Starting phenix.real_space_refine (version: dev) on Tue Feb 21 21:47:13 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wrf_21882/02_2023/6wrf_21882_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wrf_21882/02_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_21882/02_2023/6wrf_21882.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wrf_21882/02_2023/6wrf_21882.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wrf_21882/02_2023/6wrf_21882_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wrf_21882/02_2023/6wrf_21882_neut_trim_updated.pdb" } resolution = 3.14 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 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: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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: 18.89, per 1000 atoms: 0.35 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: 34.69 Conformation dependent library (CDL) restraints added in 3.9 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: 2.18 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: 16.95 Time building geometry restraints manager: 36.46 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: 20900 31.61 - 63.22: 413 63.22 - 94.83: 37 94.83 - 126.43: 0 126.43 - 158.04: 3 Dihedral angle restraints: 21353 sinusoidal: 10383 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 21350 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 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. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.130 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: 1.260 Extract box with map and model: 15.330 Check model and map are aligned: 0.640 Process input model: 128.480 Find NCS groups from input model: 2.430 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Set scattering table: 0.380 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:2.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 154.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 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 : 13.248 158.043 10306 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 % 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 *********************** 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 : 3.357 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: 0.8513 time to fit residues: 625.1934 Evaluate side-chains 331 residues out of total 2882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 330 time to evaluate : 3.353 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4828 time to fit residues: 5.1800 ------------------------------------------------------------------------------- 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: 1.9990 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: 0.8980 chunk 266 optimal weight: 0.9990 chunk 103 optimal weight: 0.5980 chunk 162 optimal weight: 0.5980 chunk 198 optimal weight: 0.5980 chunk 308 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 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: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 27218 Z= 0.190 Angle : 0.535 6.042 36798 Z= 0.274 Chirality : 0.041 0.168 4262 Planarity : 0.004 0.050 4766 Dihedral : 6.340 152.482 3756 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer Outliers : 0.24 % 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: 0.95 (0.12), residues: 1679 sheet: -0.33 (0.20), residues: 565 loop : -1.55 (0.16), residues: 1174 *********************** 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 341 residues out of total 2882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 334 time to evaluate : 3.342 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: 7 outliers final: 5 residues processed: 335 average time/residue: 0.7996 time to fit residues: 425.4561 Evaluate side-chains 313 residues out of total 2882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 308 time to evaluate : 3.390 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.5883 time to fit residues: 9.4315 ------------------------------------------------------------------------------- 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: 0.9990 chunk 95 optimal weight: 3.9990 chunk 256 optimal weight: 1.9990 chunk 210 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 chunk 309 optimal weight: 0.6980 chunk 334 optimal weight: 3.9990 chunk 275 optimal weight: 2.9990 chunk 306 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 chunk 248 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 289 GLN 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 27218 Z= 0.193 Angle : 0.471 6.968 36798 Z= 0.236 Chirality : 0.040 0.150 4262 Planarity : 0.003 0.048 4766 Dihedral : 6.201 137.552 3756 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer Outliers : 0.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.14), residues: 3418 helix: 1.28 (0.13), residues: 1679 sheet: -0.09 (0.20), residues: 566 loop : -1.31 (0.17), residues: 1173 *********************** 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 334 residues out of total 2882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 324 time to evaluate : 3.365 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: 10 outliers final: 8 residues processed: 327 average time/residue: 0.7709 time to fit residues: 398.4214 Evaluate side-chains 313 residues out of total 2882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 305 time to evaluate : 3.337 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.5968 time to fit residues: 12.6098 ------------------------------------------------------------------------------- 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: 1.9990 chunk 232 optimal weight: 2.9990 chunk 160 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 147 optimal weight: 6.9990 chunk 207 optimal weight: 50.0000 chunk 310 optimal weight: 1.9990 chunk 328 optimal weight: 2.9990 chunk 162 optimal weight: 0.8980 chunk 294 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 27218 Z= 0.271 Angle : 0.484 6.401 36798 Z= 0.243 Chirality : 0.041 0.149 4262 Planarity : 0.003 0.055 4766 Dihedral : 6.085 138.656 3756 Min Nonbonded Distance : 1.754 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.14), residues: 3418 helix: 1.40 (0.13), residues: 1690 sheet: 0.12 (0.21), residues: 556 loop : -1.24 (0.17), residues: 1172 *********************** 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 316 residues out of total 2882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 313 time to evaluate : 3.425 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 outliers start: 3 outliers final: 1 residues processed: 315 average time/residue: 0.7679 time to fit residues: 380.9926 Evaluate side-chains 300 residues out of total 2882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 299 time to evaluate : 3.405 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4739 time to fit residues: 5.1029 ------------------------------------------------------------------------------- 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: 6.9990 chunk 186 optimal weight: 40.0000 chunk 4 optimal weight: 4.9990 chunk 244 optimal weight: 50.0000 chunk 135 optimal weight: 2.9990 chunk 280 optimal weight: 40.0000 chunk 227 optimal weight: 6.9990 chunk 0 optimal weight: 1.9990 chunk 167 optimal weight: 3.9990 chunk 294 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 324 GLN C 163 GLN C 167 GLN D 342 ASN E 167 GLN 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.058 27218 Z= 0.533 Angle : 0.585 8.543 36798 Z= 0.298 Chirality : 0.045 0.184 4262 Planarity : 0.003 0.043 4766 Dihedral : 6.282 138.648 3756 Min Nonbonded Distance : 1.679 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer Outliers : 0.49 % 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: 0.09 (0.14), residues: 3418 helix: 1.15 (0.13), residues: 1697 sheet: -0.42 (0.21), residues: 600 loop : -1.28 (0.17), residues: 1121 *********************** 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 315 residues out of total 2882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 301 time to evaluate : 3.425 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: 14 outliers final: 11 residues processed: 303 average time/residue: 0.7550 time to fit residues: 360.3196 Evaluate side-chains 302 residues out of total 2882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 291 time to evaluate : 3.341 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 11 outliers final: 1 residues processed: 11 average time/residue: 0.5384 time to fit residues: 14.7781 ------------------------------------------------------------------------------- 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: 0.5980 chunk 295 optimal weight: 10.0000 chunk 64 optimal weight: 1.9990 chunk 192 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 328 optimal weight: 0.9990 chunk 273 optimal weight: 4.9990 chunk 152 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 108 optimal weight: 0.5980 chunk 172 optimal weight: 4.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- 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 E 167 GLN E 225 GLN 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 27218 Z= 0.228 Angle : 0.476 6.829 36798 Z= 0.239 Chirality : 0.040 0.146 4262 Planarity : 0.003 0.043 4766 Dihedral : 6.161 141.943 3756 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer Outliers : 0.28 % 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: 0.36 (0.15), residues: 3418 helix: 1.35 (0.13), residues: 1700 sheet: -0.34 (0.21), residues: 597 loop : -1.10 (0.18), residues: 1121 *********************** 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 311 residues out of total 2882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 303 time to evaluate : 3.396 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: 8 outliers final: 4 residues processed: 308 average time/residue: 0.7710 time to fit residues: 373.9739 Evaluate side-chains 296 residues out of total 2882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 292 time to evaluate : 3.375 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.7015 time to fit residues: 8.7795 ------------------------------------------------------------------------------- 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: 0.9980 chunk 37 optimal weight: 1.9990 chunk 187 optimal weight: 40.0000 chunk 240 optimal weight: 0.8980 chunk 186 optimal weight: 30.0000 chunk 276 optimal weight: 20.0000 chunk 183 optimal weight: 1.9990 chunk 327 optimal weight: 0.7980 chunk 205 optimal weight: 30.0000 chunk 199 optimal weight: 0.7980 chunk 151 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 27218 Z= 0.179 Angle : 0.460 6.993 36798 Z= 0.229 Chirality : 0.040 0.144 4262 Planarity : 0.003 0.042 4766 Dihedral : 5.994 146.586 3756 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer Outliers : 0.07 % 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: 0.59 (0.15), residues: 3418 helix: 1.54 (0.13), residues: 1697 sheet: -0.25 (0.21), residues: 586 loop : -0.95 (0.18), residues: 1135 *********************** 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 307 residues out of total 2882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 305 time to evaluate : 3.369 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: 2 residues processed: 305 average time/residue: 0.8078 time to fit residues: 391.6746 Evaluate side-chains 297 residues out of total 2882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 295 time to evaluate : 3.380 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.6331 time to fit residues: 6.4238 ------------------------------------------------------------------------------- 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: 0.5980 chunk 130 optimal weight: 0.5980 chunk 195 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 208 optimal weight: 0.6980 chunk 223 optimal weight: 50.0000 chunk 162 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 257 optimal weight: 6.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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** L 116 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 27218 Z= 0.212 Angle : 0.464 5.806 36798 Z= 0.232 Chirality : 0.040 0.144 4262 Planarity : 0.003 0.040 4766 Dihedral : 5.911 146.317 3756 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer Outliers : 0.10 % 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: 0.67 (0.15), residues: 3418 helix: 1.62 (0.13), residues: 1696 sheet: -0.22 (0.21), residues: 590 loop : -0.94 (0.18), residues: 1132 *********************** 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 300 residues out of total 2882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 297 time to evaluate : 3.472 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: 3 outliers final: 1 residues processed: 298 average time/residue: 0.7929 time to fit residues: 374.5884 Evaluate side-chains 292 residues out of total 2882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 291 time to evaluate : 3.337 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.6196 time to fit residues: 5.2956 ------------------------------------------------------------------------------- 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: 30.0000 chunk 313 optimal weight: 3.9990 chunk 286 optimal weight: 0.7980 chunk 305 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 chunk 133 optimal weight: 3.9990 chunk 239 optimal weight: 3.9990 chunk 93 optimal weight: 0.9980 chunk 275 optimal weight: 0.6980 chunk 288 optimal weight: 0.5980 chunk 304 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 27218 Z= 0.159 Angle : 0.450 8.265 36798 Z= 0.224 Chirality : 0.040 0.140 4262 Planarity : 0.003 0.040 4766 Dihedral : 5.817 142.653 3756 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer Outliers : 0.00 % 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: 0.81 (0.15), residues: 3418 helix: 1.73 (0.13), residues: 1694 sheet: -0.16 (0.21), residues: 590 loop : -0.87 (0.18), residues: 1134 *********************** 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 308 residues out of total 2882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 308 time to evaluate : 4.207 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: 0 outliers final: 0 residues processed: 308 average time/residue: 0.7782 time to fit residues: 380.4996 Evaluate side-chains 298 residues out of total 2882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 298 time to evaluate : 3.411 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.3224 ------------------------------------------------------------------------------- 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: 2.9990 chunk 322 optimal weight: 2.9990 chunk 197 optimal weight: 0.6980 chunk 153 optimal weight: 3.9990 chunk 224 optimal weight: 8.9990 chunk 338 optimal weight: 0.8980 chunk 311 optimal weight: 1.9990 chunk 269 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 208 optimal weight: 1.9990 chunk 165 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.3130 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= 0.278 Angle : 0.480 5.516 36798 Z= 0.240 Chirality : 0.041 0.140 4262 Planarity : 0.003 0.038 4766 Dihedral : 5.777 141.122 3756 Min Nonbonded Distance : 1.734 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer Outliers : 0.07 % 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: 0.78 (0.15), residues: 3418 helix: 1.68 (0.13), residues: 1698 sheet: 0.06 (0.21), residues: 565 loop : -0.96 (0.18), residues: 1155 ********************** 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 299 residues out of total 2882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 297 time to evaluate : 3.399 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 outliers start: 2 outliers final: 2 residues processed: 297 average time/residue: 0.7783 time to fit residues: 362.7001 Evaluate side-chains 297 residues out of total 2882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 295 time to evaluate : 3.382 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.5534 time to fit residues: 6.2502 ------------------------------------------------------------------------------- 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: 0.9990 chunk 287 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 248 optimal weight: 0.5980 chunk 39 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 270 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 277 optimal weight: 10.0000 chunk 34 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.157688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.110983 restraints weight = 151084.553| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 4.04 r_work: 0.3003 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 27218 Z= 0.170 Angle : 0.451 5.528 36798 Z= 0.225 Chirality : 0.040 0.172 4262 Planarity : 0.003 0.038 4766 Dihedral : 5.722 133.641 3756 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer Outliers : 0.00 % 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: 0.93 (0.15), residues: 3418 helix: 1.79 (0.13), residues: 1695 sheet: 0.11 (0.21), residues: 565 loop : -0.87 (0.18), residues: 1158 =============================================================================== Job complete usr+sys time: 9311.71 seconds wall clock time: 162 minutes 10.84 seconds (9730.84 seconds total)