C ARG 356": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ASP 364": "OD1" <-> "OD2" Residue "C GLU 395": "OE1" <-> "OE2" Residue "C GLU 399": "OE1" <-> "OE2" Residue "C ASP 404": "OD1" <-> "OD2" Residue "C ARG 407": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 412": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 421": "OE1" <-> "OE2" Residue "C PHE 511": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 47": "OD1" <-> "OD2" Residue "D GLU 75": "OE1" <-> "OE2" Residue "D PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 103": "OE1" <-> "OE2" Residue "D ARG 231": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 254": "OE1" <-> "OE2" Residue "D ASP 261": "OD1" <-> "OD2" Residue "D ASP 269": "OD1" <-> "OD2" Residue "D ASP 319": "OD1" <-> "OD2" Residue "D GLU 335": "OE1" <-> "OE2" Residue "D ARG 356": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ASP 364": "OD1" <-> "OD2" Residue "D GLU 395": "OE1" <-> "OE2" Residue "D GLU 399": "OE1" <-> "OE2" Residue "D ASP 404": "OD1" <-> "OD2" Residue "D ARG 407": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 412": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 511": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 47": "OD1" <-> "OD2" Residue "E GLU 75": "OE1" <-> "OE2" Residue "E PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 103": "OE1" <-> "OE2" Residue "E ASP 226": "OD1" <-> "OD2" Residue "E ARG 231": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 261": "OD1" <-> "OD2" Residue "E ASP 269": "OD1" <-> "OD2" Residue "E ASP 319": "OD1" <-> "OD2" Residue "E GLU 335": "OE1" <-> "OE2" Residue "E ARG 356": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ASP 364": "OD1" <-> "OD2" Residue "E GLU 395": "OE1" <-> "OE2" Residue "E GLU 399": "OE1" <-> "OE2" Residue "E ASP 404": "OD1" <-> "OD2" Residue "E ARG 407": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 412": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E PHE 511": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 47": "OD1" <-> "OD2" Residue "F GLU 48": "OE1" <-> "OE2" Residue "F GLU 75": "OE1" <-> "OE2" Residue "F PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 103": "OE1" <-> "OE2" Residue "F GLU 111": "OE1" <-> "OE2" Residue "F GLU 196": "OE1" <-> "OE2" Residue "F ASP 226": "OD1" <-> "OD2" Residue "F ARG 231": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ASP 232": "OD1" <-> "OD2" Residue "F TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 261": "OD1" <-> "OD2" Residue "F ASP 269": "OD1" <-> "OD2" Residue "F ASP 319": "OD1" <-> "OD2" Residue "F GLU 335": "OE1" <-> "OE2" Residue "F ARG 356": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ASP 364": "OD1" <-> "OD2" Residue "F GLU 395": "OE1" <-> "OE2" Residue "F GLU 399": "OE1" <-> "OE2" Residue "F ASP 404": "OD1" <-> "OD2" Residue "F ARG 407": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 412": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F GLU 421": "OE1" <-> "OE2" Residue "F PHE 511": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 47": "OD1" <-> "OD2" Residue "G GLU 48": "OE1" <-> "OE2" Residue "G GLU 75": "OE1" <-> "OE2" Residue "G PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 103": "OE1" <-> "OE2" Residue "G ARG 231": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 261": "OD1" <-> "OD2" Residue "G ASP 269": "OD1" <-> "OD2" Residue "G ASP 319": "OD1" <-> "OD2" Residue "G GLU 335": "OE1" <-> "OE2" Residue "G ARG 356": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ASP 364": "OD1" <-> "OD2" Residue "G GLU 395": "OE1" <-> "OE2" Residue "G GLU 399": "OE1" <-> "OE2" Residue "G ASP 404": "OD1" <-> "OD2" Residue "G ARG 407": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ARG 412": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G PHE 511": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 47": "OD1" <-> "OD2" Residue "H GLU 48": "OE1" <-> "OE2" Residue "H GLU 75": "OE1" <-> "OE2" Residue "H PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 103": "OE1" <-> "OE2" Residue "H GLU 196": "OE1" <-> "OE2" Residue "H ASP 226": "OD1" <-> "OD2" Residue "H ARG 231": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 254": "OE1" <-> "OE2" Residue "H ASP 261": "OD1" <-> "OD2" Residue "H ASP 269": "OD1" <-> "OD2" Residue "H ASP 319": "OD1" <-> "OD2" Residue "H GLU 335": "OE1" <-> "OE2" Residue "H ARG 356": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ASP 364": "OD1" <-> "OD2" Residue "H GLU 395": "OE1" <-> "OE2" Residue "H GLU 399": "OE1" <-> "OE2" Residue "H ASP 404": "OD1" <-> "OD2" Residue "H ARG 407": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ARG 412": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H GLU 421": "OE1" <-> "OE2" Residue "H PHE 511": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 50936 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 6300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 6300 Classifications: {'peptide': 416} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 15, 'TRANS': 399} Chain breaks: 4 Chain: "B" Number of atoms: 6300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 6300 Classifications: {'peptide': 416} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 15, 'TRANS': 399} Chain breaks: 4 Chain: "C" Number of atoms: 6300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 6300 Classifications: {'peptide': 416} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 15, 'TRANS': 399} Chain breaks: 4 Chain: "D" Number of atoms: 6300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 6300 Classifications: {'peptide': 416} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 15, 'TRANS': 399} Chain breaks: 4 Chain: "E" Number of atoms: 6300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 6300 Classifications: {'peptide': 416} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 15, 'TRANS': 399} Chain breaks: 4 Chain: "F" Number of atoms: 6300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 6300 Classifications: {'peptide': 416} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 15, 'TRANS': 399} Chain breaks: 4 Chain: "G" Number of atoms: 6300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 6300 Classifications: {'peptide': 416} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 15, 'TRANS': 399} Chain breaks: 4 Chain: "H" Number of atoms: 6300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 6300 Classifications: {'peptide': 416} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 15, 'TRANS': 399} Chain breaks: 4 Chain: "A" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "B" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "C" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "D" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "E" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "F" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "G" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "H" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Time building chain proxies: 21.62, per 1000 atoms: 0.42 Number of scatterers: 50936 At special positions: 0 Unit cell: (143.31, 142.467, 122.235, 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 168 16.00 P 24 15.00 O 4896 8.00 N 4328 7.00 C 16112 6.00 H 25408 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=8, symmetry=0 Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 38.53 Conformation dependent library (CDL) restraints added in 4.7 seconds 6496 Ramachandran restraints generated. 3248 Oldfield, 0 Emsley, 3248 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5952 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 143 helices and 40 sheets defined 35.8% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.93 Creating SS restraints... Processing helix chain 'A' and resid 3 through 5 No H-bonds generated for 'chain 'A' and resid 3 through 5' Processing helix chain 'A' and resid 20 through 23 No H-bonds generated for 'chain 'A' and resid 20 through 23' 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 85 Processing helix chain 'A' and resid 97 through 109 Processing helix chain 'A' and resid 194 through 197 No H-bonds generated for 'chain 'A' and resid 194 through 197' Processing helix chain 'A' and resid 224 through 228 Processing helix chain 'A' and resid 254 through 266 Processing helix chain 'A' and resid 281 through 293 Processing helix chain 'A' and resid 307 through 316 Processing helix chain 'A' and resid 333 through 337 Processing helix chain 'A' and resid 343 through 357 removed outlier: 4.040A pdb=" N ARG A 356 " --> pdb=" O GLU A 352 " (cutoff:3.500A) removed outlier: 4.329A 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 417 through 420 No H-bonds generated for 'chain 'A' and resid 417 through 420' 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 3 through 5 No H-bonds generated for 'chain 'B' and resid 3 through 5' Processing helix chain 'B' and resid 20 through 23 No H-bonds generated for 'chain 'B' and resid 20 through 23' 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 85 Processing helix chain 'B' and resid 97 through 109 Processing helix chain 'B' and resid 194 through 197 No H-bonds generated for 'chain 'B' and resid 194 through 197' Processing helix chain 'B' and resid 224 through 228 Processing helix chain 'B' and resid 254 through 266 Processing helix chain 'B' and resid 281 through 293 Processing helix chain 'B' and resid 307 through 316 Processing helix chain 'B' and resid 333 through 337 Processing helix chain 'B' and resid 343 through 357 removed outlier: 4.013A pdb=" N ARG B 356 " --> pdb=" O GLU B 352 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N PHE B 357 " --> pdb=" O TYR B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 378 Processing helix chain 'B' and resid 417 through 420 No H-bonds generated for 'chain 'B' and resid 417 through 420' Processing helix chain 'B' and resid 453 through 471 Proline residue: B 458 - end of helix Processing helix chain 'B' and resid 476 through 484 Processing helix chain 'B' and resid 495 through 501 Processing helix chain 'C' and resid 3 through 5 No H-bonds generated for 'chain 'C' and resid 3 through 5' Processing helix chain 'C' and resid 20 through 23 No H-bonds generated for 'chain 'C' and resid 20 through 23' 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 109 Processing helix chain 'C' and resid 194 through 197 No H-bonds generated for 'chain 'C' and resid 194 through 197' Processing helix chain 'C' and resid 224 through 228 Processing helix chain 'C' and resid 254 through 266 Processing helix chain 'C' and resid 281 through 293 Processing helix chain 'C' and resid 307 through 316 Processing helix chain 'C' and resid 333 through 337 Processing helix chain 'C' and resid 343 through 357 removed outlier: 4.022A pdb=" N ARG C 356 " --> pdb=" O GLU C 352 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N PHE C 357 " --> pdb=" O TYR C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 378 Processing helix chain 'C' and resid 417 through 420 No H-bonds generated for 'chain 'C' and resid 417 through 420' Processing helix chain 'C' and resid 453 through 471 Proline residue: C 458 - end of helix Processing helix chain 'C' and resid 476 through 484 Processing helix chain 'C' and resid 495 through 501 Processing helix chain 'D' and resid 3 through 5 No H-bonds generated for 'chain 'D' and resid 3 through 5' Processing helix chain 'D' and resid 20 through 23 No H-bonds generated for 'chain 'D' and resid 20 through 23' 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 109 Processing helix chain 'D' and resid 194 through 197 No H-bonds generated for 'chain 'D' and resid 194 through 197' Processing helix chain 'D' and resid 224 through 228 Processing helix chain 'D' and resid 254 through 266 Processing helix chain 'D' and resid 281 through 293 Processing helix chain 'D' and resid 307 through 316 Processing helix chain 'D' and resid 333 through 337 Processing helix chain 'D' and resid 343 through 357 removed outlier: 4.022A pdb=" N ARG D 356 " --> pdb=" O GLU D 352 " (cutoff:3.500A) removed outlier: 4.327A 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 417 through 420 No H-bonds generated for 'chain 'D' and resid 417 through 420' 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 3 through 5 No H-bonds generated for 'chain 'E' and resid 3 through 5' Processing helix chain 'E' and resid 20 through 23 No H-bonds generated for 'chain 'E' and resid 20 through 23' 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 No H-bonds generated for 'chain 'E' and resid 194 through 197' Processing helix chain 'E' and resid 224 through 228 Processing helix chain 'E' and resid 254 through 266 Processing helix chain 'E' and resid 281 through 293 Processing helix chain 'E' and resid 307 through 316 Processing helix chain 'E' and resid 333 through 337 Processing helix chain 'E' and resid 343 through 357 removed outlier: 4.024A pdb=" N ARG E 356 " --> pdb=" O GLU E 352 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N PHE E 357 " --> pdb=" O TYR E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 370 through 378 Processing helix chain 'E' and resid 417 through 420 No H-bonds generated for 'chain 'E' and resid 417 through 420' Processing helix chain 'E' and resid 453 through 471 Proline residue: E 458 - end of helix Processing helix chain 'E' and resid 476 through 484 Processing helix chain 'E' and resid 495 through 501 Processing helix chain 'F' and resid 3 through 6 No H-bonds generated for 'chain 'F' and resid 3 through 6' Processing helix chain 'F' and resid 20 through 23 No H-bonds generated for 'chain 'F' and resid 20 through 23' 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 No H-bonds generated for 'chain 'F' and resid 194 through 197' Processing helix chain 'F' and resid 224 through 228 Processing helix chain 'F' and resid 254 through 266 Processing helix chain 'F' and resid 281 through 293 Processing helix chain 'F' and resid 307 through 316 Processing helix chain 'F' and resid 333 through 337 Processing helix chain 'F' and resid 343 through 357 removed outlier: 4.036A pdb=" N ARG F 356 " --> pdb=" O GLU F 352 " (cutoff:3.500A) removed outlier: 4.298A 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 417 through 420 No H-bonds generated for 'chain 'F' and resid 417 through 420' 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 20 through 23 No H-bonds generated for 'chain 'G' and resid 20 through 23' 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 No H-bonds generated for 'chain 'G' and resid 194 through 197' Processing helix chain 'G' and resid 224 through 228 Processing helix chain 'G' and resid 254 through 266 Processing helix chain 'G' and resid 281 through 293 Processing helix chain 'G' and resid 307 through 316 Processing helix chain 'G' and resid 333 through 337 Processing helix chain 'G' and resid 343 through 357 removed outlier: 4.034A pdb=" N ARG G 356 " --> pdb=" O GLU G 352 " (cutoff:3.500A) removed outlier: 4.313A 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 417 through 420 No H-bonds generated for 'chain 'G' and resid 417 through 420' 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 3 through 6 No H-bonds generated for 'chain 'H' and resid 3 through 6' Processing helix chain 'H' and resid 20 through 23 No H-bonds generated for 'chain 'H' and resid 20 through 23' 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 109 Processing helix chain 'H' and resid 194 through 197 No H-bonds generated for 'chain 'H' and resid 194 through 197' Processing helix chain 'H' and resid 224 through 228 Processing helix chain 'H' and resid 254 through 266 Processing helix chain 'H' and resid 281 through 293 Processing helix chain 'H' and resid 307 through 316 Processing helix chain 'H' and resid 333 through 337 Processing helix chain 'H' and resid 343 through 357 removed outlier: 4.040A pdb=" N ARG H 356 " --> pdb=" O GLU H 352 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N PHE H 357 " --> pdb=" O TYR H 353 " (cutoff:3.500A) Processing helix chain 'H' and resid 370 through 378 Processing helix chain 'H' and resid 417 through 420 No H-bonds generated for 'chain 'H' and resid 417 through 420' Processing helix chain 'H' and resid 453 through 471 Proline residue: H 458 - end of helix Processing helix chain 'H' and resid 476 through 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: 6.329A pdb=" N VAL A 384 " --> pdb=" O ILE A 66 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR A 383 " --> pdb=" O ILE A 361 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 209 through 211 removed outlier: 4.089A pdb=" N ALA A 220 " --> pdb=" O ILE A 211 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 247 through 250 removed outlier: 6.725A pdb=" N VAL A 270 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N VAL A 250 " --> pdb=" O VAL A 270 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N VAL A 272 " --> pdb=" O VAL A 250 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N GLN A 298 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N LEU A 273 " --> pdb=" O GLN A 298 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ILE A 300 " --> pdb=" O LEU A 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 400 through 403 Processing sheet with id= F, first strand: chain 'B' and resid 35 through 37 Processing sheet with id= G, first strand: chain 'B' and resid 65 through 67 removed outlier: 6.329A pdb=" N VAL B 384 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR B 383 " --> pdb=" O ILE B 361 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 209 through 211 removed outlier: 3.924A pdb=" N ALA B 220 " --> pdb=" O ILE B 211 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 247 through 250 removed outlier: 6.723A pdb=" N VAL B 270 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N VAL B 250 " --> pdb=" O VAL B 270 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N VAL B 272 " --> pdb=" O VAL B 250 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N GLN B 298 " --> pdb=" O ILE B 271 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N LEU B 273 " --> pdb=" O GLN B 298 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N ILE B 300 " --> pdb=" O LEU B 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'B' and resid 400 through 403 Processing sheet with id= K, first strand: chain 'C' and resid 35 through 37 Processing sheet with id= L, first strand: chain 'C' and resid 65 through 67 removed outlier: 6.329A pdb=" N VAL C 384 " --> pdb=" O ILE C 66 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR C 383 " --> pdb=" O ILE C 361 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 209 through 211 removed outlier: 3.846A pdb=" N ALA C 220 " --> pdb=" O ILE C 211 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 247 through 250 removed outlier: 6.722A pdb=" N VAL C 270 " --> pdb=" O ALA C 248 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N VAL C 250 " --> pdb=" O VAL C 270 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N VAL C 272 " --> pdb=" O VAL C 250 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N GLN C 298 " --> pdb=" O ILE C 271 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N LEU C 273 " --> pdb=" O GLN C 298 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ILE C 300 " --> pdb=" O LEU C 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'C' and resid 400 through 403 Processing sheet with id= P, first strand: chain 'D' and resid 35 through 37 Processing sheet with id= Q, first strand: chain 'D' and resid 65 through 67 removed outlier: 6.329A pdb=" N VAL D 384 " --> pdb=" O ILE D 66 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR D 383 " --> pdb=" O ILE D 361 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 209 through 211 Processing sheet with id= S, first strand: chain 'D' and resid 247 through 250 removed outlier: 6.723A pdb=" N VAL D 270 " --> pdb=" O ALA D 248 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N VAL D 250 " --> pdb=" O VAL D 270 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N VAL D 272 " --> pdb=" O VAL D 250 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLN D 298 " --> pdb=" O ILE D 271 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N LEU D 273 " --> pdb=" O GLN D 298 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ILE D 300 " --> pdb=" O LEU D 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'D' and resid 400 through 403 Processing sheet with id= U, first strand: chain 'E' and resid 35 through 37 Processing sheet with id= V, first strand: chain 'E' and resid 65 through 67 removed outlier: 6.329A pdb=" N VAL E 384 " --> pdb=" O ILE E 66 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR E 383 " --> pdb=" O ILE E 361 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'E' and resid 209 through 211 removed outlier: 3.717A pdb=" N ALA E 220 " --> pdb=" O ILE E 211 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'E' and resid 247 through 250 removed outlier: 6.724A pdb=" N VAL E 270 " --> pdb=" O ALA E 248 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N VAL E 250 " --> pdb=" O VAL E 270 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N VAL E 272 " --> pdb=" O VAL E 250 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N GLN E 298 " --> pdb=" O ILE E 271 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N LEU E 273 " --> pdb=" O GLN E 298 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ILE E 300 " --> pdb=" O LEU E 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'E' and resid 400 through 403 Processing sheet with id= Z, first strand: chain 'F' and resid 35 through 37 Processing sheet with id= AA, first strand: chain 'F' and resid 65 through 67 removed outlier: 6.330A pdb=" N VAL F 384 " --> pdb=" O ILE F 66 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR F 383 " --> pdb=" O ILE F 361 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'F' and resid 209 through 211 removed outlier: 3.841A pdb=" N ALA F 220 " --> pdb=" O ILE F 211 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'F' and resid 247 through 250 removed outlier: 6.725A pdb=" N VAL F 270 " --> pdb=" O ALA F 248 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N VAL F 250 " --> pdb=" O VAL F 270 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N VAL F 272 " --> pdb=" O VAL F 250 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N GLN F 298 " --> pdb=" O ILE F 271 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N LEU F 273 " --> pdb=" O GLN F 298 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ILE F 300 " --> pdb=" O LEU F 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= AC Processing sheet with id= AD, first strand: chain 'F' and resid 400 through 403 Processing sheet with id= AE, first strand: chain 'G' and resid 35 through 37 Processing sheet with id= AF, first strand: chain 'G' and resid 65 through 67 removed outlier: 6.329A pdb=" N VAL G 384 " --> pdb=" O ILE G 66 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR G 383 " --> pdb=" O ILE G 361 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'G' and resid 209 through 211 Processing sheet with id= AH, first strand: chain 'G' and resid 247 through 250 removed outlier: 6.725A pdb=" N VAL G 270 " --> pdb=" O ALA G 248 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N VAL G 250 " --> pdb=" O VAL G 270 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N VAL G 272 " --> pdb=" O VAL G 250 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N GLN G 298 " --> pdb=" O ILE G 271 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N LEU G 273 " --> pdb=" O GLN G 298 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ILE G 300 " --> pdb=" O LEU G 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= AH Processing sheet with id= AI, first strand: chain 'G' and resid 400 through 403 Processing sheet with id= AJ, first strand: chain 'H' and resid 35 through 37 Processing sheet with id= AK, first strand: chain 'H' and resid 65 through 67 removed outlier: 6.330A pdb=" N VAL H 384 " --> pdb=" O ILE H 66 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR H 383 " --> pdb=" O ILE H 361 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'H' and resid 209 through 211 removed outlier: 3.681A pdb=" N ALA H 220 " --> pdb=" O ILE H 211 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'H' and resid 247 through 250 removed outlier: 6.723A pdb=" N VAL H 270 " --> pdb=" O ALA H 248 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N VAL H 250 " --> pdb=" O VAL H 270 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N VAL H 272 " --> pdb=" O VAL H 250 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N GLN H 298 " --> pdb=" O ILE H 271 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N LEU H 273 " --> pdb=" O GLN H 298 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ILE H 300 " --> pdb=" O LEU H 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= AM Processing sheet with id= AN, first strand: chain 'H' and resid 400 through 403 762 hydrogen bonds defined for protein. 1992 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 20.38 Time building geometry restraints manager: 39.96 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: 25360 1.12 - 1.29: 4261 1.29 - 1.47: 9807 1.47 - 1.64: 11647 1.64 - 1.82: 293 Bond restraints: 51368 Sorted by residual: bond pdb=" C3B NAD A 602 " pdb=" C4B NAD A 602 " ideal model delta sigma weight residual 1.523 1.293 0.230 2.00e-02 2.50e+03 1.33e+02 bond pdb=" C3B NAD H 602 " pdb=" C4B NAD H 602 " ideal model delta sigma weight residual 1.523 1.293 0.230 2.00e-02 2.50e+03 1.32e+02 bond pdb=" C3D NAD G 602 " pdb=" C4D NAD G 602 " ideal model delta sigma weight residual 1.531 1.303 0.228 2.00e-02 2.50e+03 1.30e+02 bond pdb=" C3D NAD D 602 " pdb=" C4D NAD D 602 " ideal model delta sigma weight residual 1.531 1.303 0.228 2.00e-02 2.50e+03 1.30e+02 bond pdb=" C3B NAD D 602 " pdb=" C4B NAD D 602 " ideal model delta sigma weight residual 1.523 1.295 0.228 2.00e-02 2.50e+03 1.30e+02 ... (remaining 51363 not shown) Histogram of bond angle deviations from ideal: 96.55 - 106.22: 805 106.22 - 115.90: 63665 115.90 - 125.58: 27826 125.58 - 135.26: 552 135.26 - 144.93: 24 Bond angle restraints: 92872 Sorted by residual: angle pdb=" C1' IMP C 601 " pdb=" N9 IMP C 601 " pdb=" C4 IMP C 601 " ideal model delta sigma weight residual 126.00 106.14 19.86 3.00e+00 1.11e-01 4.38e+01 angle pdb=" C1' IMP E 601 " pdb=" N9 IMP E 601 " pdb=" C4 IMP E 601 " ideal model delta sigma weight residual 126.00 106.15 19.85 3.00e+00 1.11e-01 4.38e+01 angle pdb=" C1' IMP B 601 " pdb=" N9 IMP B 601 " pdb=" C4 IMP B 601 " ideal model delta sigma weight residual 126.00 106.15 19.85 3.00e+00 1.11e-01 4.38e+01 angle pdb=" C1' IMP F 601 " pdb=" N9 IMP F 601 " pdb=" C4 IMP F 601 " ideal model delta sigma weight residual 126.00 106.16 19.84 3.00e+00 1.11e-01 4.37e+01 angle pdb=" C1' IMP G 601 " pdb=" N9 IMP G 601 " pdb=" C4 IMP G 601 " ideal model delta sigma weight residual 126.00 106.18 19.82 3.00e+00 1.11e-01 4.36e+01 ... (remaining 92867 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.19: 22769 33.19 - 66.39: 1396 66.39 - 99.58: 111 99.58 - 132.78: 0 132.78 - 165.97: 4 Dihedral angle restraints: 24280 sinusoidal: 13648 harmonic: 10632 Sorted by residual: dihedral pdb=" C5' IMP E 601 " pdb=" O5' IMP E 601 " pdb=" P IMP E 601 " pdb=" O2P IMP E 601 " ideal model delta sinusoidal sigma weight residual -168.07 -2.10 -165.97 1 2.00e+01 2.50e-03 4.73e+01 dihedral pdb=" C5' IMP G 601 " pdb=" O5' IMP G 601 " pdb=" P IMP G 601 " pdb=" O2P IMP G 601 " ideal model delta sinusoidal sigma weight residual -168.07 -2.11 -165.96 1 2.00e+01 2.50e-03 4.73e+01 dihedral pdb=" C5' IMP F 601 " pdb=" O5' IMP F 601 " pdb=" P IMP F 601 " pdb=" O2P IMP F 601 " ideal model delta sinusoidal sigma weight residual -168.07 -2.17 -165.90 1 2.00e+01 2.50e-03 4.73e+01 ... (remaining 24277 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 3039 0.067 - 0.135: 921 0.135 - 0.202: 81 0.202 - 0.270: 4 0.270 - 0.337: 19 Chirality restraints: 4064 Sorted by residual: chirality pdb=" CA ARG A 474 " pdb=" N ARG A 474 " pdb=" C ARG A 474 " pdb=" CB ARG A 474 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.84e+00 chirality pdb=" CA ARG C 474 " pdb=" N ARG C 474 " pdb=" C ARG C 474 " pdb=" CB ARG C 474 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.73e+00 chirality pdb=" CA ARG B 474 " pdb=" N ARG B 474 " pdb=" C ARG B 474 " pdb=" CB ARG B 474 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.63e+00 ... (remaining 4061 not shown) Planarity restraints: 7592 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 353 " 0.125 2.00e-02 2.50e+03 5.18e-02 8.06e+01 pdb=" CG TYR A 353 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR A 353 " -0.038 2.00e-02 2.50e+03 pdb=" CD2 TYR A 353 " -0.044 2.00e-02 2.50e+03 pdb=" CE1 TYR A 353 " -0.024 2.00e-02 2.50e+03 pdb=" CE2 TYR A 353 " -0.032 2.00e-02 2.50e+03 pdb=" CZ TYR A 353 " -0.006 2.00e-02 2.50e+03 pdb=" OH TYR A 353 " 0.100 2.00e-02 2.50e+03 pdb=" HD1 TYR A 353 " -0.025 2.00e-02 2.50e+03 pdb=" HD2 TYR A 353 " -0.023 2.00e-02 2.50e+03 pdb=" HE1 TYR A 353 " -0.008 2.00e-02 2.50e+03 pdb=" HE2 TYR A 353 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 353 " -0.120 2.00e-02 2.50e+03 4.96e-02 7.38e+01 pdb=" CG TYR B 353 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR B 353 " 0.037 2.00e-02 2.50e+03 pdb=" CD2 TYR B 353 " 0.045 2.00e-02 2.50e+03 pdb=" CE1 TYR B 353 " 0.028 2.00e-02 2.50e+03 pdb=" CE2 TYR B 353 " 0.028 2.00e-02 2.50e+03 pdb=" CZ TYR B 353 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR B 353 " -0.092 2.00e-02 2.50e+03 pdb=" HD1 TYR B 353 " 0.016 2.00e-02 2.50e+03 pdb=" HD2 TYR B 353 " 0.023 2.00e-02 2.50e+03 pdb=" HE1 TYR B 353 " 0.005 2.00e-02 2.50e+03 pdb=" HE2 TYR B 353 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 353 " -0.117 2.00e-02 2.50e+03 4.87e-02 7.10e+01 pdb=" CG TYR C 353 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR C 353 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 TYR C 353 " 0.043 2.00e-02 2.50e+03 pdb=" CE1 TYR C 353 " 0.025 2.00e-02 2.50e+03 pdb=" CE2 TYR C 353 " 0.027 2.00e-02 2.50e+03 pdb=" CZ TYR C 353 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR C 353 " -0.092 2.00e-02 2.50e+03 pdb=" HD1 TYR C 353 " 0.017 2.00e-02 2.50e+03 pdb=" HD2 TYR C 353 " 0.024 2.00e-02 2.50e+03 pdb=" HE1 TYR C 353 " 0.011 2.00e-02 2.50e+03 pdb=" HE2 TYR C 353 " -0.005 2.00e-02 2.50e+03 ... (remaining 7589 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.10: 2687 2.10 - 2.73: 82922 2.73 - 3.35: 149822 3.35 - 3.98: 209139 3.98 - 4.60: 307719 Nonbonded interactions: 752289 Sorted by model distance: nonbonded pdb=" HA LYS A 228 " pdb=" HD3 LYS A 228 " model vdw 1.481 2.440 nonbonded pdb=" HB2 GLN D 283 " pdb="HE21 GLN D 283 " model vdw 1.542 2.270 nonbonded pdb=" HB2 GLN F 283 " pdb="HE21 GLN F 283 " model vdw 1.543 2.270 nonbonded pdb=" HB2 GLN C 283 " pdb="HE21 GLN C 283 " model vdw 1.543 2.270 nonbonded pdb=" HB2 GLN E 283 " pdb="HE21 GLN E 283 " model vdw 1.543 2.270 ... (remaining 752284 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.810 Extract box with map and model: 16.060 Check model and map are aligned: 0.790 Set scattering table: 0.480 Process input model: 152.830 Find NCS groups from input model: 2.390 Set up NCS constraints: 0.290 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:12.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 190.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.230 25960 Z= 0.887 Angle : 1.196 19.856 35128 Z= 0.619 Chirality : 0.063 0.337 4064 Planarity : 0.008 0.093 4424 Dihedral : 16.031 165.972 9808 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.66 % Favored : 96.18 % Rotamer: Outliers : 3.66 % Allowed : 9.86 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % 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: -1.40 (0.13), residues: 3248 helix: -0.72 (0.13), residues: 1320 sheet: -0.15 (0.27), residues: 288 loop : -1.18 (0.14), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 466 PHE 0.077 0.004 PHE B 357 TYR 0.112 0.006 TYR A 353 ARG 0.010 0.001 ARG H 356 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6496 Ramachandran restraints generated. 3248 Oldfield, 0 Emsley, 3248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6496 Ramachandran restraints generated. 3248 Oldfield, 0 Emsley, 3248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 2648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 526 time to evaluate : 3.551 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 3 ASP cc_start: 0.6040 (OUTLIER) cc_final: 0.5661 (m-30) REVERT: A 243 GLN cc_start: 0.7995 (mm-40) cc_final: 0.7640 (mm-40) REVERT: A 292 GLN cc_start: 0.8238 (tm-30) cc_final: 0.7968 (tm130) REVERT: A 330 ILE cc_start: 0.9275 (OUTLIER) cc_final: 0.9070 (pp) REVERT: A 441 GLN cc_start: 0.8466 (mt0) cc_final: 0.8119 (mt0) REVERT: B 211 ILE cc_start: 0.8411 (OUTLIER) cc_final: 0.8185 (mp) REVERT: B 243 GLN cc_start: 0.8003 (mm-40) cc_final: 0.7690 (mm-40) REVERT: B 292 GLN cc_start: 0.8257 (tm-30) cc_final: 0.7971 (tm130) REVERT: B 330 ILE cc_start: 0.9265 (OUTLIER) cc_final: 0.9056 (pp) REVERT: C 243 GLN cc_start: 0.8002 (mm-40) cc_final: 0.7683 (mm-40) REVERT: C 292 GLN cc_start: 0.8236 (tm-30) cc_final: 0.7935 (tm130) REVERT: C 330 ILE cc_start: 0.9278 (OUTLIER) cc_final: 0.9070 (pp) REVERT: C 441 GLN cc_start: 0.8414 (mt0) cc_final: 0.8164 (mt0) REVERT: D 224 ARG cc_start: 0.7936 (OUTLIER) cc_final: 0.7474 (ptp-170) REVERT: D 243 GLN cc_start: 0.7999 (mm-40) cc_final: 0.7673 (mm-40) REVERT: D 292 GLN cc_start: 0.8235 (tm-30) cc_final: 0.7956 (tm130) REVERT: D 330 ILE cc_start: 0.9268 (OUTLIER) cc_final: 0.9064 (pp) REVERT: D 441 GLN cc_start: 0.8437 (mt0) cc_final: 0.8119 (mt0) REVERT: E 243 GLN cc_start: 0.7974 (mm-40) cc_final: 0.7661 (mm-40) REVERT: E 292 GLN cc_start: 0.8255 (tm-30) cc_final: 0.7965 (tm130) REVERT: E 330 ILE cc_start: 0.9282 (OUTLIER) cc_final: 0.9079 (pp) REVERT: F 243 GLN cc_start: 0.8020 (mm-40) cc_final: 0.7713 (mm-40) REVERT: F 292 GLN cc_start: 0.8258 (tm-30) cc_final: 0.7958 (tm130) REVERT: F 441 GLN cc_start: 0.8401 (mt0) cc_final: 0.8179 (mt0) REVERT: G 243 GLN cc_start: 0.8004 (mm-40) cc_final: 0.7675 (mm-40) REVERT: G 292 GLN cc_start: 0.8246 (tm-30) cc_final: 0.7939 (tm130) REVERT: G 330 ILE cc_start: 0.9275 (OUTLIER) cc_final: 0.9068 (pp) REVERT: G 441 GLN cc_start: 0.8484 (mt0) cc_final: 0.8151 (mt0) REVERT: H 243 GLN cc_start: 0.8004 (mm-40) cc_final: 0.7640 (mm-40) REVERT: H 292 GLN cc_start: 0.8255 (tm-30) cc_final: 0.7973 (tm130) REVERT: H 330 ILE cc_start: 0.9270 (OUTLIER) cc_final: 0.9064 (pp) REVERT: H 441 GLN cc_start: 0.8428 (mt0) cc_final: 0.8145 (mt0) outliers start: 97 outliers final: 37 residues processed: 603 average time/residue: 2.8072 time to fit residues: 1979.4060 Evaluate side-chains 513 residues out of total 2648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 466 time to evaluate : 4.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ASP Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain D residue 198 ASN Chi-restraints excluded: chain D residue 224 ARG Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 336 VAL Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain F residue 3 ASP Chi-restraints excluded: chain F residue 225 THR Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain G residue 224 ARG Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 336 VAL Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 3 ASP Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 225 THR Chi-restraints excluded: chain H residue 250 VAL Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 336 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 276 optimal weight: 0.8980 chunk 248 optimal weight: 0.9990 chunk 137 optimal weight: 5.9990 chunk 84 optimal weight: 0.7980 chunk 167 optimal weight: 0.6980 chunk 132 optimal weight: 0.9980 chunk 257 optimal weight: 0.8980 chunk 99 optimal weight: 0.8980 chunk 156 optimal weight: 0.9980 chunk 191 optimal weight: 0.7980 chunk 297 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 GLN A 296 HIS A 454 GLN B 277 GLN B 296 HIS C 277 GLN C 296 HIS C 454 GLN D 21 GLN D 277 GLN D 296 HIS D 454 GLN E 21 GLN E 277 GLN E 296 HIS E 454 GLN F 277 GLN F 296 HIS F 454 GLN G 21 GLN G 277 GLN G 296 HIS G 454 GLN H 21 GLN H 277 GLN H 296 HIS H 454 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 25960 Z= 0.181 Angle : 0.518 3.984 35128 Z= 0.274 Chirality : 0.041 0.153 4064 Planarity : 0.004 0.043 4424 Dihedral : 10.438 164.435 4131 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.44 % Allowed : 16.01 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % 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 (0.15), residues: 3248 helix: 0.55 (0.15), residues: 1304 sheet: 0.30 (0.29), residues: 288 loop : -0.78 (0.15), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 92 PHE 0.011 0.001 PHE A 357 TYR 0.010 0.001 TYR D 348 ARG 0.004 0.000 ARG E 231 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6496 Ramachandran restraints generated. 3248 Oldfield, 0 Emsley, 3248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6496 Ramachandran restraints generated. 3248 Oldfield, 0 Emsley, 3248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 2648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 482 time to evaluate : 3.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.9378 (tpp) cc_final: 0.9167 (tpp) REVERT: A 109 LYS cc_start: 0.7744 (mmtp) cc_final: 0.7417 (mmtm) REVERT: A 243 GLN cc_start: 0.7870 (mm-40) cc_final: 0.7596 (mm-40) REVERT: A 292 GLN cc_start: 0.8222 (tm-30) cc_final: 0.7931 (tm130) REVERT: A 441 GLN cc_start: 0.8387 (mt0) cc_final: 0.7987 (mt0) REVERT: B 78 MET cc_start: 0.9391 (tpp) cc_final: 0.9155 (tpp) REVERT: B 109 LYS cc_start: 0.7732 (mmtp) cc_final: 0.7422 (mmtm) REVERT: B 211 ILE cc_start: 0.8403 (OUTLIER) cc_final: 0.8202 (mp) REVERT: B 243 GLN cc_start: 0.7865 (mm-40) cc_final: 0.7622 (mm-40) REVERT: B 292 GLN cc_start: 0.8250 (tm-30) cc_final: 0.7944 (tm130) REVERT: C 78 MET cc_start: 0.9387 (tpp) cc_final: 0.9150 (tpp) REVERT: C 243 GLN cc_start: 0.7868 (mm-40) cc_final: 0.7575 (mm-40) REVERT: C 292 GLN cc_start: 0.8222 (tm-30) cc_final: 0.7908 (tm130) REVERT: C 441 GLN cc_start: 0.8301 (mt0) cc_final: 0.8004 (mt0) REVERT: D 78 MET cc_start: 0.9380 (tpp) cc_final: 0.9158 (tpp) REVERT: D 111 GLU cc_start: 0.7071 (tp30) cc_final: 0.6860 (tp30) REVERT: D 224 ARG cc_start: 0.7859 (OUTLIER) cc_final: 0.7484 (ptp-170) REVERT: D 243 GLN cc_start: 0.7856 (mm-40) cc_final: 0.7573 (mm-40) REVERT: D 292 GLN cc_start: 0.8225 (tm-30) cc_final: 0.7925 (tm130) REVERT: D 441 GLN cc_start: 0.8419 (mt0) cc_final: 0.8067 (mt0) REVERT: D 495 MET cc_start: 0.7019 (OUTLIER) cc_final: 0.6791 (tpt) REVERT: E 78 MET cc_start: 0.9391 (tpp) cc_final: 0.9167 (tpp) REVERT: E 109 LYS cc_start: 0.7781 (mmtp) cc_final: 0.7449 (mmtm) REVERT: E 243 GLN cc_start: 0.7847 (mm-40) cc_final: 0.7595 (mm-40) REVERT: E 292 GLN cc_start: 0.8233 (tm-30) cc_final: 0.7927 (tm130) REVERT: F 78 MET cc_start: 0.9376 (tpp) cc_final: 0.9168 (tpp) REVERT: F 243 GLN cc_start: 0.7896 (mm-40) cc_final: 0.7604 (mm-40) REVERT: F 292 GLN cc_start: 0.8209 (tm-30) cc_final: 0.7912 (tm130) REVERT: F 441 GLN cc_start: 0.8359 (mt0) cc_final: 0.8085 (mt0) REVERT: G 78 MET cc_start: 0.9377 (tpp) cc_final: 0.9169 (tpp) REVERT: G 243 GLN cc_start: 0.7859 (mm-40) cc_final: 0.7572 (mm-40) REVERT: G 292 GLN cc_start: 0.8212 (tm-30) cc_final: 0.7908 (tm130) REVERT: G 441 GLN cc_start: 0.8433 (mt0) cc_final: 0.8064 (mt0) REVERT: H 78 MET cc_start: 0.9377 (tpp) cc_final: 0.9155 (tpp) REVERT: H 243 GLN cc_start: 0.7882 (mm-40) cc_final: 0.7585 (mm-40) REVERT: H 292 GLN cc_start: 0.8223 (tm-30) cc_final: 0.7930 (tm130) REVERT: H 441 GLN cc_start: 0.8362 (mt0) cc_final: 0.8011 (mt0) outliers start: 38 outliers final: 4 residues processed: 509 average time/residue: 3.0388 time to fit residues: 1793.1115 Evaluate side-chains 479 residues out of total 2648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 472 time to evaluate : 3.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ASP Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain D residue 224 ARG Chi-restraints excluded: chain D residue 495 MET Chi-restraints excluded: chain E residue 495 MET Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 192 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 165 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 247 optimal weight: 2.9990 chunk 202 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 298 optimal weight: 3.9990 chunk 322 optimal weight: 4.9990 chunk 265 optimal weight: 2.9990 chunk 295 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 chunk 239 optimal weight: 6.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 454 GLN B 21 GLN B 441 GLN B 454 GLN C 454 GLN D 21 GLN D 198 ASN D 454 GLN E 21 GLN E 441 GLN E 454 GLN F 21 GLN F 454 GLN G 21 GLN G 454 GLN H 454 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 25960 Z= 0.381 Angle : 0.587 4.623 35128 Z= 0.312 Chirality : 0.045 0.150 4064 Planarity : 0.005 0.054 4424 Dihedral : 9.276 104.989 4060 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.21 % Allowed : 16.05 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.15), residues: 3248 helix: 0.42 (0.15), residues: 1320 sheet: 0.37 (0.29), residues: 288 loop : -0.71 (0.15), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 466 PHE 0.014 0.002 PHE C 357 TYR 0.012 0.002 TYR B 348 ARG 0.006 0.001 ARG C 341 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6496 Ramachandran restraints generated. 3248 Oldfield, 0 Emsley, 3248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6496 Ramachandran restraints generated. 3248 Oldfield, 0 Emsley, 3248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 2648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 463 time to evaluate : 3.736 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 243 GLN cc_start: 0.7930 (mm-40) cc_final: 0.7615 (mm-40) REVERT: A 292 GLN cc_start: 0.8233 (tm-30) cc_final: 0.7953 (tm130) REVERT: A 441 GLN cc_start: 0.8444 (mt0) cc_final: 0.8142 (mt0) REVERT: B 243 GLN cc_start: 0.7951 (mm-40) cc_final: 0.7643 (mm-40) REVERT: B 292 GLN cc_start: 0.8280 (tm-30) cc_final: 0.7970 (tm130) REVERT: C 109 LYS cc_start: 0.7998 (mmtp) cc_final: 0.7708 (mmtm) REVERT: C 243 GLN cc_start: 0.7950 (mm-40) cc_final: 0.7672 (mm-40) REVERT: C 292 GLN cc_start: 0.8236 (tm-30) cc_final: 0.7931 (tm130) REVERT: C 441 GLN cc_start: 0.8352 (mt0) cc_final: 0.8143 (mt0) REVERT: D 78 MET cc_start: 0.9388 (tpp) cc_final: 0.9100 (tpp) REVERT: D 111 GLU cc_start: 0.7169 (tp30) cc_final: 0.6918 (tp30) REVERT: D 224 ARG cc_start: 0.7941 (OUTLIER) cc_final: 0.7590 (ptp-170) REVERT: D 243 GLN cc_start: 0.7918 (mm-40) cc_final: 0.7635 (mm-40) REVERT: D 292 GLN cc_start: 0.8249 (tm-30) cc_final: 0.7942 (tm130) REVERT: D 441 GLN cc_start: 0.8379 (mt0) cc_final: 0.7989 (mt0) REVERT: D 495 MET cc_start: 0.7048 (OUTLIER) cc_final: 0.6813 (tpt) REVERT: E 78 MET cc_start: 0.9393 (tpp) cc_final: 0.9099 (tpp) REVERT: E 243 GLN cc_start: 0.7920 (mm-40) cc_final: 0.7622 (mm-40) REVERT: E 292 GLN cc_start: 0.8253 (tm-30) cc_final: 0.7956 (tm130) REVERT: F 109 LYS cc_start: 0.7985 (mmtp) cc_final: 0.7713 (mmtm) REVERT: F 243 GLN cc_start: 0.7965 (mm-40) cc_final: 0.7693 (mm-40) REVERT: F 292 GLN cc_start: 0.8245 (tm-30) cc_final: 0.7940 (tm130) REVERT: F 441 GLN cc_start: 0.8356 (mt0) cc_final: 0.8140 (mt0) REVERT: G 78 MET cc_start: 0.9388 (tpp) cc_final: 0.9099 (tpp) REVERT: G 243 GLN cc_start: 0.7940 (mm-40) cc_final: 0.7635 (mm-40) REVERT: G 292 GLN cc_start: 0.8246 (tm-30) cc_final: 0.7937 (tm130) REVERT: G 441 GLN cc_start: 0.8389 (mt0) cc_final: 0.7978 (mt0) REVERT: H 78 MET cc_start: 0.9389 (tpp) cc_final: 0.9100 (tpp) REVERT: H 243 GLN cc_start: 0.7942 (mm-40) cc_final: 0.7637 (mm-40) REVERT: H 292 GLN cc_start: 0.8229 (tm-30) cc_final: 0.7954 (tm130) REVERT: H 441 GLN cc_start: 0.8385 (mt0) cc_final: 0.8114 (mt0) outliers start: 32 outliers final: 21 residues processed: 485 average time/residue: 3.0856 time to fit residues: 1727.0445 Evaluate side-chains 479 residues out of total 2648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 456 time to evaluate : 3.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ASP Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 455 LYS Chi-restraints excluded: chain C residue 48 GLU Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain D residue 48 GLU Chi-restraints excluded: chain D residue 198 ASN Chi-restraints excluded: chain D residue 224 ARG Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 495 MET Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 495 MET Chi-restraints excluded: chain F residue 48 GLU Chi-restraints excluded: chain F residue 211 ILE Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain G residue 3 ASP Chi-restraints excluded: chain G residue 48 GLU Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 443 VAL Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 48 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 294 optimal weight: 2.9990 chunk 224 optimal weight: 2.9990 chunk 154 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 142 optimal weight: 2.9990 chunk 200 optimal weight: 1.9990 chunk 299 optimal weight: 7.9990 chunk 317 optimal weight: 2.9990 chunk 156 optimal weight: 2.9990 chunk 283 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 454 GLN B 21 GLN B 454 GLN C 454 GLN D 21 GLN D 198 ASN D 454 GLN E 21 GLN E 454 GLN F 21 GLN F 454 GLN G 21 GLN G 454 GLN H 454 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 25960 Z= 0.418 Angle : 0.600 5.772 35128 Z= 0.318 Chirality : 0.046 0.147 4064 Planarity : 0.005 0.059 4424 Dihedral : 9.263 98.464 4057 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.70 % Allowed : 15.26 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % 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: -0.27 (0.15), residues: 3248 helix: 0.40 (0.15), residues: 1320 sheet: 0.42 (0.30), residues: 288 loop : -0.71 (0.15), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 466 PHE 0.014 0.002 PHE C 357 TYR 0.012 0.002 TYR B 348 ARG 0.004 0.001 ARG G 341 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6496 Ramachandran restraints generated. 3248 Oldfield, 0 Emsley, 3248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6496 Ramachandran restraints generated. 3248 Oldfield, 0 Emsley, 3248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 2648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 466 time to evaluate : 3.928 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 109 LYS cc_start: 0.7980 (mmtp) cc_final: 0.7641 (mmtm) REVERT: A 111 GLU cc_start: 0.7202 (tp30) cc_final: 0.6985 (tp30) REVERT: A 243 GLN cc_start: 0.7930 (mm-40) cc_final: 0.7659 (mm-40) REVERT: A 277 GLN cc_start: 0.9187 (OUTLIER) cc_final: 0.7125 (tm-30) REVERT: A 292 GLN cc_start: 0.8226 (tm-30) cc_final: 0.7947 (tm130) REVERT: A 441 GLN cc_start: 0.8406 (mt0) cc_final: 0.8127 (mt0) REVERT: B 109 LYS cc_start: 0.7995 (mmtp) cc_final: 0.7671 (mmtm) REVERT: B 243 GLN cc_start: 0.7944 (mm-40) cc_final: 0.7691 (mm-40) REVERT: B 277 GLN cc_start: 0.9179 (OUTLIER) cc_final: 0.7117 (tm-30) REVERT: B 292 GLN cc_start: 0.8272 (tm-30) cc_final: 0.7952 (tm130) REVERT: C 109 LYS cc_start: 0.8010 (mmtp) cc_final: 0.7717 (mmtm) REVERT: C 243 GLN cc_start: 0.7947 (mm-40) cc_final: 0.7651 (mm-40) REVERT: C 277 GLN cc_start: 0.9180 (OUTLIER) cc_final: 0.7110 (tm-30) REVERT: C 292 GLN cc_start: 0.8233 (tm-30) cc_final: 0.7926 (tm130) REVERT: D 109 LYS cc_start: 0.7964 (mmtp) cc_final: 0.7646 (mmtm) REVERT: D 111 GLU cc_start: 0.7176 (tp30) cc_final: 0.6952 (tp30) REVERT: D 224 ARG cc_start: 0.7984 (OUTLIER) cc_final: 0.7673 (ptp-170) REVERT: D 243 GLN cc_start: 0.7933 (mm-40) cc_final: 0.7677 (mm-40) REVERT: D 277 GLN cc_start: 0.9179 (OUTLIER) cc_final: 0.7106 (tm-30) REVERT: D 292 GLN cc_start: 0.8247 (tm-30) cc_final: 0.7937 (tm130) REVERT: D 441 GLN cc_start: 0.8424 (mt0) cc_final: 0.8096 (mt0) REVERT: E 15 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7284 (tp30) REVERT: E 109 LYS cc_start: 0.8003 (mmtp) cc_final: 0.7659 (mmtm) REVERT: E 243 GLN cc_start: 0.7925 (mm-40) cc_final: 0.7658 (mm-40) REVERT: E 277 GLN cc_start: 0.9179 (OUTLIER) cc_final: 0.7116 (tm-30) REVERT: E 292 GLN cc_start: 0.8264 (tm-30) cc_final: 0.7948 (tm130) REVERT: F 109 LYS cc_start: 0.7999 (mmtp) cc_final: 0.7724 (mmtm) REVERT: F 243 GLN cc_start: 0.7959 (mm-40) cc_final: 0.7694 (mm-40) REVERT: F 277 GLN cc_start: 0.9181 (OUTLIER) cc_final: 0.7114 (tm-30) REVERT: F 292 GLN cc_start: 0.8236 (tm-30) cc_final: 0.7932 (tm130) REVERT: G 109 LYS cc_start: 0.7968 (mmtp) cc_final: 0.7633 (mmtm) REVERT: G 111 GLU cc_start: 0.7197 (tp30) cc_final: 0.6988 (tp30) REVERT: G 243 GLN cc_start: 0.7932 (mm-40) cc_final: 0.7674 (mm-40) REVERT: G 277 GLN cc_start: 0.9182 (OUTLIER) cc_final: 0.7119 (tm-30) REVERT: G 292 GLN cc_start: 0.8239 (tm-30) cc_final: 0.7930 (tm130) REVERT: G 441 GLN cc_start: 0.8389 (mt0) cc_final: 0.7968 (mt0) REVERT: H 109 LYS cc_start: 0.7998 (mmtp) cc_final: 0.7674 (mmtm) REVERT: H 243 GLN cc_start: 0.7937 (mm-40) cc_final: 0.7672 (mm-40) REVERT: H 277 GLN cc_start: 0.9186 (OUTLIER) cc_final: 0.7117 (tm-30) REVERT: H 292 GLN cc_start: 0.8224 (tm-30) cc_final: 0.7954 (tm130) outliers start: 45 outliers final: 29 residues processed: 499 average time/residue: 3.1425 time to fit residues: 1824.0639 Evaluate side-chains 500 residues out of total 2648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 461 time to evaluate : 3.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain C residue 48 GLU Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain D residue 48 GLU Chi-restraints excluded: chain D residue 198 ASN Chi-restraints excluded: chain D residue 224 ARG Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 495 MET Chi-restraints excluded: chain E residue 15 GLU Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 421 GLU Chi-restraints excluded: chain E residue 495 MET Chi-restraints excluded: chain F residue 48 GLU Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain G residue 3 ASP Chi-restraints excluded: chain G residue 48 GLU Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 443 VAL Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 48 GLU Chi-restraints excluded: chain H residue 250 VAL Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 333 THR Chi-restraints excluded: chain H residue 336 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 264 optimal weight: 1.9990 chunk 179 optimal weight: 0.9990 chunk 4 optimal weight: 0.2980 chunk 236 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 270 optimal weight: 2.9990 chunk 219 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 161 optimal weight: 1.9990 chunk 284 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 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 454 GLN B 21 GLN B 441 GLN B 454 GLN C 454 GLN D 21 GLN D 198 ASN D 454 GLN E 21 GLN E 441 GLN E 454 GLN F 21 GLN F 454 GLN G 21 GLN G 454 GLN H 454 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 25960 Z= 0.223 Angle : 0.518 5.290 35128 Z= 0.269 Chirality : 0.042 0.149 4064 Planarity : 0.005 0.053 4424 Dihedral : 8.648 82.742 4055 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.25 % Allowed : 15.48 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % 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 (0.15), residues: 3248 helix: 0.71 (0.15), residues: 1312 sheet: 0.54 (0.30), residues: 288 loop : -0.55 (0.15), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 92 PHE 0.010 0.001 PHE C 357 TYR 0.010 0.001 TYR A 348 ARG 0.002 0.000 ARG H 341 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6496 Ramachandran restraints generated. 3248 Oldfield, 0 Emsley, 3248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6496 Ramachandran restraints generated. 3248 Oldfield, 0 Emsley, 3248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 2648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 470 time to evaluate : 3.703 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 109 LYS cc_start: 0.7816 (mmtp) cc_final: 0.7487 (mmtm) REVERT: A 111 GLU cc_start: 0.7130 (tp30) cc_final: 0.6891 (tp30) REVERT: A 243 GLN cc_start: 0.7878 (mm-40) cc_final: 0.7633 (mm-40) REVERT: A 277 GLN cc_start: 0.9141 (OUTLIER) cc_final: 0.7046 (tm-30) REVERT: A 292 GLN cc_start: 0.8221 (tm-30) cc_final: 0.7932 (tm130) REVERT: B 109 LYS cc_start: 0.7824 (mmtp) cc_final: 0.7513 (mmtm) REVERT: B 243 GLN cc_start: 0.7887 (mm-40) cc_final: 0.7626 (mm-40) REVERT: B 277 GLN cc_start: 0.9134 (OUTLIER) cc_final: 0.7043 (tm-30) REVERT: B 292 GLN cc_start: 0.8271 (tm-30) cc_final: 0.7936 (tm130) REVERT: C 109 LYS cc_start: 0.7821 (mmtp) cc_final: 0.7519 (mmtm) REVERT: C 243 GLN cc_start: 0.7884 (mm-40) cc_final: 0.7604 (mm-40) REVERT: C 277 GLN cc_start: 0.9138 (OUTLIER) cc_final: 0.7048 (tm-30) REVERT: C 292 GLN cc_start: 0.8224 (tm-30) cc_final: 0.7907 (tm130) REVERT: D 15 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7254 (tp30) REVERT: D 78 MET cc_start: 0.9376 (tpp) cc_final: 0.9130 (tpp) REVERT: D 109 LYS cc_start: 0.7790 (mmtp) cc_final: 0.7473 (mmtm) REVERT: D 111 GLU cc_start: 0.7101 (tp30) cc_final: 0.6885 (tp30) REVERT: D 224 ARG cc_start: 0.8006 (OUTLIER) cc_final: 0.7726 (ptp-170) REVERT: D 243 GLN cc_start: 0.7862 (mm-40) cc_final: 0.7602 (mm-40) REVERT: D 277 GLN cc_start: 0.9131 (OUTLIER) cc_final: 0.7032 (tm-30) REVERT: D 292 GLN cc_start: 0.8231 (tm-30) cc_final: 0.7914 (tm130) REVERT: D 441 GLN cc_start: 0.8381 (mt0) cc_final: 0.8048 (mt0) REVERT: D 495 MET cc_start: 0.7053 (OUTLIER) cc_final: 0.6823 (tpt) REVERT: E 109 LYS cc_start: 0.7844 (mmtp) cc_final: 0.7509 (mmtm) REVERT: E 243 GLN cc_start: 0.7867 (mm-40) cc_final: 0.7592 (mm-40) REVERT: E 277 GLN cc_start: 0.9132 (OUTLIER) cc_final: 0.7040 (tm-30) REVERT: E 292 GLN cc_start: 0.8263 (tm-30) cc_final: 0.7932 (tm130) REVERT: F 78 MET cc_start: 0.9374 (tpp) cc_final: 0.9126 (tpp) REVERT: F 109 LYS cc_start: 0.7823 (mmtp) cc_final: 0.7545 (mmtm) REVERT: F 243 GLN cc_start: 0.7897 (mm-40) cc_final: 0.7626 (mm-40) REVERT: F 277 GLN cc_start: 0.9134 (OUTLIER) cc_final: 0.7038 (tm-30) REVERT: F 292 GLN cc_start: 0.8233 (tm-30) cc_final: 0.7920 (tm130) REVERT: G 78 MET cc_start: 0.9378 (tpp) cc_final: 0.9128 (tpp) REVERT: G 109 LYS cc_start: 0.7802 (mmtp) cc_final: 0.7468 (mmtm) REVERT: G 243 GLN cc_start: 0.7881 (mm-40) cc_final: 0.7608 (mm-40) REVERT: G 277 GLN cc_start: 0.9135 (OUTLIER) cc_final: 0.7041 (tm-30) REVERT: G 292 GLN cc_start: 0.8227 (tm-30) cc_final: 0.7905 (tm130) REVERT: G 441 GLN cc_start: 0.8441 (mt0) cc_final: 0.8098 (mt0) REVERT: H 15 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.7213 (tp30) REVERT: H 78 MET cc_start: 0.9373 (tpp) cc_final: 0.9125 (tpp) REVERT: H 109 LYS cc_start: 0.7819 (mmtp) cc_final: 0.7503 (mmtm) REVERT: H 243 GLN cc_start: 0.7890 (mm-40) cc_final: 0.7617 (mm-40) REVERT: H 277 GLN cc_start: 0.9138 (OUTLIER) cc_final: 0.7038 (tm-30) REVERT: H 292 GLN cc_start: 0.8222 (tm-30) cc_final: 0.7937 (tm130) REVERT: H 441 GLN cc_start: 0.8363 (mt0) cc_final: 0.8009 (mt0) outliers start: 33 outliers final: 15 residues processed: 491 average time/residue: 3.1390 time to fit residues: 1778.1845 Evaluate side-chains 492 residues out of total 2648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 465 time to evaluate : 3.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 319 ASP Chi-restraints excluded: chain D residue 15 GLU Chi-restraints excluded: chain D residue 198 ASN Chi-restraints excluded: chain D residue 224 ARG Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 495 MET Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 495 MET Chi-restraints excluded: chain F residue 48 GLU Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 319 ASP Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 319 ASP Chi-restraints excluded: chain G residue 443 VAL Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 15 GLU Chi-restraints excluded: chain H residue 48 GLU Chi-restraints excluded: chain H residue 250 VAL Chi-restraints excluded: chain H residue 277 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 106 optimal weight: 2.9990 chunk 285 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 186 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 317 optimal weight: 1.9990 chunk 263 optimal weight: 0.6980 chunk 146 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 166 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 454 GLN ** B 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 454 GLN C 21 GLN ** C 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 454 GLN C 498 GLN D 198 ASN D 454 GLN ** E 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 454 GLN ** F 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 454 GLN F 498 GLN G 454 GLN G 498 GLN H 198 ASN H 454 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 25960 Z= 0.266 Angle : 0.532 5.614 35128 Z= 0.277 Chirality : 0.042 0.147 4064 Planarity : 0.005 0.053 4424 Dihedral : 8.633 77.090 4055 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.21 % Allowed : 15.45 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % 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: 0.09 (0.15), residues: 3248 helix: 0.73 (0.15), residues: 1320 sheet: 0.52 (0.30), residues: 288 loop : -0.52 (0.15), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 466 PHE 0.010 0.002 PHE C 357 TYR 0.010 0.001 TYR B 348 ARG 0.003 0.000 ARG C 341 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6496 Ramachandran restraints generated. 3248 Oldfield, 0 Emsley, 3248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6496 Ramachandran restraints generated. 3248 Oldfield, 0 Emsley, 3248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 2648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 473 time to evaluate : 3.947 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 15 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7304 (tp30) REVERT: A 109 LYS cc_start: 0.7858 (mmtp) cc_final: 0.7534 (mmtm) REVERT: A 111 GLU cc_start: 0.7157 (tp30) cc_final: 0.6948 (tp30) REVERT: A 243 GLN cc_start: 0.7895 (mm-40) cc_final: 0.7653 (mm-40) REVERT: A 277 GLN cc_start: 0.9149 (OUTLIER) cc_final: 0.7063 (tm-30) REVERT: A 292 GLN cc_start: 0.8223 (tm-30) cc_final: 0.7937 (tm130) REVERT: A 441 GLN cc_start: 0.8390 (mt0) cc_final: 0.8008 (mt0) REVERT: B 15 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.7252 (tp30) REVERT: B 109 LYS cc_start: 0.7838 (mmtp) cc_final: 0.7561 (mmtm) REVERT: B 243 GLN cc_start: 0.7909 (mm-40) cc_final: 0.7626 (mm-40) REVERT: B 277 GLN cc_start: 0.9139 (OUTLIER) cc_final: 0.7059 (tm-30) REVERT: B 292 GLN cc_start: 0.8268 (tm-30) cc_final: 0.7936 (tm130) REVERT: C 109 LYS cc_start: 0.7853 (mmtp) cc_final: 0.7550 (mmtm) REVERT: C 243 GLN cc_start: 0.7891 (mm-40) cc_final: 0.7639 (mm-40) REVERT: C 277 GLN cc_start: 0.9143 (OUTLIER) cc_final: 0.7063 (tm-30) REVERT: C 292 GLN cc_start: 0.8227 (tm-30) cc_final: 0.7914 (tm130) REVERT: D 15 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7243 (tp30) REVERT: D 78 MET cc_start: 0.9388 (tpp) cc_final: 0.9121 (tpp) REVERT: D 109 LYS cc_start: 0.7820 (mmtp) cc_final: 0.7530 (mmtm) REVERT: D 111 GLU cc_start: 0.7109 (tp30) cc_final: 0.6885 (tp30) REVERT: D 224 ARG cc_start: 0.7992 (OUTLIER) cc_final: 0.7729 (ptp-170) REVERT: D 243 GLN cc_start: 0.7898 (mm-40) cc_final: 0.7642 (mm-40) REVERT: D 277 GLN cc_start: 0.9142 (OUTLIER) cc_final: 0.7050 (tm-30) REVERT: D 292 GLN cc_start: 0.8238 (tm-30) cc_final: 0.7923 (tm130) REVERT: D 441 GLN cc_start: 0.8392 (mt0) cc_final: 0.8087 (mt0) REVERT: D 495 MET cc_start: 0.7062 (OUTLIER) cc_final: 0.6837 (tpt) REVERT: E 78 MET cc_start: 0.9383 (tpp) cc_final: 0.9128 (tpp) REVERT: E 109 LYS cc_start: 0.7885 (mmtp) cc_final: 0.7593 (mmtm) REVERT: E 243 GLN cc_start: 0.7881 (mm-40) cc_final: 0.7602 (mm-40) REVERT: E 277 GLN cc_start: 0.9140 (OUTLIER) cc_final: 0.7059 (tm-30) REVERT: E 292 GLN cc_start: 0.8265 (tm-30) cc_final: 0.7932 (tm130) REVERT: F 109 LYS cc_start: 0.7837 (mmtp) cc_final: 0.7554 (mmtm) REVERT: F 243 GLN cc_start: 0.7906 (mm-40) cc_final: 0.7651 (mm-40) REVERT: F 277 GLN cc_start: 0.9141 (OUTLIER) cc_final: 0.7056 (tm-30) REVERT: F 292 GLN cc_start: 0.8237 (tm-30) cc_final: 0.7926 (tm130) REVERT: G 78 MET cc_start: 0.9389 (tpp) cc_final: 0.9118 (tpp) REVERT: G 109 LYS cc_start: 0.7836 (mmtp) cc_final: 0.7531 (mmtm) REVERT: G 243 GLN cc_start: 0.7900 (mm-40) cc_final: 0.7602 (mm-40) REVERT: G 277 GLN cc_start: 0.9145 (OUTLIER) cc_final: 0.7050 (tm-30) REVERT: G 292 GLN cc_start: 0.8235 (tm-30) cc_final: 0.7919 (tm130) REVERT: G 441 GLN cc_start: 0.8442 (mt0) cc_final: 0.8105 (mt0) REVERT: H 78 MET cc_start: 0.9385 (tpp) cc_final: 0.9113 (tpp) REVERT: H 109 LYS cc_start: 0.7865 (mmtp) cc_final: 0.7553 (mmtm) REVERT: H 243 GLN cc_start: 0.7899 (mm-40) cc_final: 0.7622 (mm-40) REVERT: H 277 GLN cc_start: 0.9146 (OUTLIER) cc_final: 0.7056 (tm-30) REVERT: H 292 GLN cc_start: 0.8225 (tm-30) cc_final: 0.7942 (tm130) REVERT: H 441 GLN cc_start: 0.8398 (mt0) cc_final: 0.8044 (mt0) outliers start: 32 outliers final: 16 residues processed: 492 average time/residue: 3.1235 time to fit residues: 1771.4986 Evaluate side-chains 497 residues out of total 2648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 468 time to evaluate : 4.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain B residue 15 GLU Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 455 LYS Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain D residue 15 GLU Chi-restraints excluded: chain D residue 198 ASN Chi-restraints excluded: chain D residue 224 ARG Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 495 MET Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 495 MET Chi-restraints excluded: chain F residue 48 GLU Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain G residue 3 ASP Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 443 VAL Chi-restraints excluded: chain G residue 455 LYS Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 48 GLU Chi-restraints excluded: chain H residue 250 VAL Chi-restraints excluded: chain H residue 277 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 305 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 180 optimal weight: 3.9990 chunk 231 optimal weight: 1.9990 chunk 179 optimal weight: 0.8980 chunk 267 optimal weight: 2.9990 chunk 177 optimal weight: 0.0170 chunk 316 optimal weight: 1.9990 chunk 197 optimal weight: 2.9990 chunk 192 optimal weight: 2.9990 chunk 145 optimal weight: 1.9990 overall best weight: 1.3824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 454 GLN B 21 GLN B 441 GLN B 454 GLN C 21 GLN ** C 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 454 GLN D 21 GLN D 198 ASN D 454 GLN E 21 GLN ** E 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 454 GLN F 21 GLN ** F 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 454 GLN G 21 GLN G 454 GLN H 454 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 25960 Z= 0.240 Angle : 0.524 6.538 35128 Z= 0.272 Chirality : 0.042 0.147 4064 Planarity : 0.005 0.051 4424 Dihedral : 8.513 75.670 4055 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.47 % Allowed : 15.60 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.15), residues: 3248 helix: 0.84 (0.15), residues: 1312 sheet: 0.50 (0.30), residues: 288 loop : -0.47 (0.15), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 466 PHE 0.009 0.001 PHE C 357 TYR 0.010 0.001 TYR B 348 ARG 0.002 0.000 ARG F 341 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6496 Ramachandran restraints generated. 3248 Oldfield, 0 Emsley, 3248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6496 Ramachandran restraints generated. 3248 Oldfield, 0 Emsley, 3248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 2648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 474 time to evaluate : 3.944 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 15 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.7289 (tp30) REVERT: A 109 LYS cc_start: 0.7811 (mmtp) cc_final: 0.7510 (mmtm) REVERT: A 111 GLU cc_start: 0.7147 (tp30) cc_final: 0.6929 (tp30) REVERT: A 243 GLN cc_start: 0.7883 (mm-40) cc_final: 0.7627 (mm-40) REVERT: A 277 GLN cc_start: 0.9142 (OUTLIER) cc_final: 0.7055 (tm-30) REVERT: A 292 GLN cc_start: 0.8225 (tm-30) cc_final: 0.7935 (tm130) REVERT: A 441 GLN cc_start: 0.8393 (mt0) cc_final: 0.7989 (mt0) REVERT: B 15 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7258 (tp30) REVERT: B 109 LYS cc_start: 0.7791 (mmtp) cc_final: 0.7505 (mmtm) REVERT: B 243 GLN cc_start: 0.7883 (mm-40) cc_final: 0.7585 (mm-40) REVERT: B 277 GLN cc_start: 0.9133 (OUTLIER) cc_final: 0.7048 (tm-30) REVERT: B 292 GLN cc_start: 0.8278 (tm-30) cc_final: 0.7944 (tm130) REVERT: C 109 LYS cc_start: 0.7825 (mmtp) cc_final: 0.7525 (mmtm) REVERT: C 243 GLN cc_start: 0.7905 (mm-40) cc_final: 0.7650 (mm-40) REVERT: C 277 GLN cc_start: 0.9136 (OUTLIER) cc_final: 0.7048 (tm-30) REVERT: C 292 GLN cc_start: 0.8221 (tm-30) cc_final: 0.7903 (tm130) REVERT: D 15 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.7239 (tp30) REVERT: D 78 MET cc_start: 0.9382 (tpp) cc_final: 0.9135 (tpp) REVERT: D 109 LYS cc_start: 0.7779 (mmtp) cc_final: 0.7490 (mmtm) REVERT: D 111 GLU cc_start: 0.7087 (tp30) cc_final: 0.6880 (tp30) REVERT: D 224 ARG cc_start: 0.7998 (OUTLIER) cc_final: 0.7752 (ptp-170) REVERT: D 243 GLN cc_start: 0.7879 (mm-40) cc_final: 0.7628 (mm-40) REVERT: D 277 GLN cc_start: 0.9133 (OUTLIER) cc_final: 0.7049 (tm-30) REVERT: D 292 GLN cc_start: 0.8230 (tm-30) cc_final: 0.7911 (tm130) REVERT: D 441 GLN cc_start: 0.8380 (mt0) cc_final: 0.8076 (mt0) REVERT: D 495 MET cc_start: 0.7068 (OUTLIER) cc_final: 0.6863 (tpt) REVERT: E 78 MET cc_start: 0.9380 (tpp) cc_final: 0.9128 (tpp) REVERT: E 109 LYS cc_start: 0.7820 (mmtp) cc_final: 0.7515 (mmtm) REVERT: E 243 GLN cc_start: 0.7879 (mm-40) cc_final: 0.7564 (mm-40) REVERT: E 277 GLN cc_start: 0.9131 (OUTLIER) cc_final: 0.7035 (tm-30) REVERT: E 292 GLN cc_start: 0.8272 (tm-30) cc_final: 0.7939 (tm130) REVERT: F 78 MET cc_start: 0.9383 (tpp) cc_final: 0.9127 (tpp) REVERT: F 109 LYS cc_start: 0.7806 (mmtp) cc_final: 0.7527 (mmtm) REVERT: F 243 GLN cc_start: 0.7918 (mm-40) cc_final: 0.7673 (mm-40) REVERT: F 277 GLN cc_start: 0.9133 (OUTLIER) cc_final: 0.7047 (tm-30) REVERT: F 292 GLN cc_start: 0.8238 (tm-30) cc_final: 0.7926 (tm130) REVERT: G 78 MET cc_start: 0.9382 (tpp) cc_final: 0.9131 (tpp) REVERT: G 109 LYS cc_start: 0.7803 (mmtp) cc_final: 0.7498 (mmtm) REVERT: G 243 GLN cc_start: 0.7883 (mm-40) cc_final: 0.7623 (mm-40) REVERT: G 277 GLN cc_start: 0.9133 (OUTLIER) cc_final: 0.7034 (tm-30) REVERT: G 292 GLN cc_start: 0.8232 (tm-30) cc_final: 0.7914 (tm130) REVERT: G 441 GLN cc_start: 0.8434 (mt0) cc_final: 0.8109 (mt0) REVERT: H 15 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.7211 (tp30) REVERT: H 78 MET cc_start: 0.9379 (tpp) cc_final: 0.9125 (tpp) REVERT: H 109 LYS cc_start: 0.7795 (mmtp) cc_final: 0.7506 (mmtm) REVERT: H 243 GLN cc_start: 0.7883 (mm-40) cc_final: 0.7594 (mm-40) REVERT: H 277 GLN cc_start: 0.9136 (OUTLIER) cc_final: 0.7030 (tm-30) REVERT: H 292 GLN cc_start: 0.8225 (tm-30) cc_final: 0.7940 (tm130) REVERT: H 441 GLN cc_start: 0.8391 (mt0) cc_final: 0.8016 (mt0) outliers start: 39 outliers final: 20 residues processed: 495 average time/residue: 3.1243 time to fit residues: 1779.4455 Evaluate side-chains 496 residues out of total 2648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 462 time to evaluate : 4.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ASP Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain B residue 15 GLU Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 455 LYS Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain D residue 15 GLU Chi-restraints excluded: chain D residue 48 GLU Chi-restraints excluded: chain D residue 224 ARG Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 495 MET Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 455 LYS Chi-restraints excluded: chain E residue 495 MET Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 48 GLU Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain G residue 48 GLU Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 443 VAL Chi-restraints excluded: chain G residue 455 LYS Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 15 GLU Chi-restraints excluded: chain H residue 48 GLU Chi-restraints excluded: chain H residue 250 VAL Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 333 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 195 optimal weight: 3.9990 chunk 126 optimal weight: 0.9980 chunk 188 optimal weight: 3.9990 chunk 95 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 200 optimal weight: 1.9990 chunk 215 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 248 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 454 GLN B 21 GLN ** B 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 454 GLN C 21 GLN ** C 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 454 GLN D 454 GLN ** E 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 454 GLN F 21 GLN ** F 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 454 GLN G 454 GLN H 454 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 25960 Z= 0.237 Angle : 0.521 6.771 35128 Z= 0.270 Chirality : 0.042 0.147 4064 Planarity : 0.005 0.051 4424 Dihedral : 8.442 76.727 4055 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.70 % Allowed : 15.45 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.15), residues: 3248 helix: 0.90 (0.15), residues: 1312 sheet: 0.52 (0.30), residues: 288 loop : -0.42 (0.15), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 466 PHE 0.019 0.001 PHE E 401 TYR 0.009 0.001 TYR C 348 ARG 0.002 0.000 ARG G 341 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6496 Ramachandran restraints generated. 3248 Oldfield, 0 Emsley, 3248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6496 Ramachandran restraints generated. 3248 Oldfield, 0 Emsley, 3248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 2648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 465 time to evaluate : 3.664 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 15 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.7292 (tp30) REVERT: A 109 LYS cc_start: 0.7807 (mmtp) cc_final: 0.7506 (mmtm) REVERT: A 111 GLU cc_start: 0.7147 (tp30) cc_final: 0.6937 (tp30) REVERT: A 243 GLN cc_start: 0.7874 (mm-40) cc_final: 0.7619 (mm-40) REVERT: A 277 GLN cc_start: 0.9140 (OUTLIER) cc_final: 0.7032 (tm-30) REVERT: A 292 GLN cc_start: 0.8220 (tm-30) cc_final: 0.7930 (tm130) REVERT: A 441 GLN cc_start: 0.8387 (mt0) cc_final: 0.7993 (mt0) REVERT: B 109 LYS cc_start: 0.7774 (mmtp) cc_final: 0.7497 (mmtm) REVERT: B 243 GLN cc_start: 0.7908 (mm-40) cc_final: 0.7602 (mm-40) REVERT: B 277 GLN cc_start: 0.9126 (OUTLIER) cc_final: 0.7021 (tm-30) REVERT: B 292 GLN cc_start: 0.8282 (tm-30) cc_final: 0.7926 (tm130) REVERT: C 243 GLN cc_start: 0.7899 (mm-40) cc_final: 0.7616 (mm-40) REVERT: C 277 GLN cc_start: 0.9130 (OUTLIER) cc_final: 0.7026 (tm-30) REVERT: C 292 GLN cc_start: 0.8220 (tm-30) cc_final: 0.7901 (tm130) REVERT: D 15 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.7247 (tp30) REVERT: D 78 MET cc_start: 0.9384 (tpp) cc_final: 0.9138 (tpp) REVERT: D 109 LYS cc_start: 0.7762 (mmtp) cc_final: 0.7481 (mmtm) REVERT: D 111 GLU cc_start: 0.7089 (tp30) cc_final: 0.6877 (tp30) REVERT: D 224 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.7792 (ptp-170) REVERT: D 243 GLN cc_start: 0.7890 (mm-40) cc_final: 0.7644 (mm-40) REVERT: D 277 GLN cc_start: 0.9132 (OUTLIER) cc_final: 0.7019 (tm-30) REVERT: D 292 GLN cc_start: 0.8233 (tm-30) cc_final: 0.7890 (tm130) REVERT: D 441 GLN cc_start: 0.8370 (mt0) cc_final: 0.8070 (mt0) REVERT: D 495 MET cc_start: 0.7078 (OUTLIER) cc_final: 0.6866 (tpt) REVERT: E 78 MET cc_start: 0.9383 (tpp) cc_final: 0.9128 (tpp) REVERT: E 243 GLN cc_start: 0.7875 (mm-40) cc_final: 0.7537 (mm-40) REVERT: E 277 GLN cc_start: 0.9138 (OUTLIER) cc_final: 0.6979 (tm-30) REVERT: E 292 GLN cc_start: 0.8258 (tm-30) cc_final: 0.7921 (tm130) REVERT: E 495 MET cc_start: 0.7082 (OUTLIER) cc_final: 0.6774 (tpt) REVERT: F 78 MET cc_start: 0.9388 (tpp) cc_final: 0.9131 (tpp) REVERT: F 243 GLN cc_start: 0.7904 (mm-40) cc_final: 0.7634 (mm-40) REVERT: F 277 GLN cc_start: 0.9133 (OUTLIER) cc_final: 0.7025 (tm-30) REVERT: F 292 GLN cc_start: 0.8238 (tm-30) cc_final: 0.7925 (tm130) REVERT: G 78 MET cc_start: 0.9385 (tpp) cc_final: 0.9134 (tpp) REVERT: G 109 LYS cc_start: 0.7789 (mmtp) cc_final: 0.7489 (mmtm) REVERT: G 243 GLN cc_start: 0.7894 (mm-40) cc_final: 0.7642 (mm-40) REVERT: G 277 GLN cc_start: 0.9140 (OUTLIER) cc_final: 0.6979 (tm-30) REVERT: G 292 GLN cc_start: 0.8225 (tm-30) cc_final: 0.7882 (tm130) REVERT: G 441 GLN cc_start: 0.8432 (mt0) cc_final: 0.8109 (mt0) REVERT: H 15 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7211 (tp30) REVERT: H 78 MET cc_start: 0.9382 (tpp) cc_final: 0.9125 (tpp) REVERT: H 243 GLN cc_start: 0.7878 (mm-40) cc_final: 0.7569 (mm-40) REVERT: H 277 GLN cc_start: 0.9143 (OUTLIER) cc_final: 0.6976 (tm-30) REVERT: H 292 GLN cc_start: 0.8221 (tm-30) cc_final: 0.7932 (tm130) REVERT: H 441 GLN cc_start: 0.8406 (mt0) cc_final: 0.8041 (mt0) outliers start: 45 outliers final: 21 residues processed: 493 average time/residue: 3.0778 time to fit residues: 1762.3362 Evaluate side-chains 494 residues out of total 2648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 459 time to evaluate : 3.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 455 LYS Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain D residue 15 GLU Chi-restraints excluded: chain D residue 48 GLU Chi-restraints excluded: chain D residue 224 ARG Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 495 MET Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 455 LYS Chi-restraints excluded: chain E residue 495 MET Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 48 GLU Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain G residue 48 GLU Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 443 VAL Chi-restraints excluded: chain G residue 455 LYS Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 15 GLU Chi-restraints excluded: chain H residue 48 GLU Chi-restraints excluded: chain H residue 250 VAL Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 333 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 287 optimal weight: 3.9990 chunk 302 optimal weight: 2.9990 chunk 276 optimal weight: 3.9990 chunk 294 optimal weight: 2.9990 chunk 177 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 231 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 266 optimal weight: 2.9990 chunk 278 optimal weight: 2.9990 chunk 293 optimal weight: 0.9980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 454 GLN A 498 GLN B 21 GLN ** B 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 454 GLN C 21 GLN ** C 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 454 GLN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 454 GLN ** E 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 454 GLN F 21 GLN F 230 ASN ** F 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 454 GLN G 454 GLN H 454 GLN H 498 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 25960 Z= 0.326 Angle : 0.567 6.922 35128 Z= 0.296 Chirality : 0.044 0.145 4064 Planarity : 0.005 0.053 4424 Dihedral : 8.805 81.966 4055 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.51 % Allowed : 15.79 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % 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 (0.15), residues: 3248 helix: 0.80 (0.15), residues: 1312 sheet: 0.48 (0.30), residues: 288 loop : -0.51 (0.15), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 466 PHE 0.019 0.002 PHE G 401 TYR 0.010 0.001 TYR B 353 ARG 0.004 0.000 ARG A 341 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6496 Ramachandran restraints generated. 3248 Oldfield, 0 Emsley, 3248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6496 Ramachandran restraints generated. 3248 Oldfield, 0 Emsley, 3248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 2648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 471 time to evaluate : 3.535 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 15 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7260 (tp30) REVERT: A 109 LYS cc_start: 0.7914 (mmtp) cc_final: 0.7635 (mmtm) REVERT: A 111 GLU cc_start: 0.7193 (tp30) cc_final: 0.6966 (tp30) REVERT: A 243 GLN cc_start: 0.7908 (mm-40) cc_final: 0.7659 (mm-40) REVERT: A 277 GLN cc_start: 0.9165 (OUTLIER) cc_final: 0.7082 (tm-30) REVERT: A 292 GLN cc_start: 0.8227 (tm-30) cc_final: 0.7943 (tm130) REVERT: A 441 GLN cc_start: 0.8404 (mt0) cc_final: 0.7986 (mt0) REVERT: B 109 LYS cc_start: 0.7890 (mmtp) cc_final: 0.7619 (mmtm) REVERT: B 243 GLN cc_start: 0.7926 (mm-40) cc_final: 0.7625 (mm-40) REVERT: B 277 GLN cc_start: 0.9157 (OUTLIER) cc_final: 0.7076 (tm-30) REVERT: B 292 GLN cc_start: 0.8273 (tm-30) cc_final: 0.7947 (tm130) REVERT: C 109 LYS cc_start: 0.7906 (mmtp) cc_final: 0.7623 (mmtm) REVERT: C 243 GLN cc_start: 0.7928 (mm-40) cc_final: 0.7686 (mm-40) REVERT: C 277 GLN cc_start: 0.9161 (OUTLIER) cc_final: 0.7080 (tm-30) REVERT: C 292 GLN cc_start: 0.8267 (tm-30) cc_final: 0.7946 (tm130) REVERT: D 15 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7251 (tp30) REVERT: D 78 MET cc_start: 0.9397 (tpp) cc_final: 0.9123 (tpp) REVERT: D 109 LYS cc_start: 0.7883 (mmtp) cc_final: 0.7613 (mmtm) REVERT: D 111 GLU cc_start: 0.7138 (tp30) cc_final: 0.6930 (tp30) REVERT: D 224 ARG cc_start: 0.8069 (OUTLIER) cc_final: 0.7814 (ptp-170) REVERT: D 243 GLN cc_start: 0.7924 (mm-40) cc_final: 0.7684 (mm-40) REVERT: D 277 GLN cc_start: 0.9158 (OUTLIER) cc_final: 0.7078 (tm-30) REVERT: D 292 GLN cc_start: 0.8232 (tm-30) cc_final: 0.7915 (tm130) REVERT: D 441 GLN cc_start: 0.8385 (mt0) cc_final: 0.8072 (mt0) REVERT: D 495 MET cc_start: 0.7094 (OUTLIER) cc_final: 0.6881 (tpt) REVERT: E 15 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7200 (tp30) REVERT: E 78 MET cc_start: 0.9399 (tpp) cc_final: 0.9119 (tpp) REVERT: E 109 LYS cc_start: 0.7896 (mmtp) cc_final: 0.7602 (mmtm) REVERT: E 243 GLN cc_start: 0.7902 (mm-40) cc_final: 0.7610 (mm-40) REVERT: E 277 GLN cc_start: 0.9157 (OUTLIER) cc_final: 0.7077 (tm-30) REVERT: E 292 GLN cc_start: 0.8261 (tm-30) cc_final: 0.7933 (tm130) REVERT: F 78 MET cc_start: 0.9398 (tpp) cc_final: 0.9114 (tpp) REVERT: F 109 LYS cc_start: 0.7875 (mmtp) cc_final: 0.7606 (mmtm) REVERT: F 243 GLN cc_start: 0.7937 (mm-40) cc_final: 0.7671 (mm-40) REVERT: F 277 GLN cc_start: 0.9159 (OUTLIER) cc_final: 0.7073 (tm-30) REVERT: F 292 GLN cc_start: 0.8229 (tm-30) cc_final: 0.7920 (tm130) REVERT: G 78 MET cc_start: 0.9396 (tpp) cc_final: 0.9111 (tpp) REVERT: G 109 LYS cc_start: 0.7873 (mmtp) cc_final: 0.7589 (mmtm) REVERT: G 243 GLN cc_start: 0.7906 (mm-40) cc_final: 0.7655 (mm-40) REVERT: G 277 GLN cc_start: 0.9162 (OUTLIER) cc_final: 0.7087 (tm-30) REVERT: G 292 GLN cc_start: 0.8222 (tm-30) cc_final: 0.7904 (tm130) REVERT: G 441 GLN cc_start: 0.8386 (mt0) cc_final: 0.7990 (mt0) REVERT: H 15 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7215 (tp30) REVERT: H 78 MET cc_start: 0.9394 (tpp) cc_final: 0.9111 (tpp) REVERT: H 109 LYS cc_start: 0.7884 (mmtp) cc_final: 0.7609 (mmtm) REVERT: H 243 GLN cc_start: 0.7914 (mm-40) cc_final: 0.7636 (mm-40) REVERT: H 277 GLN cc_start: 0.9168 (OUTLIER) cc_final: 0.7087 (tm-30) REVERT: H 292 GLN cc_start: 0.8236 (tm-30) cc_final: 0.7954 (tm130) REVERT: H 441 GLN cc_start: 0.8428 (mt0) cc_final: 0.8033 (mt0) outliers start: 40 outliers final: 25 residues processed: 494 average time/residue: 3.2787 time to fit residues: 1902.8068 Evaluate side-chains 504 residues out of total 2648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 465 time to evaluate : 3.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ASP Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 455 LYS Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain D residue 15 GLU Chi-restraints excluded: chain D residue 224 ARG Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 455 LYS Chi-restraints excluded: chain D residue 495 MET Chi-restraints excluded: chain E residue 15 GLU Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 455 LYS Chi-restraints excluded: chain E residue 495 MET Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 48 GLU Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain G residue 3 ASP Chi-restraints excluded: chain G residue 48 GLU Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 443 VAL Chi-restraints excluded: chain G residue 455 LYS Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 15 GLU Chi-restraints excluded: chain H residue 48 GLU Chi-restraints excluded: chain H residue 250 VAL Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 333 THR Chi-restraints excluded: chain H residue 336 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 193 optimal weight: 1.9990 chunk 311 optimal weight: 3.9990 chunk 190 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 216 optimal weight: 3.9990 chunk 326 optimal weight: 0.8980 chunk 300 optimal weight: 0.9980 chunk 260 optimal weight: 6.9990 chunk 27 optimal weight: 0.5980 chunk 200 optimal weight: 0.9990 chunk 159 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 454 GLN B 21 GLN ** B 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 454 GLN C 21 GLN ** C 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 454 GLN D 454 GLN E 21 GLN ** E 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 454 GLN F 21 GLN ** F 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 454 GLN G 454 GLN H 454 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 25960 Z= 0.202 Angle : 0.508 7.018 35128 Z= 0.262 Chirality : 0.041 0.148 4064 Planarity : 0.004 0.050 4424 Dihedral : 8.339 84.300 4055 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.21 % Allowed : 15.86 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % 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: 0.35 (0.15), residues: 3248 helix: 1.06 (0.16), residues: 1304 sheet: 0.49 (0.30), residues: 288 loop : -0.43 (0.15), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 92 PHE 0.019 0.001 PHE D 401 TYR 0.009 0.001 TYR H 348 ARG 0.003 0.000 ARG F 412 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6496 Ramachandran restraints generated. 3248 Oldfield, 0 Emsley, 3248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6496 Ramachandran restraints generated. 3248 Oldfield, 0 Emsley, 3248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 2648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 460 time to evaluate : 3.738 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 15 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7255 (tp30) REVERT: A 78 MET cc_start: 0.9389 (tpp) cc_final: 0.9135 (tpp) REVERT: A 109 LYS cc_start: 0.7795 (mmtp) cc_final: 0.7496 (mmtm) REVERT: A 111 GLU cc_start: 0.7132 (tp30) cc_final: 0.6924 (tp30) REVERT: A 243 GLN cc_start: 0.7860 (mm-40) cc_final: 0.7611 (mm-40) REVERT: A 277 GLN cc_start: 0.9136 (OUTLIER) cc_final: 0.6956 (tm-30) REVERT: A 292 GLN cc_start: 0.8215 (tm-30) cc_final: 0.7918 (tm130) REVERT: A 441 GLN cc_start: 0.8390 (mt0) cc_final: 0.7983 (mt0) REVERT: B 243 GLN cc_start: 0.7890 (mm-40) cc_final: 0.7575 (mm-40) REVERT: B 277 GLN cc_start: 0.9127 (OUTLIER) cc_final: 0.6951 (tm-30) REVERT: B 292 GLN cc_start: 0.8266 (tm-30) cc_final: 0.7931 (tm130) REVERT: C 78 MET cc_start: 0.9379 (tpp) cc_final: 0.9122 (tpp) REVERT: C 243 GLN cc_start: 0.7879 (mm-40) cc_final: 0.7596 (mm-40) REVERT: C 277 GLN cc_start: 0.9132 (OUTLIER) cc_final: 0.6957 (tm-30) REVERT: C 292 GLN cc_start: 0.8225 (tm-30) cc_final: 0.7901 (tm130) REVERT: D 15 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7244 (tp30) REVERT: D 78 MET cc_start: 0.9388 (tpp) cc_final: 0.9152 (tpp) REVERT: D 109 LYS cc_start: 0.7760 (mmtp) cc_final: 0.7486 (mmtm) REVERT: D 224 ARG cc_start: 0.8093 (OUTLIER) cc_final: 0.7857 (ptp-170) REVERT: D 243 GLN cc_start: 0.7862 (mm-40) cc_final: 0.7617 (mm-40) REVERT: D 277 GLN cc_start: 0.9129 (OUTLIER) cc_final: 0.6953 (tm-30) REVERT: D 292 GLN cc_start: 0.8237 (tm-30) cc_final: 0.7911 (tm130) REVERT: D 441 GLN cc_start: 0.8363 (mt0) cc_final: 0.8058 (mt0) REVERT: D 495 MET cc_start: 0.7072 (OUTLIER) cc_final: 0.6787 (tpt) REVERT: E 243 GLN cc_start: 0.7852 (mm-40) cc_final: 0.7568 (mm-40) REVERT: E 277 GLN cc_start: 0.9129 (OUTLIER) cc_final: 0.6954 (tm-30) REVERT: E 292 GLN cc_start: 0.8255 (tm-30) cc_final: 0.7917 (tm130) REVERT: E 495 MET cc_start: 0.7102 (OUTLIER) cc_final: 0.6867 (tpt) REVERT: F 78 MET cc_start: 0.9384 (tpp) cc_final: 0.9136 (tpp) REVERT: F 243 GLN cc_start: 0.7893 (mm-40) cc_final: 0.7621 (mm-40) REVERT: F 277 GLN cc_start: 0.9130 (OUTLIER) cc_final: 0.6952 (tm-30) REVERT: F 292 GLN cc_start: 0.8229 (tm-30) cc_final: 0.7914 (tm130) REVERT: G 78 MET cc_start: 0.9387 (tpp) cc_final: 0.9137 (tpp) REVERT: G 243 GLN cc_start: 0.7860 (mm-40) cc_final: 0.7579 (mm-40) REVERT: G 277 GLN cc_start: 0.9131 (OUTLIER) cc_final: 0.6954 (tm-30) REVERT: G 292 GLN cc_start: 0.8236 (tm-30) cc_final: 0.7910 (tm130) REVERT: G 441 GLN cc_start: 0.8417 (mt0) cc_final: 0.8098 (mt0) REVERT: H 78 MET cc_start: 0.9378 (tpp) cc_final: 0.9129 (tpp) REVERT: H 243 GLN cc_start: 0.7857 (mm-40) cc_final: 0.7538 (mm-40) REVERT: H 277 GLN cc_start: 0.9134 (OUTLIER) cc_final: 0.6949 (tm-30) REVERT: H 292 GLN cc_start: 0.8222 (tm-30) cc_final: 0.7930 (tm130) REVERT: H 441 GLN cc_start: 0.8400 (mt0) cc_final: 0.8032 (mt0) outliers start: 32 outliers final: 13 residues processed: 478 average time/residue: 3.0188 time to fit residues: 1662.1439 Evaluate side-chains 481 residues out of total 2648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 455 time to evaluate : 3.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ASP Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 455 LYS Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain D residue 15 GLU Chi-restraints excluded: chain D residue 224 ARG Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 495 MET Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 495 MET Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain G residue 48 GLU Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 443 VAL Chi-restraints excluded: chain G residue 455 LYS Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 250 VAL Chi-restraints excluded: chain H residue 277 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 206 optimal weight: 0.8980 chunk 277 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 239 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 260 optimal weight: 6.9990 chunk 109 optimal weight: 0.9980 chunk 267 optimal weight: 0.7980 chunk 32 optimal weight: 4.9990 chunk 48 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 454 GLN B 21 GLN ** B 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 454 GLN C 21 GLN ** C 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 454 GLN D 21 GLN D 454 GLN ** E 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 454 GLN F 21 GLN ** F 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 454 GLN G 454 GLN H 454 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.120582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.084879 restraints weight = 78561.818| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 1.71 r_work: 0.2727 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2604 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 25960 Z= 0.208 Angle : 0.510 6.619 35128 Z= 0.264 Chirality : 0.041 0.154 4064 Planarity : 0.004 0.051 4424 Dihedral : 8.271 89.674 4055 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.13 % Allowed : 16.01 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % 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: 0.38 (0.15), residues: 3248 helix: 1.05 (0.15), residues: 1312 sheet: 0.43 (0.30), residues: 288 loop : -0.38 (0.15), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 466 PHE 0.018 0.001 PHE G 401 TYR 0.009 0.001 TYR B 348 ARG 0.003 0.000 ARG A 412 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23996.57 seconds wall clock time: 417 minutes 23.84 seconds (25043.84 seconds total)