Starting phenix.real_space_refine on Thu Dec 7 22:23:04 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wrf_21882/12_2023/6wrf_21882_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wrf_21882/12_2023/6wrf_21882.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wrf_21882/12_2023/6wrf_21882.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wrf_21882/12_2023/6wrf_21882.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wrf_21882/12_2023/6wrf_21882_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wrf_21882/12_2023/6wrf_21882_neut_trim_updated.pdb" } resolution = 3.14 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= 1.000 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: 7 Type Number sf(0) Gaussians P 17 5.49 5 Mg 5 5.21 5 S 119 5.16 5 C 16882 2.51 5 N 4581 2.21 5 O 5231 1.98 5 H 27016 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 194": "OD1" <-> "OD2" Residue "B PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 261": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 285": "OE1" <-> "OE2" Residue "B ASP 352": "OD1" <-> "OD2" Residue "B ARG 370": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 399": "OD1" <-> "OD2" Residue "B ASP 404": "OD1" <-> "OD2" Residue "C ASP 103": "OD1" <-> "OD2" Residue "C PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 170": "OD1" <-> "OD2" Residue "C TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 187": "OD1" <-> "OD2" Residue "C ASP 194": "OD1" <-> "OD2" Residue "C ARG 200": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 261": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 347": "OD1" <-> "OD2" Residue "C ARG 370": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 200": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 234": "OE1" <-> "OE2" Residue "D PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 261": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 347": "OD1" <-> "OD2" Residue "D ARG 370": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 413": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 185": "OE1" <-> "OE2" Residue "E ASP 201": "OD1" <-> "OD2" Residue "E ARG 261": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 352": "OD1" <-> "OD2" Residue "E ARG 370": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 137": "OD1" <-> "OD2" Residue "F GLU 156": "OE1" <-> "OE2" Residue "F GLU 185": "OE1" <-> "OE2" Residue "F ASP 187": "OD1" <-> "OD2" Residue "F ARG 261": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 352": "OD1" <-> "OD2" Residue "F ASP 356": "OD1" <-> "OD2" Residue "F ARG 370": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F GLU 394": "OE1" <-> "OE2" Residue "F ASP 404": "OD1" <-> "OD2" Residue "H ARG 12": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H GLU 136": "OE1" <-> "OE2" Residue "H ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H GLU 162": "OE1" <-> "OE2" Residue "H ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ASP 171": "OD1" <-> "OD2" Residue "H PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I ARG 12": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I GLU 14": "OE1" <-> "OE2" Residue "I ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I GLU 162": "OE1" <-> "OE2" Residue "I ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I GLU 169": "OE1" <-> "OE2" Residue "I ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 12": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J GLU 141": "OE1" <-> "OE2" Residue "J ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J GLU 162": "OE1" <-> "OE2" Residue "J ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 12": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ASP 171": "OD1" <-> "OD2" Residue "L ARG 12": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L GLU 14": "OE1" <-> "OE2" Residue "L ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ASP 134": "OD1" <-> "OD2" Residue "L ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ASP 171": "OD1" <-> "OD2" Residue "M ARG 12": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M GLU 56": "OE1" <-> "OE2" Residue "M ASP 58": "OD1" <-> "OD2" Residue "M TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ASP 167": "OD1" <-> "OD2" Residue "M ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N ARG 12": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N ASP 134": "OD1" <-> "OD2" Residue "N ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 109": "OE1" <-> "OE2" Residue "A PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 194": "OD1" <-> "OD2" Residue "A PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 261": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 279": "OD1" <-> "OD2" Residue "A GLU 283": "OE1" <-> "OE2" Residue "A PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 370": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 399": "OD1" <-> "OD2" Residue "A ASP 404": "OD1" <-> "OD2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 53851 Number of models: 1 Model: "" Number of chains: 27 Chain: "B" Number of atoms: 5438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 5438 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 14, 'TRANS': 337} Chain: "C" Number of atoms: 5448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 5448 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 14, 'TRANS': 338} Chain: "D" Number of atoms: 5448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 5448 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 14, 'TRANS': 338} Chain: "E" Number of atoms: 5361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 5361 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 14, 'TRANS': 332} Chain breaks: 1 Chain: "F" Number of atoms: 5246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 5246 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 13, 'TRANS': 325} Chain breaks: 1 Chain: "H" Number of atoms: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3016 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "I" Number of atoms: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3016 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "J" Number of atoms: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3016 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "K" Number of atoms: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3016 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "L" Number of atoms: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3016 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "M" Number of atoms: 3105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 3105 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 7, 'TRANS': 189} Chain: "N" Number of atoms: 3002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 3002 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 7, 'TRANS': 183} Chain: "S" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 100 Classifications: {'peptide': 7} Modifications used: {'COO': 1} Link IDs: {'TRANS': 6} Chain: "A" Number of atoms: 5429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 5429 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 14, 'TRANS': 336} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 17.37, per 1000 atoms: 0.32 Number of scatterers: 53851 At special positions: 0 Unit cell: (147.03, 134.85, 138.33, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 119 16.00 P 17 15.00 Mg 5 11.99 O 5231 8.00 N 4581 7.00 C 16882 6.00 H 27016 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 32.41 Conformation dependent library (CDL) restraints added in 4.0 seconds 6836 Ramachandran restraints generated. 3418 Oldfield, 0 Emsley, 3418 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6330 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 150 helices and 46 sheets defined 45.1% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.76 Creating SS restraints... Processing helix chain 'B' and resid 67 through 75 Processing helix chain 'B' and resid 82 through 100 Processing helix chain 'B' and resid 125 through 135 Processing helix chain 'B' and resid 158 through 169 removed outlier: 3.650A pdb=" N GLN B 167 " --> pdb=" O LYS B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 177 Processing helix chain 'B' and resid 186 through 188 No H-bonds generated for 'chain 'B' and resid 186 through 188' Processing helix chain 'B' and resid 205 through 216 removed outlier: 4.637A pdb=" N LYS B 213 " --> pdb=" O GLN B 209 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU B 214 " --> pdb=" O ALA B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 262 Processing helix chain 'B' and resid 283 through 289 removed outlier: 3.638A pdb=" N ALA B 288 " --> pdb=" O GLY B 284 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLN B 289 " --> pdb=" O GLU B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 298 Processing helix chain 'B' and resid 302 through 305 No H-bonds generated for 'chain 'B' and resid 302 through 305' Processing helix chain 'B' and resid 319 through 327 removed outlier: 3.873A pdb=" N LYS B 327 " --> pdb=" O ILE B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 344 removed outlier: 3.665A pdb=" N GLU B 344 " --> pdb=" O LEU B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 365 removed outlier: 3.534A pdb=" N ARG B 365 " --> pdb=" O LYS B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 379 removed outlier: 3.503A pdb=" N VAL B 376 " --> pdb=" O ARG B 373 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU B 377 " --> pdb=" O SER B 374 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA B 378 " --> pdb=" O ILE B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 387 Processing helix chain 'B' and resid 400 through 404 removed outlier: 3.700A pdb=" N ASP B 404 " --> pdb=" O GLU B 400 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 400 through 404' Processing helix chain 'C' and resid 67 through 75 Processing helix chain 'C' and resid 82 through 100 Processing helix chain 'C' and resid 125 through 135 Processing helix chain 'C' and resid 158 through 168 removed outlier: 3.559A pdb=" N ILE C 161 " --> pdb=" O VAL C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 176 No H-bonds generated for 'chain 'C' and resid 173 through 176' Processing helix chain 'C' and resid 205 through 216 removed outlier: 4.687A pdb=" N LYS C 213 " --> pdb=" O GLN C 209 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU C 214 " --> pdb=" O ALA C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 262 Processing helix chain 'C' and resid 283 through 289 removed outlier: 4.065A pdb=" N GLN C 289 " --> pdb=" O GLU C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 298 Processing helix chain 'C' and resid 302 through 307 Processing helix chain 'C' and resid 319 through 327 removed outlier: 3.883A pdb=" N LYS C 327 " --> pdb=" O ILE C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 344 removed outlier: 3.734A pdb=" N GLU C 344 " --> pdb=" O LEU C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 365 Processing helix chain 'C' and resid 368 through 379 removed outlier: 3.720A pdb=" N VAL C 376 " --> pdb=" O ARG C 373 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLU C 377 " --> pdb=" O SER C 374 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA C 379 " --> pdb=" O VAL C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 387 Processing helix chain 'C' and resid 400 through 404 removed outlier: 3.536A pdb=" N ASP C 404 " --> pdb=" O GLU C 400 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 400 through 404' Processing helix chain 'D' and resid 67 through 75 Processing helix chain 'D' and resid 82 through 100 Processing helix chain 'D' and resid 125 through 135 removed outlier: 3.649A pdb=" N LEU D 135 " --> pdb=" O THR D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 168 Processing helix chain 'D' and resid 173 through 176 No H-bonds generated for 'chain 'D' and resid 173 through 176' Processing helix chain 'D' and resid 186 through 188 No H-bonds generated for 'chain 'D' and resid 186 through 188' Processing helix chain 'D' and resid 205 through 216 removed outlier: 4.672A pdb=" N LYS D 213 " --> pdb=" O GLN D 209 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU D 214 " --> pdb=" O ALA D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 262 removed outlier: 3.857A pdb=" N ARG D 261 " --> pdb=" O VAL D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 289 removed outlier: 3.823A pdb=" N GLN D 289 " --> pdb=" O GLU D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 298 Processing helix chain 'D' and resid 302 through 307 Processing helix chain 'D' and resid 319 through 327 removed outlier: 3.857A pdb=" N LYS D 327 " --> pdb=" O ILE D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 344 removed outlier: 3.845A pdb=" N GLU D 344 " --> pdb=" O LEU D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 352 through 365 Processing helix chain 'D' and resid 368 through 379 removed outlier: 3.731A pdb=" N VAL D 376 " --> pdb=" O ARG D 373 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA D 379 " --> pdb=" O VAL D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 381 through 387 Processing helix chain 'D' and resid 400 through 404 removed outlier: 3.541A pdb=" N ASP D 404 " --> pdb=" O GLU D 400 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 400 through 404' Processing helix chain 'E' and resid 67 through 75 Processing helix chain 'E' and resid 82 through 100 Processing helix chain 'E' and resid 125 through 135 Processing helix chain 'E' and resid 160 through 169 Processing helix chain 'E' and resid 173 through 176 No H-bonds generated for 'chain 'E' and resid 173 through 176' Processing helix chain 'E' and resid 187 through 189 No H-bonds generated for 'chain 'E' and resid 187 through 189' Processing helix chain 'E' and resid 205 through 216 removed outlier: 3.720A pdb=" N ALA E 210 " --> pdb=" O GLY E 206 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N LYS E 213 " --> pdb=" O GLN E 209 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU E 214 " --> pdb=" O ALA E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 262 Processing helix chain 'E' and resid 283 through 289 removed outlier: 3.904A pdb=" N GLN E 289 " --> pdb=" O GLU E 285 " (cutoff:3.500A) Processing helix chain 'E' and resid 292 through 297 Processing helix chain 'E' and resid 302 through 307 Processing helix chain 'E' and resid 319 through 327 removed outlier: 3.693A pdb=" N LYS E 327 " --> pdb=" O ILE E 323 " (cutoff:3.500A) Processing helix chain 'E' and resid 333 through 343 Processing helix chain 'E' and resid 352 through 365 Processing helix chain 'E' and resid 370 through 379 removed outlier: 3.522A pdb=" N VAL E 376 " --> pdb=" O ARG E 373 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA E 378 " --> pdb=" O ILE E 375 " (cutoff:3.500A) Processing helix chain 'E' and resid 381 through 387 Processing helix chain 'E' and resid 400 through 404 Processing helix chain 'F' and resid 67 through 77 removed outlier: 3.665A pdb=" N ASP F 76 " --> pdb=" O ASN F 72 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N TYR F 77 " --> pdb=" O HIS F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 100 Processing helix chain 'F' and resid 125 through 135 Processing helix chain 'F' and resid 147 through 150 removed outlier: 4.039A pdb=" N GLU F 150 " --> pdb=" O THR F 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 147 through 150' Processing helix chain 'F' and resid 154 through 169 removed outlier: 3.758A pdb=" N ILE F 162 " --> pdb=" O VAL F 158 " (cutoff:3.500A) Processing helix chain 'F' and resid 173 through 178 removed outlier: 3.522A pdb=" N ARG F 178 " --> pdb=" O GLN F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 216 Processing helix chain 'F' and resid 232 through 234 No H-bonds generated for 'chain 'F' and resid 232 through 234' Processing helix chain 'F' and resid 253 through 262 removed outlier: 3.727A pdb=" N VAL F 262 " --> pdb=" O SER F 259 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 289 removed outlier: 3.655A pdb=" N GLN F 289 " --> pdb=" O GLU F 285 " (cutoff:3.500A) Processing helix chain 'F' and resid 292 through 298 Processing helix chain 'F' and resid 302 through 306 Processing helix chain 'F' and resid 319 through 327 removed outlier: 3.723A pdb=" N LYS F 327 " --> pdb=" O ILE F 323 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 344 removed outlier: 3.877A pdb=" N GLU F 344 " --> pdb=" O LEU F 340 " (cutoff:3.500A) Processing helix chain 'F' and resid 352 through 365 Processing helix chain 'F' and resid 368 through 387 removed outlier: 3.574A pdb=" N GLY F 371 " --> pdb=" O GLY F 368 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG F 373 " --> pdb=" O ARG F 370 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL F 376 " --> pdb=" O ARG F 373 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA F 379 " --> pdb=" O VAL F 376 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ASP F 382 " --> pdb=" O ALA F 379 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET F 384 " --> pdb=" O LEU F 381 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU F 387 " --> pdb=" O MET F 384 " (cutoff:3.500A) Processing helix chain 'F' and resid 400 through 404 removed outlier: 3.591A pdb=" N ASP F 404 " --> pdb=" O GLU F 400 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 400 through 404' Processing helix chain 'H' and resid 19 through 26 removed outlier: 3.505A pdb=" N GLU H 26 " --> pdb=" O ARG H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 53 Processing helix chain 'H' and resid 71 through 82 removed outlier: 3.530A pdb=" N ILE H 76 " --> pdb=" O ALA H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 104 Processing helix chain 'H' and resid 132 through 157 Processing helix chain 'H' and resid 161 through 168 Processing helix chain 'H' and resid 176 through 182 Processing helix chain 'I' and resid 19 through 26 removed outlier: 3.613A pdb=" N LEU I 23 " --> pdb=" O ILE I 19 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU I 26 " --> pdb=" O ARG I 22 " (cutoff:3.500A) Processing helix chain 'I' and resid 37 through 53 Processing helix chain 'I' and resid 71 through 82 removed outlier: 3.556A pdb=" N ILE I 76 " --> pdb=" O ALA I 72 " (cutoff:3.500A) Processing helix chain 'I' and resid 97 through 104 Processing helix chain 'I' and resid 132 through 157 Processing helix chain 'I' and resid 161 through 168 Processing helix chain 'I' and resid 176 through 182 Processing helix chain 'J' and resid 19 through 26 removed outlier: 3.660A pdb=" N GLU J 26 " --> pdb=" O ARG J 22 " (cutoff:3.500A) Processing helix chain 'J' and resid 37 through 53 Processing helix chain 'J' and resid 71 through 82 removed outlier: 3.527A pdb=" N ILE J 76 " --> pdb=" O ALA J 72 " (cutoff:3.500A) Processing helix chain 'J' and resid 97 through 104 Processing helix chain 'J' and resid 132 through 157 Processing helix chain 'J' and resid 161 through 168 Processing helix chain 'J' and resid 176 through 182 Processing helix chain 'K' and resid 19 through 26 removed outlier: 3.809A pdb=" N LEU K 23 " --> pdb=" O ILE K 19 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU K 26 " --> pdb=" O ARG K 22 " (cutoff:3.500A) Processing helix chain 'K' and resid 37 through 53 Processing helix chain 'K' and resid 70 through 82 Processing helix chain 'K' and resid 97 through 104 Processing helix chain 'K' and resid 132 through 157 Processing helix chain 'K' and resid 161 through 168 Processing helix chain 'K' and resid 176 through 182 Processing helix chain 'L' and resid 19 through 26 removed outlier: 3.607A pdb=" N GLU L 26 " --> pdb=" O ARG L 22 " (cutoff:3.500A) Processing helix chain 'L' and resid 37 through 53 Processing helix chain 'L' and resid 70 through 82 Processing helix chain 'L' and resid 97 through 104 Processing helix chain 'L' and resid 132 through 157 Processing helix chain 'L' and resid 161 through 168 Processing helix chain 'L' and resid 176 through 182 Processing helix chain 'M' and resid 19 through 26 removed outlier: 3.627A pdb=" N GLU M 26 " --> pdb=" O ARG M 22 " (cutoff:3.500A) Processing helix chain 'M' and resid 37 through 53 Processing helix chain 'M' and resid 71 through 82 Processing helix chain 'M' and resid 97 through 104 Processing helix chain 'M' and resid 132 through 157 Processing helix chain 'M' and resid 161 through 168 Processing helix chain 'M' and resid 176 through 182 Processing helix chain 'N' and resid 19 through 26 removed outlier: 3.728A pdb=" N LEU N 23 " --> pdb=" O ILE N 19 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU N 26 " --> pdb=" O ARG N 22 " (cutoff:3.500A) Processing helix chain 'N' and resid 37 through 53 Processing helix chain 'N' and resid 70 through 82 Processing helix chain 'N' and resid 97 through 104 Processing helix chain 'N' and resid 132 through 157 Processing helix chain 'N' and resid 161 through 168 Processing helix chain 'N' and resid 176 through 182 Processing helix chain 'A' and resid 67 through 77 removed outlier: 3.738A pdb=" N TYR A 77 " --> pdb=" O HIS A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 100 Processing helix chain 'A' and resid 125 through 135 removed outlier: 3.512A pdb=" N ALA A 129 " --> pdb=" O LYS A 125 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU A 130 " --> pdb=" O THR A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 168 Processing helix chain 'A' and resid 173 through 178 removed outlier: 3.869A pdb=" N ARG A 178 " --> pdb=" O GLN A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 189 Processing helix chain 'A' and resid 205 through 216 Processing helix chain 'A' and resid 254 through 262 Processing helix chain 'A' and resid 277 through 279 No H-bonds generated for 'chain 'A' and resid 277 through 279' Processing helix chain 'A' and resid 292 through 298 Processing helix chain 'A' and resid 302 through 307 Processing helix chain 'A' and resid 319 through 327 removed outlier: 3.509A pdb=" N LYS A 327 " --> pdb=" O ILE A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 344 removed outlier: 3.563A pdb=" N GLU A 344 " --> pdb=" O LEU A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 365 Processing helix chain 'A' and resid 368 through 379 removed outlier: 3.526A pdb=" N VAL A 376 " --> pdb=" O ARG A 373 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU A 377 " --> pdb=" O SER A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 387 Processing helix chain 'A' and resid 400 through 404 removed outlier: 3.626A pdb=" N ASP A 404 " --> pdb=" O GLU A 400 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 400 through 404' Processing sheet with id= A, first strand: chain 'B' and resid 310 through 313 Processing sheet with id= B, first strand: chain 'B' and resid 219 through 222 Processing sheet with id= C, first strand: chain 'B' and resid 347 through 350 removed outlier: 6.955A pdb=" N ILE B 412 " --> pdb=" O GLU B 394 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N VAL B 396 " --> pdb=" O LEU B 410 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N LEU B 410 " --> pdb=" O VAL B 396 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 310 through 313 Processing sheet with id= E, first strand: chain 'C' and resid 219 through 222 Processing sheet with id= F, first strand: chain 'C' and resid 347 through 350 removed outlier: 7.013A pdb=" N ILE C 412 " --> pdb=" O GLU C 394 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N VAL C 396 " --> pdb=" O LEU C 410 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LEU C 410 " --> pdb=" O VAL C 396 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 310 through 314 removed outlier: 3.746A pdb=" N GLY D 119 " --> pdb=" O GLY D 249 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 219 through 222 Processing sheet with id= I, first strand: chain 'D' and resid 347 through 350 removed outlier: 6.864A pdb=" N ILE D 412 " --> pdb=" O GLU D 394 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N VAL D 396 " --> pdb=" O LEU D 410 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LEU D 410 " --> pdb=" O VAL D 396 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 312 through 314 removed outlier: 3.576A pdb=" N GLY E 119 " --> pdb=" O GLY E 249 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 219 through 223 removed outlier: 3.550A pdb=" N LEU E 236 " --> pdb=" O VAL E 222 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 347 through 350 removed outlier: 6.812A pdb=" N ILE E 412 " --> pdb=" O GLU E 394 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N VAL E 396 " --> pdb=" O LEU E 410 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU E 410 " --> pdb=" O VAL E 396 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'F' and resid 115 through 118 removed outlier: 6.643A pdb=" N VAL F 310 " --> pdb=" O LEU F 116 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N ILE F 118 " --> pdb=" O VAL F 310 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ALA F 312 " --> pdb=" O ILE F 118 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'F' and resid 140 through 144 removed outlier: 6.621A pdb=" N ILE F 180 " --> pdb=" O THR F 141 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N ALA F 143 " --> pdb=" O ILE F 180 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N TYR F 182 " --> pdb=" O ALA F 143 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LEU F 244 " --> pdb=" O VAL F 181 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N ILE F 183 " --> pdb=" O LEU F 244 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ILE F 246 " --> pdb=" O ILE F 183 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'F' and resid 219 through 222 Processing sheet with id= P, first strand: chain 'F' and resid 347 through 350 removed outlier: 7.227A pdb=" N ILE F 412 " --> pdb=" O GLU F 394 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'H' and resid 5 through 8 Processing sheet with id= R, first strand: chain 'H' and resid 28 through 32 removed outlier: 6.350A pdb=" N TYR H 60 " --> pdb=" O ILE H 29 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N LEU H 31 " --> pdb=" O TYR H 60 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N TYR H 62 " --> pdb=" O LEU H 31 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'H' and resid 112 through 114 removed outlier: 6.653A pdb=" N SER H 187 " --> pdb=" O CYS H 113 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'H' and resid 118 through 121 Processing sheet with id= U, first strand: chain 'I' and resid 5 through 9 Processing sheet with id= V, first strand: chain 'I' and resid 28 through 32 removed outlier: 6.357A pdb=" N TYR I 60 " --> pdb=" O ILE I 29 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N LEU I 31 " --> pdb=" O TYR I 60 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N TYR I 62 " --> pdb=" O LEU I 31 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'I' and resid 112 through 114 removed outlier: 6.701A pdb=" N SER I 187 " --> pdb=" O CYS I 113 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'I' and resid 118 through 121 Processing sheet with id= Y, first strand: chain 'J' and resid 5 through 9 Processing sheet with id= Z, first strand: chain 'J' and resid 28 through 32 removed outlier: 6.373A pdb=" N TYR J 60 " --> pdb=" O ILE J 29 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N LEU J 31 " --> pdb=" O TYR J 60 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N TYR J 62 " --> pdb=" O LEU J 31 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'J' and resid 112 through 114 removed outlier: 6.677A pdb=" N SER J 187 " --> pdb=" O CYS J 113 " (cutoff:3.500A) No H-bonds generated for sheet with id= AA Processing sheet with id= AB, first strand: chain 'J' and resid 118 through 121 Processing sheet with id= AC, first strand: chain 'K' and resid 5 through 10 Processing sheet with id= AD, first strand: chain 'K' and resid 28 through 32 removed outlier: 6.385A pdb=" N TYR K 60 " --> pdb=" O ILE K 29 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N LEU K 31 " --> pdb=" O TYR K 60 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N TYR K 62 " --> pdb=" O LEU K 31 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'K' and resid 112 through 114 removed outlier: 6.751A pdb=" N SER K 187 " --> pdb=" O CYS K 113 " (cutoff:3.500A) No H-bonds generated for sheet with id= AE Processing sheet with id= AF, first strand: chain 'K' and resid 118 through 121 Processing sheet with id= AG, first strand: chain 'L' and resid 5 through 10 Processing sheet with id= AH, first strand: chain 'L' and resid 28 through 32 removed outlier: 6.461A pdb=" N TYR L 60 " --> pdb=" O ILE L 29 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N LEU L 31 " --> pdb=" O TYR L 60 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N TYR L 62 " --> pdb=" O LEU L 31 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N SER L 187 " --> pdb=" O CYS L 113 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'L' and resid 118 through 121 Processing sheet with id= AJ, first strand: chain 'M' and resid 5 through 9 Processing sheet with id= AK, first strand: chain 'M' and resid 28 through 32 removed outlier: 6.383A pdb=" N TYR M 60 " --> pdb=" O ILE M 29 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N LEU M 31 " --> pdb=" O TYR M 60 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N TYR M 62 " --> pdb=" O LEU M 31 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'M' and resid 112 through 114 removed outlier: 6.963A pdb=" N SER M 187 " --> pdb=" O CYS M 113 " (cutoff:3.500A) No H-bonds generated for sheet with id= AL Processing sheet with id= AM, first strand: chain 'M' and resid 118 through 121 Processing sheet with id= AN, first strand: chain 'N' and resid 5 through 8 Processing sheet with id= AO, first strand: chain 'N' and resid 28 through 32 removed outlier: 6.367A pdb=" N TYR N 60 " --> pdb=" O ILE N 29 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N LEU N 31 " --> pdb=" O TYR N 60 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N TYR N 62 " --> pdb=" O LEU N 31 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'N' and resid 112 through 114 removed outlier: 6.700A pdb=" N SER N 187 " --> pdb=" O CYS N 113 " (cutoff:3.500A) No H-bonds generated for sheet with id= AP Processing sheet with id= AQ, first strand: chain 'N' and resid 118 through 121 Processing sheet with id= AR, first strand: chain 'A' and resid 310 through 314 removed outlier: 3.842A pdb=" N THR A 141 " --> pdb=" O ILE A 180 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'A' and resid 219 through 222 Processing sheet with id= AT, first strand: chain 'A' and resid 347 through 350 1112 hydrogen bonds defined for protein. 3021 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: 17.94 Time building geometry restraints manager: 34.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.05: 26996 1.05 - 1.27: 4715 1.27 - 1.50: 11823 1.50 - 1.72: 10487 1.72 - 1.95: 213 Bond restraints: 54234 Sorted by residual: bond pdb=" CG1 ILE D 215 " pdb=" CD1 ILE D 215 " ideal model delta sigma weight residual 1.513 1.405 0.108 3.90e-02 6.57e+02 7.64e+00 bond pdb=" CG1 ILE C 215 " pdb=" CD1 ILE C 215 " ideal model delta sigma weight residual 1.513 1.428 0.085 3.90e-02 6.57e+02 4.70e+00 bond pdb=" CG1 ILE I 63 " pdb=" CD1 ILE I 63 " ideal model delta sigma weight residual 1.513 1.429 0.084 3.90e-02 6.57e+02 4.65e+00 bond pdb=" CG1 ILE E 215 " pdb=" CD1 ILE E 215 " ideal model delta sigma weight residual 1.513 1.431 0.082 3.90e-02 6.57e+02 4.47e+00 bond pdb=" CG LEU B 314 " pdb=" CD2 LEU B 314 " ideal model delta sigma weight residual 1.521 1.456 0.065 3.30e-02 9.18e+02 3.91e+00 ... (remaining 54229 not shown) Histogram of bond angle deviations from ideal: 96.89 - 104.70: 473 104.70 - 112.51: 64838 112.51 - 120.33: 17622 120.33 - 128.14: 15304 128.14 - 135.96: 203 Bond angle restraints: 98440 Sorted by residual: angle pdb=" C PRO E 196 " pdb=" N SER E 197 " pdb=" CA SER E 197 " ideal model delta sigma weight residual 122.66 134.01 -11.35 1.63e+00 3.76e-01 4.85e+01 angle pdb=" N GLU B 328 " pdb=" CA GLU B 328 " pdb=" C GLU B 328 " ideal model delta sigma weight residual 109.81 118.91 -9.10 2.21e+00 2.05e-01 1.69e+01 angle pdb=" CA PRO E 196 " pdb=" C PRO E 196 " pdb=" N SER E 197 " ideal model delta sigma weight residual 116.70 108.57 8.13 2.07e+00 2.33e-01 1.54e+01 angle pdb=" C ILE M 83 " pdb=" N LYS M 84 " pdb=" CA LYS M 84 " ideal model delta sigma weight residual 119.78 124.60 -4.82 1.24e+00 6.50e-01 1.51e+01 angle pdb=" N ASP J 18 " pdb=" CA ASP J 18 " pdb=" C ASP J 18 " ideal model delta sigma weight residual 110.55 105.66 4.89 1.35e+00 5.49e-01 1.31e+01 ... (remaining 98435 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.61: 23807 31.61 - 63.22: 531 63.22 - 94.83: 37 94.83 - 126.43: 0 126.43 - 158.04: 3 Dihedral angle restraints: 24378 sinusoidal: 13408 harmonic: 10970 Sorted by residual: dihedral pdb=" C5' ADP F 600 " pdb=" O5' ADP F 600 " pdb=" PA ADP F 600 " pdb=" O2A ADP F 600 " ideal model delta sinusoidal sigma weight residual -60.00 98.05 -158.04 1 2.00e+01 2.50e-03 4.63e+01 dihedral pdb=" O2A ADP F 600 " pdb=" O3A ADP F 600 " pdb=" PA ADP F 600 " pdb=" PB ADP F 600 " ideal model delta sinusoidal sigma weight residual -60.00 72.42 -132.42 1 2.00e+01 2.50e-03 4.02e+01 dihedral pdb=" O1B ADP F 600 " pdb=" O3A ADP F 600 " pdb=" PB ADP F 600 " pdb=" PA ADP F 600 " ideal model delta sinusoidal sigma weight residual -60.00 66.48 -126.48 1 2.00e+01 2.50e-03 3.83e+01 ... (remaining 24375 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 2615 0.044 - 0.088: 1157 0.088 - 0.132: 422 0.132 - 0.175: 65 0.175 - 0.219: 3 Chirality restraints: 4262 Sorted by residual: chirality pdb=" CA PRO E 196 " pdb=" N PRO E 196 " pdb=" C PRO E 196 " pdb=" CB PRO E 196 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CB ILE B 268 " pdb=" CA ILE B 268 " pdb=" CG1 ILE B 268 " pdb=" CG2 ILE B 268 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.11e-01 chirality pdb=" CA GLU B 328 " pdb=" N GLU B 328 " pdb=" C GLU B 328 " pdb=" CB GLU B 328 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.01e-01 ... (remaining 4259 not shown) Planarity restraints: 8068 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP E 194 " -0.014 2.00e-02 2.50e+03 2.73e-02 7.45e+00 pdb=" C ASP E 194 " 0.047 2.00e-02 2.50e+03 pdb=" O ASP E 194 " -0.017 2.00e-02 2.50e+03 pdb=" N ASN E 195 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU E 328 " 0.038 5.00e-02 4.00e+02 5.71e-02 5.22e+00 pdb=" N PRO E 329 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO E 329 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO E 329 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN M 54 " -0.037 5.00e-02 4.00e+02 5.50e-02 4.85e+00 pdb=" N PRO M 55 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO M 55 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO M 55 " -0.030 5.00e-02 4.00e+02 ... (remaining 8065 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.16: 1838 2.16 - 2.77: 108234 2.77 - 3.38: 149211 3.38 - 3.99: 199918 3.99 - 4.60: 321070 Nonbonded interactions: 780271 Sorted by model distance: nonbonded pdb=" HG1 THR D 149 " pdb=" O GLU D 156 " model vdw 1.545 1.850 nonbonded pdb=" O ALA J 96 " pdb=" H ALA J 100 " model vdw 1.603 1.850 nonbonded pdb=" O ALA I 96 " pdb=" H ALA I 100 " model vdw 1.612 1.850 nonbonded pdb=" HG1 THR D 126 " pdb="MG MG D 502 " model vdw 1.619 1.700 nonbonded pdb=" O ALA L 96 " pdb=" H ALA L 100 " model vdw 1.621 1.850 ... (remaining 780266 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' and ((resid 64 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name HG \ or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23)) \ or resid 65 through 94 or (resid 95 and (name N or name CA or name C or name O \ or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H \ or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name HE2)) or resi \ d 96 through 191 or (resid 204 and (name N or name CA or name C or name O or nam \ e HA2 or name HA3)) or resid 205 through 275 or resid 282 through 414)) selection = (chain 'B' and ((resid 64 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name HG \ or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23)) \ or resid 65 through 191 or (resid 204 and (name N or name CA or name C or name \ O or name HA2 or name HA3)) or resid 205 through 275 or resid 282 through 414)) selection = (chain 'C' and ((resid 64 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name HG \ or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23)) \ or resid 65 through 191 or (resid 204 and (name N or name CA or name C or name \ O or name HA2 or name HA3)) or resid 205 through 275 or resid 282 through 414)) selection = (chain 'D' and ((resid 64 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name HG \ or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23)) \ or resid 65 through 191 or (resid 204 and (name N or name CA or name C or name \ O or name HA2 or name HA3)) or resid 205 through 275 or resid 282 through 414)) selection = (chain 'E' and ((resid 64 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name HG \ or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23)) \ or resid 65 through 191 or (resid 204 and (name N or name CA or name C or name \ O or name HA2 or name HA3)) or resid 205 through 414)) selection = (chain 'F' and (resid 64 through 275 or resid 282 through 414)) } ncs_group { reference = (chain 'H' and resid 2 through 192) selection = (chain 'I' and resid 2 through 192) selection = (chain 'J' and resid 2 through 192) selection = (chain 'K' and resid 2 through 192) selection = (chain 'L' and resid 2 through 192) selection = (chain 'M' and resid 2 through 192) selection = chain 'N' } 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: 3.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.640 Extract box with map and model: 13.660 Check model and map are aligned: 0.580 Set scattering table: 0.380 Process input model: 130.220 Find NCS groups from input model: 2.450 Set up NCS constraints: 0.170 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 153.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 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 : 0.011 0.108 27218 Z= 0.711 Angle : 0.864 11.354 36798 Z= 0.464 Chirality : 0.054 0.219 4262 Planarity : 0.005 0.057 4766 Dihedral : 13.564 158.043 10361 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 0.07 % Allowed : 1.18 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.13), residues: 3418 helix: 0.36 (0.12), residues: 1655 sheet: -0.69 (0.20), residues: 541 loop : -1.85 (0.15), residues: 1222 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS E 230 PHE 0.031 0.003 PHE K 17 TYR 0.021 0.002 TYR B 153 ARG 0.007 0.001 ARG K 15 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6836 Ramachandran restraints generated. 3418 Oldfield, 0 Emsley, 3418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6836 Ramachandran restraints generated. 3418 Oldfield, 0 Emsley, 3418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 2882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 486 time to evaluate : 3.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 488 average time/residue: 0.8809 time to fit residues: 652.4188 Evaluate side-chains 331 residues out of total 2882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 330 time to evaluate : 3.196 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.5049 time to fit residues: 4.9737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 287 optimal weight: 0.9980 chunk 257 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 88 optimal weight: 0.5980 chunk 173 optimal weight: 0.9990 chunk 137 optimal weight: 1.9990 chunk 266 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 162 optimal weight: 0.5980 chunk 198 optimal weight: 0.5980 chunk 308 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 195 ASN C 342 ASN D 230 HIS E 163 GLN E 167 GLN E 289 GLN E 406 GLN F 106 ASN F 160 ASN H 46 GLN ** J 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 116 ASN ** K 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 46 GLN ** M 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 41 ASN A 209 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 27218 Z= 0.197 Angle : 0.533 5.980 36798 Z= 0.273 Chirality : 0.041 0.168 4262 Planarity : 0.004 0.048 4766 Dihedral : 7.908 152.503 3811 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.31 % Allowed : 5.83 % Favored : 93.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.14), residues: 3418 helix: 0.96 (0.12), residues: 1679 sheet: -0.32 (0.20), residues: 565 loop : -1.53 (0.16), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 95 PHE 0.009 0.001 PHE L 17 TYR 0.011 0.001 TYR F 96 ARG 0.010 0.000 ARG N 15 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6836 Ramachandran restraints generated. 3418 Oldfield, 0 Emsley, 3418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6836 Ramachandran restraints generated. 3418 Oldfield, 0 Emsley, 3418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 337 time to evaluate : 3.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 7 residues processed: 339 average time/residue: 0.7702 time to fit residues: 412.7153 Evaluate side-chains 315 residues out of total 2882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 308 time to evaluate : 3.138 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.5706 time to fit residues: 11.1087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 171 optimal weight: 0.4980 chunk 95 optimal weight: 0.6980 chunk 256 optimal weight: 1.9990 chunk 210 optimal weight: 0.6980 chunk 85 optimal weight: 0.8980 chunk 309 optimal weight: 7.9990 chunk 334 optimal weight: 3.9990 chunk 275 optimal weight: 2.9990 chunk 306 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 248 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 41 ASN ** J 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 116 ASN ** K 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 94 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 27218 Z= 0.179 Angle : 0.468 6.280 36798 Z= 0.235 Chirality : 0.040 0.148 4262 Planarity : 0.003 0.046 4766 Dihedral : 7.622 139.009 3811 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.21 % Allowed : 6.21 % Favored : 93.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.14), residues: 3418 helix: 1.28 (0.13), residues: 1678 sheet: -0.12 (0.20), residues: 556 loop : -1.29 (0.17), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS I 38 PHE 0.008 0.001 PHE M 30 TYR 0.031 0.001 TYR J 77 ARG 0.004 0.000 ARG N 15 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6836 Ramachandran restraints generated. 3418 Oldfield, 0 Emsley, 3418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6836 Ramachandran restraints generated. 3418 Oldfield, 0 Emsley, 3418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 325 time to evaluate : 3.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 328 average time/residue: 0.7587 time to fit residues: 394.2482 Evaluate side-chains 313 residues out of total 2882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 309 time to evaluate : 3.103 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.5027 time to fit residues: 7.6696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 305 optimal weight: 2.9990 chunk 232 optimal weight: 2.9990 chunk 160 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 147 optimal weight: 7.9990 chunk 207 optimal weight: 10.0000 chunk 310 optimal weight: 1.9990 chunk 328 optimal weight: 2.9990 chunk 162 optimal weight: 0.2980 chunk 294 optimal weight: 0.2980 chunk 88 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 225 GLN C 260 HIS C 324 GLN H 41 ASN H 46 GLN I 94 GLN ** I 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 41 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 27218 Z= 0.238 Angle : 0.472 6.356 36798 Z= 0.238 Chirality : 0.040 0.148 4262 Planarity : 0.003 0.060 4766 Dihedral : 7.381 139.162 3811 Min Nonbonded Distance : 1.765 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.17 % Allowed : 6.49 % Favored : 93.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.14), residues: 3418 helix: 1.44 (0.13), residues: 1691 sheet: 0.11 (0.21), residues: 556 loop : -1.22 (0.17), residues: 1171 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 260 PHE 0.013 0.001 PHE L 17 TYR 0.012 0.001 TYR A 96 ARG 0.004 0.000 ARG L 15 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6836 Ramachandran restraints generated. 3418 Oldfield, 0 Emsley, 3418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6836 Ramachandran restraints generated. 3418 Oldfield, 0 Emsley, 3418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 316 time to evaluate : 3.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 316 average time/residue: 0.7827 time to fit residues: 393.5001 Evaluate side-chains 309 residues out of total 2882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 306 time to evaluate : 3.110 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.6239 time to fit residues: 7.2138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 273 optimal weight: 3.9990 chunk 186 optimal weight: 50.0000 chunk 4 optimal weight: 4.9990 chunk 244 optimal weight: 50.0000 chunk 135 optimal weight: 2.9990 chunk 280 optimal weight: 20.0000 chunk 227 optimal weight: 6.9990 chunk 0 optimal weight: 1.9990 chunk 167 optimal weight: 3.9990 chunk 294 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 260 HIS D 342 ASN H 46 GLN I 116 ASN ** J 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 27218 Z= 0.468 Angle : 0.563 8.237 36798 Z= 0.286 Chirality : 0.043 0.192 4262 Planarity : 0.004 0.042 4766 Dihedral : 7.425 139.981 3811 Min Nonbonded Distance : 1.695 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.31 % Allowed : 6.80 % Favored : 92.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.14), residues: 3418 helix: 1.22 (0.13), residues: 1700 sheet: -0.38 (0.21), residues: 597 loop : -1.25 (0.17), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 230 PHE 0.012 0.001 PHE K 112 TYR 0.018 0.001 TYR F 96 ARG 0.006 0.000 ARG B 370 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6836 Ramachandran restraints generated. 3418 Oldfield, 0 Emsley, 3418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6836 Ramachandran restraints generated. 3418 Oldfield, 0 Emsley, 3418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 307 time to evaluate : 3.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 7 residues processed: 308 average time/residue: 0.7643 time to fit residues: 373.3210 Evaluate side-chains 303 residues out of total 2882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 296 time to evaluate : 3.213 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.5351 time to fit residues: 10.7077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 110 optimal weight: 0.8980 chunk 295 optimal weight: 8.9990 chunk 64 optimal weight: 2.9990 chunk 192 optimal weight: 0.9990 chunk 81 optimal weight: 0.6980 chunk 328 optimal weight: 0.6980 chunk 273 optimal weight: 0.9980 chunk 152 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 108 optimal weight: 0.4980 chunk 172 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 41 ASN H 46 GLN ** J 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 94 GLN ** K 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 27218 Z= 0.163 Angle : 0.456 6.276 36798 Z= 0.229 Chirality : 0.040 0.146 4262 Planarity : 0.003 0.043 4766 Dihedral : 6.843 143.304 3811 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.21 % Allowed : 7.63 % Favored : 92.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.15), residues: 3418 helix: 1.48 (0.13), residues: 1696 sheet: -0.29 (0.20), residues: 596 loop : -1.08 (0.17), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS D 95 PHE 0.012 0.001 PHE N 17 TYR 0.013 0.001 TYR A 96 ARG 0.007 0.000 ARG N 22 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6836 Ramachandran restraints generated. 3418 Oldfield, 0 Emsley, 3418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6836 Ramachandran restraints generated. 3418 Oldfield, 0 Emsley, 3418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 312 time to evaluate : 3.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 313 average time/residue: 0.7978 time to fit residues: 397.2216 Evaluate side-chains 304 residues out of total 2882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 300 time to evaluate : 3.099 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.6289 time to fit residues: 8.3056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 317 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 187 optimal weight: 40.0000 chunk 240 optimal weight: 2.9990 chunk 186 optimal weight: 10.0000 chunk 276 optimal weight: 50.0000 chunk 183 optimal weight: 0.8980 chunk 327 optimal weight: 1.9990 chunk 205 optimal weight: 10.0000 chunk 199 optimal weight: 2.9990 chunk 151 optimal weight: 4.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 163 GLN C 167 GLN D 406 GLN E 167 GLN H 46 GLN ** J 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 27218 Z= 0.354 Angle : 0.512 6.807 36798 Z= 0.259 Chirality : 0.041 0.162 4262 Planarity : 0.003 0.041 4766 Dihedral : 6.659 148.806 3811 Min Nonbonded Distance : 1.704 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 0.21 % Allowed : 8.15 % Favored : 91.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.15), residues: 3418 helix: 1.42 (0.13), residues: 1699 sheet: -0.34 (0.20), residues: 600 loop : -1.11 (0.18), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 95 PHE 0.009 0.001 PHE J 17 TYR 0.016 0.001 TYR F 96 ARG 0.005 0.000 ARG N 22 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6836 Ramachandran restraints generated. 3418 Oldfield, 0 Emsley, 3418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6836 Ramachandran restraints generated. 3418 Oldfield, 0 Emsley, 3418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 297 time to evaluate : 3.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 302 average time/residue: 0.7570 time to fit residues: 361.4110 Evaluate side-chains 293 residues out of total 2882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 291 time to evaluate : 3.107 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.4587 time to fit residues: 5.7019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 202 optimal weight: 0.7980 chunk 130 optimal weight: 0.8980 chunk 195 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 208 optimal weight: 0.9980 chunk 223 optimal weight: 30.0000 chunk 162 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 257 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 163 GLN C 167 GLN D 406 GLN E 167 GLN E 225 GLN H 46 GLN ** J 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 94 GLN ** K 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 116 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 27218 Z= 0.190 Angle : 0.460 6.376 36798 Z= 0.231 Chirality : 0.040 0.143 4262 Planarity : 0.003 0.041 4766 Dihedral : 6.409 146.223 3811 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.15), residues: 3418 helix: 1.60 (0.13), residues: 1697 sheet: -0.26 (0.21), residues: 590 loop : -0.96 (0.18), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS E 230 PHE 0.008 0.001 PHE M 101 TYR 0.013 0.001 TYR A 96 ARG 0.004 0.000 ARG J 12 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6836 Ramachandran restraints generated. 3418 Oldfield, 0 Emsley, 3418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6836 Ramachandran restraints generated. 3418 Oldfield, 0 Emsley, 3418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 299 time to evaluate : 3.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 299 average time/residue: 0.7694 time to fit residues: 365.7491 Evaluate side-chains 295 residues out of total 2882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 295 time to evaluate : 3.107 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.9949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 298 optimal weight: 40.0000 chunk 313 optimal weight: 3.9990 chunk 286 optimal weight: 1.9990 chunk 305 optimal weight: 1.9990 chunk 183 optimal weight: 3.9990 chunk 133 optimal weight: 3.9990 chunk 239 optimal weight: 3.9990 chunk 93 optimal weight: 0.7980 chunk 275 optimal weight: 2.9990 chunk 288 optimal weight: 1.9990 chunk 304 optimal weight: 4.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 163 GLN C 167 GLN H 46 GLN ** J 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 27218 Z= 0.330 Angle : 0.501 8.250 36798 Z= 0.252 Chirality : 0.041 0.144 4262 Planarity : 0.003 0.039 4766 Dihedral : 6.385 144.568 3811 Min Nonbonded Distance : 1.723 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 0.10 % Allowed : 8.33 % Favored : 91.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.15), residues: 3418 helix: 1.54 (0.13), residues: 1697 sheet: -0.07 (0.21), residues: 565 loop : -1.03 (0.18), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 95 PHE 0.007 0.001 PHE J 17 TYR 0.015 0.001 TYR F 96 ARG 0.004 0.000 ARG C 307 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6836 Ramachandran restraints generated. 3418 Oldfield, 0 Emsley, 3418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6836 Ramachandran restraints generated. 3418 Oldfield, 0 Emsley, 3418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 296 time to evaluate : 3.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 297 average time/residue: 0.7763 time to fit residues: 365.1449 Evaluate side-chains 291 residues out of total 2882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 289 time to evaluate : 3.101 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.5497 time to fit residues: 5.9274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 200 optimal weight: 3.9990 chunk 322 optimal weight: 3.9990 chunk 197 optimal weight: 0.5980 chunk 153 optimal weight: 3.9990 chunk 224 optimal weight: 20.0000 chunk 338 optimal weight: 0.6980 chunk 311 optimal weight: 1.9990 chunk 269 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 208 optimal weight: 0.9990 chunk 165 optimal weight: 2.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 406 GLN E 342 ASN H 46 GLN ** J 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 27218 Z= 0.245 Angle : 0.470 5.548 36798 Z= 0.237 Chirality : 0.040 0.173 4262 Planarity : 0.003 0.039 4766 Dihedral : 6.332 139.335 3811 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.07 % Allowed : 8.40 % Favored : 91.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.15), residues: 3418 helix: 1.62 (0.13), residues: 1695 sheet: -0.07 (0.21), residues: 565 loop : -0.96 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS D 68 PHE 0.020 0.001 PHE L 17 TYR 0.013 0.001 TYR A 96 ARG 0.004 0.000 ARG J 12 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6836 Ramachandran restraints generated. 3418 Oldfield, 0 Emsley, 3418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6836 Ramachandran restraints generated. 3418 Oldfield, 0 Emsley, 3418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 298 time to evaluate : 3.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 299 average time/residue: 0.7959 time to fit residues: 373.5166 Evaluate side-chains 293 residues out of total 2882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 292 time to evaluate : 3.118 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 1.2534 time to fit residues: 5.7400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 214 optimal weight: 0.9980 chunk 287 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 248 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 270 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 277 optimal weight: 9.9990 chunk 34 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 406 GLN H 46 GLN ** J 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.158810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.110798 restraints weight = 153356.221| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 4.10 r_work: 0.2980 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 27218 Z= 0.208 Angle : 0.465 7.899 36798 Z= 0.233 Chirality : 0.040 0.150 4262 Planarity : 0.003 0.039 4766 Dihedral : 6.261 134.362 3811 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.10 % Allowed : 8.43 % Favored : 91.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.15), residues: 3418 helix: 1.70 (0.13), residues: 1695 sheet: -0.03 (0.21), residues: 565 loop : -0.91 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS D 68 PHE 0.010 0.001 PHE J 17 TYR 0.013 0.001 TYR F 96 ARG 0.004 0.000 ARG J 12 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9434.55 seconds wall clock time: 164 minutes 17.55 seconds (9857.55 seconds total)