Starting phenix.real_space_refine (version: dev) on Tue May 17 19:47:08 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ppe_20434/05_2022/6ppe_20434.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ppe_20434/05_2022/6ppe_20434.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ppe_20434/05_2022/6ppe_20434.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ppe_20434/05_2022/6ppe_20434.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ppe_20434/05_2022/6ppe_20434.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ppe_20434/05_2022/6ppe_20434.pdb" } resolution = 3.19 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 12": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 12": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 12": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 12": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 12": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 12": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ARG 12": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I ARG 12": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 30": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ARG 12": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 TYR 60": "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 ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M PHE 173": "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 PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 43736 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3017 Classifications: {'peptide': 192} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "B" Number of atoms: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3017 Classifications: {'peptide': 192} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "C" Number of atoms: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3017 Classifications: {'peptide': 192} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "D" Number of atoms: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3017 Classifications: {'peptide': 192} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "E" Number of atoms: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3017 Classifications: {'peptide': 192} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "F" Number of atoms: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3017 Classifications: {'peptide': 192} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "G" Number of atoms: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3017 Classifications: {'peptide': 192} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "H" Number of atoms: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3017 Classifications: {'peptide': 192} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "I" Number of atoms: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3017 Classifications: {'peptide': 192} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "J" Number of atoms: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3017 Classifications: {'peptide': 192} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "K" Number of atoms: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3017 Classifications: {'peptide': 192} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "L" Number of atoms: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3017 Classifications: {'peptide': 192} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "M" Number of atoms: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3017 Classifications: {'peptide': 192} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "N" Number of atoms: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 3017 Classifications: {'peptide': 192} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "O" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 106 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "P" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 106 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "Q" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 106 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "R" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 106 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "S" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 106 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "T" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 106 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "U" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 106 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "V" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 106 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "X" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 106 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "Y" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 106 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "Z" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 106 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "1" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 106 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "2" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 106 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "3" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 106 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 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: 19.76, per 1000 atoms: 0.45 Number of scatterers: 43736 At special positions: 0 Unit cell: (112.52, 114.84, 128.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 168 16.00 O 4130 8.00 N 3780 7.00 C 13762 6.00 H 21896 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: 37.47 Conformation dependent library (CDL) restraints added in 3.8 seconds 5516 Ramachandran restraints generated. 2758 Oldfield, 0 Emsley, 2758 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5124 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 49 sheets defined 47.3% alpha, 29.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.79 Creating SS restraints... Processing helix chain 'A' and resid 19 through 26 removed outlier: 3.608A pdb=" N GLU A 26 " --> pdb=" O ARG A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 54 Processing helix chain 'A' and resid 69 through 83 removed outlier: 3.758A pdb=" N ILE A 76 " --> pdb=" O ALA A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 105 Processing helix chain 'A' and resid 132 through 158 Processing helix chain 'A' and resid 160 through 168 Processing helix chain 'A' and resid 176 through 182 Processing helix chain 'B' and resid 19 through 26 removed outlier: 3.608A pdb=" N GLU B 26 " --> pdb=" O ARG B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 54 Processing helix chain 'B' and resid 69 through 83 removed outlier: 3.758A pdb=" N ILE B 76 " --> pdb=" O ALA B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 105 Processing helix chain 'B' and resid 132 through 158 Processing helix chain 'B' and resid 160 through 168 Processing helix chain 'B' and resid 176 through 182 Processing helix chain 'C' and resid 19 through 26 removed outlier: 3.608A pdb=" N GLU C 26 " --> pdb=" O ARG C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 54 Processing helix chain 'C' and resid 69 through 83 removed outlier: 3.758A pdb=" N ILE C 76 " --> pdb=" O ALA C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 105 Processing helix chain 'C' and resid 132 through 158 Processing helix chain 'C' and resid 160 through 168 Processing helix chain 'C' and resid 176 through 182 Processing helix chain 'D' and resid 19 through 26 removed outlier: 3.609A pdb=" N GLU D 26 " --> pdb=" O ARG D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 54 Processing helix chain 'D' and resid 69 through 83 removed outlier: 3.758A pdb=" N ILE D 76 " --> pdb=" O ALA D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 105 Processing helix chain 'D' and resid 132 through 158 Processing helix chain 'D' and resid 160 through 168 Processing helix chain 'D' and resid 176 through 182 Processing helix chain 'E' and resid 19 through 26 removed outlier: 3.608A pdb=" N GLU E 26 " --> pdb=" O ARG E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 54 Processing helix chain 'E' and resid 69 through 83 removed outlier: 3.758A pdb=" N ILE E 76 " --> pdb=" O ALA E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 105 Processing helix chain 'E' and resid 132 through 158 Processing helix chain 'E' and resid 160 through 168 Processing helix chain 'E' and resid 176 through 182 Processing helix chain 'F' and resid 19 through 26 removed outlier: 3.608A pdb=" N GLU F 26 " --> pdb=" O ARG F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 36 through 54 Processing helix chain 'F' and resid 69 through 83 removed outlier: 3.758A pdb=" N ILE F 76 " --> pdb=" O ALA F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 105 Processing helix chain 'F' and resid 132 through 158 Processing helix chain 'F' and resid 160 through 168 Processing helix chain 'F' and resid 176 through 182 Processing helix chain 'G' and resid 19 through 26 removed outlier: 3.608A pdb=" N GLU G 26 " --> pdb=" O ARG G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 54 Processing helix chain 'G' and resid 69 through 83 removed outlier: 3.758A pdb=" N ILE G 76 " --> pdb=" O ALA G 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 105 Processing helix chain 'G' and resid 132 through 158 Processing helix chain 'G' and resid 160 through 168 Processing helix chain 'G' and resid 176 through 182 Processing helix chain 'H' and resid 19 through 26 removed outlier: 3.608A pdb=" N GLU H 26 " --> pdb=" O ARG H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 36 through 54 Processing helix chain 'H' and resid 69 through 83 removed outlier: 3.758A pdb=" N ILE H 76 " --> pdb=" O ALA H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 105 Processing helix chain 'H' and resid 132 through 158 Processing helix chain 'H' and resid 160 through 168 Processing helix chain 'H' and resid 176 through 182 Processing helix chain 'I' and resid 19 through 26 removed outlier: 3.609A pdb=" N GLU I 26 " --> pdb=" O ARG I 22 " (cutoff:3.500A) Processing helix chain 'I' and resid 36 through 54 Processing helix chain 'I' and resid 69 through 83 removed outlier: 3.757A pdb=" N ILE I 76 " --> pdb=" O ALA I 72 " (cutoff:3.500A) Processing helix chain 'I' and resid 96 through 105 Processing helix chain 'I' and resid 132 through 158 Processing helix chain 'I' and resid 160 through 168 Processing helix chain 'I' and resid 176 through 182 Processing helix chain 'J' and resid 19 through 26 removed outlier: 3.608A pdb=" N GLU J 26 " --> pdb=" O ARG J 22 " (cutoff:3.500A) Processing helix chain 'J' and resid 36 through 54 Processing helix chain 'J' and resid 69 through 83 removed outlier: 3.758A pdb=" N ILE J 76 " --> pdb=" O ALA J 72 " (cutoff:3.500A) Processing helix chain 'J' and resid 96 through 105 Processing helix chain 'J' and resid 132 through 158 Processing helix chain 'J' and resid 160 through 168 Processing helix chain 'J' and resid 176 through 182 Processing helix chain 'K' and resid 19 through 26 removed outlier: 3.608A pdb=" N GLU K 26 " --> pdb=" O ARG K 22 " (cutoff:3.500A) Processing helix chain 'K' and resid 36 through 54 Processing helix chain 'K' and resid 69 through 83 removed outlier: 3.759A pdb=" N ILE K 76 " --> pdb=" O ALA K 72 " (cutoff:3.500A) Processing helix chain 'K' and resid 96 through 105 Processing helix chain 'K' and resid 132 through 158 Processing helix chain 'K' and resid 160 through 168 Processing helix chain 'K' and resid 176 through 182 Processing helix chain 'L' and resid 19 through 26 removed outlier: 3.608A pdb=" N GLU L 26 " --> pdb=" O ARG L 22 " (cutoff:3.500A) Processing helix chain 'L' and resid 36 through 54 Processing helix chain 'L' and resid 69 through 83 removed outlier: 3.758A pdb=" N ILE L 76 " --> pdb=" O ALA L 72 " (cutoff:3.500A) Processing helix chain 'L' and resid 96 through 105 Processing helix chain 'L' and resid 132 through 158 Processing helix chain 'L' and resid 160 through 168 Processing helix chain 'L' and resid 176 through 182 Processing helix chain 'M' and resid 19 through 26 removed outlier: 3.609A pdb=" N GLU M 26 " --> pdb=" O ARG M 22 " (cutoff:3.500A) Processing helix chain 'M' and resid 36 through 54 Processing helix chain 'M' and resid 69 through 83 removed outlier: 3.758A pdb=" N ILE M 76 " --> pdb=" O ALA M 72 " (cutoff:3.500A) Processing helix chain 'M' and resid 96 through 105 Processing helix chain 'M' and resid 132 through 158 Processing helix chain 'M' and resid 160 through 168 Processing helix chain 'M' and resid 176 through 182 Processing helix chain 'N' and resid 19 through 26 removed outlier: 3.609A pdb=" N GLU N 26 " --> pdb=" O ARG N 22 " (cutoff:3.500A) Processing helix chain 'N' and resid 36 through 54 Processing helix chain 'N' and resid 69 through 83 removed outlier: 3.758A pdb=" N ILE N 76 " --> pdb=" O ALA N 72 " (cutoff:3.500A) Processing helix chain 'N' and resid 96 through 105 Processing helix chain 'N' and resid 132 through 158 Processing helix chain 'N' and resid 160 through 168 Processing helix chain 'N' and resid 176 through 182 Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 9 Processing sheet with id=AA2, first strand: chain 'A' and resid 28 through 32 removed outlier: 6.296A pdb=" N ILE A 59 " --> pdb=" O SER A 88 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N ILE A 90 " --> pdb=" O ILE A 59 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU A 61 " --> pdb=" O ILE A 90 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N MET A 92 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N ILE A 63 " --> pdb=" O MET A 92 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N GLN A 94 " --> pdb=" O ILE A 63 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 28 through 32 removed outlier: 6.296A pdb=" N ILE A 59 " --> pdb=" O SER A 88 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N ILE A 90 " --> pdb=" O ILE A 59 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU A 61 " --> pdb=" O ILE A 90 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N MET A 92 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N ILE A 63 " --> pdb=" O MET A 92 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N GLN A 94 " --> pdb=" O ILE A 63 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N PHE A 112 " --> pdb=" O VAL A 87 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N THR A 89 " --> pdb=" O PHE A 112 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 125 through 131 Processing sheet with id=AA5, first strand: chain 'B' and resid 5 through 9 Processing sheet with id=AA6, first strand: chain 'B' and resid 28 through 32 removed outlier: 6.296A pdb=" N ILE B 59 " --> pdb=" O SER B 88 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N ILE B 90 " --> pdb=" O ILE B 59 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU B 61 " --> pdb=" O ILE B 90 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N MET B 92 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N ILE B 63 " --> pdb=" O MET B 92 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N GLN B 94 " --> pdb=" O ILE B 63 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 28 through 32 removed outlier: 6.296A pdb=" N ILE B 59 " --> pdb=" O SER B 88 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N ILE B 90 " --> pdb=" O ILE B 59 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU B 61 " --> pdb=" O ILE B 90 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N MET B 92 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N ILE B 63 " --> pdb=" O MET B 92 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N GLN B 94 " --> pdb=" O ILE B 63 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N PHE B 112 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N THR B 89 " --> pdb=" O PHE B 112 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 125 through 131 Processing sheet with id=AA9, first strand: chain 'C' and resid 5 through 9 Processing sheet with id=AB1, first strand: chain 'C' and resid 28 through 32 removed outlier: 6.296A pdb=" N ILE C 59 " --> pdb=" O SER C 88 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N ILE C 90 " --> pdb=" O ILE C 59 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU C 61 " --> pdb=" O ILE C 90 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N MET C 92 " --> pdb=" O LEU C 61 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N ILE C 63 " --> pdb=" O MET C 92 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N GLN C 94 " --> pdb=" O ILE C 63 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 28 through 32 removed outlier: 6.296A pdb=" N ILE C 59 " --> pdb=" O SER C 88 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N ILE C 90 " --> pdb=" O ILE C 59 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU C 61 " --> pdb=" O ILE C 90 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N MET C 92 " --> pdb=" O LEU C 61 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N ILE C 63 " --> pdb=" O MET C 92 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N GLN C 94 " --> pdb=" O ILE C 63 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N PHE C 112 " --> pdb=" O VAL C 87 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N THR C 89 " --> pdb=" O PHE C 112 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 125 through 131 Processing sheet with id=AB4, first strand: chain 'D' and resid 5 through 9 Processing sheet with id=AB5, first strand: chain 'D' and resid 28 through 32 removed outlier: 6.296A pdb=" N ILE D 59 " --> pdb=" O SER D 88 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N ILE D 90 " --> pdb=" O ILE D 59 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU D 61 " --> pdb=" O ILE D 90 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N MET D 92 " --> pdb=" O LEU D 61 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N ILE D 63 " --> pdb=" O MET D 92 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N GLN D 94 " --> pdb=" O ILE D 63 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 28 through 32 removed outlier: 6.296A pdb=" N ILE D 59 " --> pdb=" O SER D 88 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N ILE D 90 " --> pdb=" O ILE D 59 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU D 61 " --> pdb=" O ILE D 90 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N MET D 92 " --> pdb=" O LEU D 61 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N ILE D 63 " --> pdb=" O MET D 92 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N GLN D 94 " --> pdb=" O ILE D 63 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N PHE D 112 " --> pdb=" O VAL D 87 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N THR D 89 " --> pdb=" O PHE D 112 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 125 through 131 removed outlier: 3.503A pdb=" N TYR D 128 " --> pdb=" O TYR L 128 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR L 128 " --> pdb=" O TYR D 128 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 5 through 9 Processing sheet with id=AB9, first strand: chain 'E' and resid 28 through 32 removed outlier: 6.296A pdb=" N ILE E 59 " --> pdb=" O SER E 88 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N ILE E 90 " --> pdb=" O ILE E 59 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LEU E 61 " --> pdb=" O ILE E 90 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N MET E 92 " --> pdb=" O LEU E 61 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N ILE E 63 " --> pdb=" O MET E 92 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N GLN E 94 " --> pdb=" O ILE E 63 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 28 through 32 removed outlier: 6.296A pdb=" N ILE E 59 " --> pdb=" O SER E 88 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N ILE E 90 " --> pdb=" O ILE E 59 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LEU E 61 " --> pdb=" O ILE E 90 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N MET E 92 " --> pdb=" O LEU E 61 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N ILE E 63 " --> pdb=" O MET E 92 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N GLN E 94 " --> pdb=" O ILE E 63 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N PHE E 112 " --> pdb=" O VAL E 87 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N THR E 89 " --> pdb=" O PHE E 112 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 125 through 131 Processing sheet with id=AC3, first strand: chain 'F' and resid 5 through 9 Processing sheet with id=AC4, first strand: chain 'F' and resid 28 through 32 removed outlier: 6.296A pdb=" N ILE F 59 " --> pdb=" O SER F 88 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N ILE F 90 " --> pdb=" O ILE F 59 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU F 61 " --> pdb=" O ILE F 90 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N MET F 92 " --> pdb=" O LEU F 61 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N ILE F 63 " --> pdb=" O MET F 92 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N GLN F 94 " --> pdb=" O ILE F 63 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 28 through 32 removed outlier: 6.296A pdb=" N ILE F 59 " --> pdb=" O SER F 88 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N ILE F 90 " --> pdb=" O ILE F 59 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU F 61 " --> pdb=" O ILE F 90 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N MET F 92 " --> pdb=" O LEU F 61 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N ILE F 63 " --> pdb=" O MET F 92 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N GLN F 94 " --> pdb=" O ILE F 63 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N PHE F 112 " --> pdb=" O VAL F 87 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N THR F 89 " --> pdb=" O PHE F 112 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 125 through 131 Processing sheet with id=AC7, first strand: chain 'G' and resid 5 through 9 Processing sheet with id=AC8, first strand: chain 'G' and resid 28 through 32 removed outlier: 6.296A pdb=" N ILE G 59 " --> pdb=" O SER G 88 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N ILE G 90 " --> pdb=" O ILE G 59 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU G 61 " --> pdb=" O ILE G 90 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N MET G 92 " --> pdb=" O LEU G 61 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N ILE G 63 " --> pdb=" O MET G 92 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N GLN G 94 " --> pdb=" O ILE G 63 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 28 through 32 removed outlier: 6.296A pdb=" N ILE G 59 " --> pdb=" O SER G 88 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N ILE G 90 " --> pdb=" O ILE G 59 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU G 61 " --> pdb=" O ILE G 90 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N MET G 92 " --> pdb=" O LEU G 61 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N ILE G 63 " --> pdb=" O MET G 92 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N GLN G 94 " --> pdb=" O ILE G 63 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N PHE G 112 " --> pdb=" O VAL G 87 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N THR G 89 " --> pdb=" O PHE G 112 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 125 through 131 Processing sheet with id=AD2, first strand: chain 'H' and resid 5 through 9 Processing sheet with id=AD3, first strand: chain 'H' and resid 28 through 32 removed outlier: 6.297A pdb=" N ILE H 59 " --> pdb=" O SER H 88 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N ILE H 90 " --> pdb=" O ILE H 59 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU H 61 " --> pdb=" O ILE H 90 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N MET H 92 " --> pdb=" O LEU H 61 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N ILE H 63 " --> pdb=" O MET H 92 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N GLN H 94 " --> pdb=" O ILE H 63 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 28 through 32 removed outlier: 6.297A pdb=" N ILE H 59 " --> pdb=" O SER H 88 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N ILE H 90 " --> pdb=" O ILE H 59 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU H 61 " --> pdb=" O ILE H 90 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N MET H 92 " --> pdb=" O LEU H 61 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N ILE H 63 " --> pdb=" O MET H 92 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N GLN H 94 " --> pdb=" O ILE H 63 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N PHE H 112 " --> pdb=" O VAL H 87 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N THR H 89 " --> pdb=" O PHE H 112 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 5 through 9 Processing sheet with id=AD6, first strand: chain 'I' and resid 28 through 32 removed outlier: 6.296A pdb=" N ILE I 59 " --> pdb=" O SER I 88 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N ILE I 90 " --> pdb=" O ILE I 59 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LEU I 61 " --> pdb=" O ILE I 90 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N MET I 92 " --> pdb=" O LEU I 61 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N ILE I 63 " --> pdb=" O MET I 92 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N GLN I 94 " --> pdb=" O ILE I 63 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 28 through 32 removed outlier: 6.296A pdb=" N ILE I 59 " --> pdb=" O SER I 88 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N ILE I 90 " --> pdb=" O ILE I 59 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LEU I 61 " --> pdb=" O ILE I 90 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N MET I 92 " --> pdb=" O LEU I 61 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N ILE I 63 " --> pdb=" O MET I 92 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N GLN I 94 " --> pdb=" O ILE I 63 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N PHE I 112 " --> pdb=" O VAL I 87 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N THR I 89 " --> pdb=" O PHE I 112 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 5 through 9 Processing sheet with id=AD9, first strand: chain 'J' and resid 28 through 32 removed outlier: 6.297A pdb=" N ILE J 59 " --> pdb=" O SER J 88 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N ILE J 90 " --> pdb=" O ILE J 59 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU J 61 " --> pdb=" O ILE J 90 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N MET J 92 " --> pdb=" O LEU J 61 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N ILE J 63 " --> pdb=" O MET J 92 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N GLN J 94 " --> pdb=" O ILE J 63 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 28 through 32 removed outlier: 6.297A pdb=" N ILE J 59 " --> pdb=" O SER J 88 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N ILE J 90 " --> pdb=" O ILE J 59 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU J 61 " --> pdb=" O ILE J 90 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N MET J 92 " --> pdb=" O LEU J 61 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N ILE J 63 " --> pdb=" O MET J 92 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N GLN J 94 " --> pdb=" O ILE J 63 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N PHE J 112 " --> pdb=" O VAL J 87 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N THR J 89 " --> pdb=" O PHE J 112 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'K' and resid 5 through 9 Processing sheet with id=AE3, first strand: chain 'K' and resid 28 through 32 removed outlier: 6.297A pdb=" N ILE K 59 " --> pdb=" O SER K 88 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N ILE K 90 " --> pdb=" O ILE K 59 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU K 61 " --> pdb=" O ILE K 90 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N MET K 92 " --> pdb=" O LEU K 61 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N ILE K 63 " --> pdb=" O MET K 92 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N GLN K 94 " --> pdb=" O ILE K 63 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 28 through 32 removed outlier: 6.297A pdb=" N ILE K 59 " --> pdb=" O SER K 88 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N ILE K 90 " --> pdb=" O ILE K 59 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU K 61 " --> pdb=" O ILE K 90 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N MET K 92 " --> pdb=" O LEU K 61 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N ILE K 63 " --> pdb=" O MET K 92 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N GLN K 94 " --> pdb=" O ILE K 63 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N PHE K 112 " --> pdb=" O VAL K 87 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N THR K 89 " --> pdb=" O PHE K 112 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'L' and resid 5 through 9 Processing sheet with id=AE6, first strand: chain 'L' and resid 28 through 32 removed outlier: 6.296A pdb=" N ILE L 59 " --> pdb=" O SER L 88 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N ILE L 90 " --> pdb=" O ILE L 59 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU L 61 " --> pdb=" O ILE L 90 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N MET L 92 " --> pdb=" O LEU L 61 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N ILE L 63 " --> pdb=" O MET L 92 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N GLN L 94 " --> pdb=" O ILE L 63 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'L' and resid 28 through 32 removed outlier: 6.296A pdb=" N ILE L 59 " --> pdb=" O SER L 88 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N ILE L 90 " --> pdb=" O ILE L 59 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU L 61 " --> pdb=" O ILE L 90 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N MET L 92 " --> pdb=" O LEU L 61 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N ILE L 63 " --> pdb=" O MET L 92 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N GLN L 94 " --> pdb=" O ILE L 63 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N PHE L 112 " --> pdb=" O VAL L 87 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N THR L 89 " --> pdb=" O PHE L 112 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'M' and resid 5 through 9 Processing sheet with id=AE9, first strand: chain 'M' and resid 28 through 32 removed outlier: 6.296A pdb=" N ILE M 59 " --> pdb=" O SER M 88 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N ILE M 90 " --> pdb=" O ILE M 59 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU M 61 " --> pdb=" O ILE M 90 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N MET M 92 " --> pdb=" O LEU M 61 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N ILE M 63 " --> pdb=" O MET M 92 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N GLN M 94 " --> pdb=" O ILE M 63 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'M' and resid 28 through 32 removed outlier: 6.296A pdb=" N ILE M 59 " --> pdb=" O SER M 88 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N ILE M 90 " --> pdb=" O ILE M 59 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU M 61 " --> pdb=" O ILE M 90 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N MET M 92 " --> pdb=" O LEU M 61 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N ILE M 63 " --> pdb=" O MET M 92 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N GLN M 94 " --> pdb=" O ILE M 63 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N PHE M 112 " --> pdb=" O VAL M 87 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N THR M 89 " --> pdb=" O PHE M 112 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'N' and resid 5 through 9 Processing sheet with id=AF3, first strand: chain 'N' and resid 28 through 32 removed outlier: 6.296A pdb=" N ILE N 59 " --> pdb=" O SER N 88 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N ILE N 90 " --> pdb=" O ILE N 59 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU N 61 " --> pdb=" O ILE N 90 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N MET N 92 " --> pdb=" O LEU N 61 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N ILE N 63 " --> pdb=" O MET N 92 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N GLN N 94 " --> pdb=" O ILE N 63 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'N' and resid 28 through 32 removed outlier: 6.296A pdb=" N ILE N 59 " --> pdb=" O SER N 88 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N ILE N 90 " --> pdb=" O ILE N 59 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU N 61 " --> pdb=" O ILE N 90 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N MET N 92 " --> pdb=" O LEU N 61 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N ILE N 63 " --> pdb=" O MET N 92 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N GLN N 94 " --> pdb=" O ILE N 63 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N PHE N 112 " --> pdb=" O VAL N 87 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N THR N 89 " --> pdb=" O PHE N 112 " (cutoff:3.500A) 1272 hydrogen bonds defined for protein. 3690 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: 19.18 Time building geometry restraints manager: 38.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 21868 1.03 - 1.22: 28 1.22 - 1.42: 8979 1.42 - 1.61: 12875 1.61 - 1.80: 308 Bond restraints: 44058 Sorted by residual: bond pdb=" N SER N 97 " pdb=" CA SER N 97 " ideal model delta sigma weight residual 1.457 1.480 -0.023 1.17e-02 7.31e+03 3.80e+00 bond pdb=" N SER B 97 " pdb=" CA SER B 97 " ideal model delta sigma weight residual 1.457 1.480 -0.023 1.17e-02 7.31e+03 3.79e+00 bond pdb=" N SER G 97 " pdb=" CA SER G 97 " ideal model delta sigma weight residual 1.457 1.480 -0.023 1.17e-02 7.31e+03 3.77e+00 bond pdb=" N SER F 97 " pdb=" CA SER F 97 " ideal model delta sigma weight residual 1.457 1.480 -0.023 1.17e-02 7.31e+03 3.71e+00 bond pdb=" N SER H 97 " pdb=" CA SER H 97 " ideal model delta sigma weight residual 1.457 1.480 -0.022 1.17e-02 7.31e+03 3.63e+00 ... (remaining 44053 not shown) Histogram of bond angle deviations from ideal: 99.62 - 106.16: 686 106.16 - 112.70: 51505 112.70 - 119.24: 9619 119.24 - 125.78: 17429 125.78 - 132.32: 407 Bond angle restraints: 79646 Sorted by residual: angle pdb=" C ALA I 96 " pdb=" N SER I 97 " pdb=" CA SER I 97 " ideal model delta sigma weight residual 121.19 127.67 -6.48 1.59e+00 3.96e-01 1.66e+01 angle pdb=" C ALA G 96 " pdb=" N SER G 97 " pdb=" CA SER G 97 " ideal model delta sigma weight residual 121.19 127.67 -6.48 1.59e+00 3.96e-01 1.66e+01 angle pdb=" C ALA L 96 " pdb=" N SER L 97 " pdb=" CA SER L 97 " ideal model delta sigma weight residual 121.19 127.67 -6.48 1.59e+00 3.96e-01 1.66e+01 angle pdb=" C ALA M 96 " pdb=" N SER M 97 " pdb=" CA SER M 97 " ideal model delta sigma weight residual 121.19 127.66 -6.47 1.59e+00 3.96e-01 1.66e+01 angle pdb=" C ALA H 96 " pdb=" N SER H 97 " pdb=" CA SER H 97 " ideal model delta sigma weight residual 121.19 127.66 -6.47 1.59e+00 3.96e-01 1.66e+01 ... (remaining 79641 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.41: 16129 15.41 - 30.83: 1198 30.83 - 46.24: 131 46.24 - 61.66: 28 61.66 - 77.07: 14 Dihedral angle restraints: 17500 sinusoidal: 8400 harmonic: 9100 Sorted by residual: dihedral pdb=" CA ALA D 96 " pdb=" C ALA D 96 " pdb=" N SER D 97 " pdb=" CA SER D 97 " ideal model delta harmonic sigma weight residual 180.00 -154.55 -25.45 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA ALA C 96 " pdb=" C ALA C 96 " pdb=" N SER C 97 " pdb=" CA SER C 97 " ideal model delta harmonic sigma weight residual -180.00 -154.56 -25.44 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA ALA G 96 " pdb=" C ALA G 96 " pdb=" N SER G 97 " pdb=" CA SER G 97 " ideal model delta harmonic sigma weight residual 180.00 -154.56 -25.44 0 5.00e+00 4.00e-02 2.59e+01 ... (remaining 17497 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1947 0.029 - 0.058: 889 0.058 - 0.087: 341 0.087 - 0.116: 153 0.116 - 0.145: 58 Chirality restraints: 3388 Sorted by residual: chirality pdb=" CA VAL E 3 " pdb=" N VAL E 3 " pdb=" C VAL E 3 " pdb=" CB VAL E 3 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.26e-01 chirality pdb=" CA VAL J 3 " pdb=" N VAL J 3 " pdb=" C VAL J 3 " pdb=" CB VAL J 3 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.14 2.00e-01 2.50e+01 5.24e-01 chirality pdb=" CA VAL K 3 " pdb=" N VAL K 3 " pdb=" C VAL K 3 " pdb=" CB VAL K 3 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.14 2.00e-01 2.50e+01 5.22e-01 ... (remaining 3385 not shown) Planarity restraints: 6580 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA G 176 " -0.020 5.00e-02 4.00e+02 2.98e-02 1.42e+00 pdb=" N PRO G 177 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO G 177 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO G 177 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA I 176 " 0.020 5.00e-02 4.00e+02 2.98e-02 1.42e+00 pdb=" N PRO I 177 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO I 177 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO I 177 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA J 176 " 0.020 5.00e-02 4.00e+02 2.97e-02 1.41e+00 pdb=" N PRO J 177 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO J 177 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO J 177 " 0.017 5.00e-02 4.00e+02 ... (remaining 6577 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.27: 5605 2.27 - 2.85: 101011 2.85 - 3.43: 113604 3.43 - 4.02: 164675 4.02 - 4.60: 253435 Nonbonded interactions: 638330 Sorted by model distance: nonbonded pdb="HE22 GLN E 123 " pdb=" HG1 THR K 133 " model vdw 1.683 2.100 nonbonded pdb=" O MET I 153 " pdb=" HG1 THR I 157 " model vdw 1.712 1.850 nonbonded pdb=" O MET E 153 " pdb=" HG1 THR E 157 " model vdw 1.712 1.850 nonbonded pdb=" O MET G 153 " pdb=" HG1 THR G 157 " model vdw 1.712 1.850 nonbonded pdb=" O MET L 153 " pdb=" HG1 THR L 157 " model vdw 1.712 1.850 ... (remaining 638325 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 '1' selection = chain '2' selection = chain '3' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' } ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' 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: 5 Type Number sf(0) Gaussians S 168 5.16 5 C 13762 2.51 5 N 3780 2.21 5 O 4130 1.98 5 H 21896 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: 0.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.690 Extract box with map and model: 9.610 Check model and map are aligned: 0.630 Convert atoms to be neutral: 0.380 Process input model: 137.830 Find NCS groups from input model: 2.060 Set up NCS constraints: 0.440 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 155.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8981 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 : 0.006 0.050 22162 Z= 0.371 Angle : 0.671 6.479 29862 Z= 0.381 Chirality : 0.043 0.145 3388 Planarity : 0.004 0.030 3892 Dihedral : 9.862 77.075 8344 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 0.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % 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: -2.78 (0.12), residues: 2758 helix: -2.12 (0.10), residues: 1358 sheet: 0.30 (0.25), residues: 308 loop : -1.94 (0.15), residues: 1092 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5516 Ramachandran restraints generated. 2758 Oldfield, 0 Emsley, 2758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5516 Ramachandran restraints generated. 2758 Oldfield, 0 Emsley, 2758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 758 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 758 time to evaluate : 3.631 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 outliers start: 0 outliers final: 0 residues processed: 758 average time/residue: 0.9631 time to fit residues: 1060.2888 Evaluate side-chains 481 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 481 time to evaluate : 3.828 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.6576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 224 optimal weight: 2.9990 chunk 201 optimal weight: 0.2980 chunk 111 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 135 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 208 optimal weight: 0.7980 chunk 80 optimal weight: 0.9980 chunk 126 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 241 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 ASN ** C 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 ASN D 41 ASN D 193 ASN E 41 ASN E 193 ASN F 41 ASN F 193 ASN G 41 ASN G 193 ASN H 41 ASN H 193 ASN I 41 ASN J 41 ASN K 41 ASN K 193 ASN L 193 ASN M 41 ASN N 41 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9018 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 22162 Z= 0.226 Angle : 0.536 6.270 29862 Z= 0.285 Chirality : 0.042 0.143 3388 Planarity : 0.004 0.058 3892 Dihedral : 4.599 27.516 3052 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer Outliers : 1.28 % 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: 0.18 (0.15), residues: 2758 helix: 1.14 (0.14), residues: 1358 sheet: 0.77 (0.27), residues: 308 loop : -1.42 (0.16), residues: 1092 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5516 Ramachandran restraints generated. 2758 Oldfield, 0 Emsley, 2758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5516 Ramachandran restraints generated. 2758 Oldfield, 0 Emsley, 2758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 524 time to evaluate : 4.118 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 outliers start: 30 outliers final: 22 residues processed: 546 average time/residue: 0.8568 time to fit residues: 693.9057 Evaluate side-chains 522 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 500 time to evaluate : 3.687 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 22 outliers final: 1 residues processed: 22 average time/residue: 0.4724 time to fit residues: 23.3868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 134 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 201 optimal weight: 1.9990 chunk 164 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 241 optimal weight: 2.9990 chunk 261 optimal weight: 1.9990 chunk 215 optimal weight: 1.9990 chunk 239 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 194 optimal weight: 0.9980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 ASN ** E 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 193 ASN L 41 ASN L 193 ASN M 41 ASN N 123 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9068 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.033 22162 Z= 0.320 Angle : 0.533 5.585 29862 Z= 0.284 Chirality : 0.042 0.154 3388 Planarity : 0.004 0.051 3892 Dihedral : 4.585 24.010 3052 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer Outliers : 0.56 % 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: 0.91 (0.16), residues: 2758 helix: 1.96 (0.14), residues: 1372 sheet: 1.14 (0.26), residues: 336 loop : -1.50 (0.16), residues: 1050 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5516 Ramachandran restraints generated. 2758 Oldfield, 0 Emsley, 2758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5516 Ramachandran restraints generated. 2758 Oldfield, 0 Emsley, 2758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 532 time to evaluate : 3.726 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 outliers start: 13 outliers final: 8 residues processed: 535 average time/residue: 0.9403 time to fit residues: 741.2592 Evaluate side-chains 501 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 493 time to evaluate : 3.732 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.5201 time to fit residues: 12.1088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 239 optimal weight: 2.9990 chunk 181 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 162 optimal weight: 0.9980 chunk 242 optimal weight: 1.9990 chunk 257 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 230 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 ASN ** E 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 41 ASN H 193 ASN I 193 ASN ** L 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 41 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9067 moved from start: 0.4100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.036 22162 Z= 0.312 Angle : 0.516 5.794 29862 Z= 0.274 Chirality : 0.042 0.147 3388 Planarity : 0.003 0.035 3892 Dihedral : 4.634 25.962 3052 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer Outliers : 0.43 % 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: 1.22 (0.16), residues: 2758 helix: 2.25 (0.14), residues: 1372 sheet: 1.27 (0.26), residues: 336 loop : -1.41 (0.16), residues: 1050 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5516 Ramachandran restraints generated. 2758 Oldfield, 0 Emsley, 2758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5516 Ramachandran restraints generated. 2758 Oldfield, 0 Emsley, 2758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 514 time to evaluate : 3.743 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 outliers start: 10 outliers final: 9 residues processed: 517 average time/residue: 0.8771 time to fit residues: 667.9676 Evaluate side-chains 502 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 493 time to evaluate : 3.703 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.4615 time to fit residues: 12.2067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 214 optimal weight: 0.5980 chunk 145 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 191 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 chunk 219 optimal weight: 1.9990 chunk 177 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 230 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 ASN ** E 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 193 ASN ** L 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9059 moved from start: 0.4241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 22162 Z= 0.247 Angle : 0.491 5.579 29862 Z= 0.259 Chirality : 0.041 0.141 3388 Planarity : 0.003 0.034 3892 Dihedral : 4.454 22.414 3052 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer Outliers : 0.09 % 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: 1.48 (0.16), residues: 2758 helix: 2.48 (0.14), residues: 1372 sheet: 0.40 (0.21), residues: 532 loop : -1.19 (0.19), residues: 854 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5516 Ramachandran restraints generated. 2758 Oldfield, 0 Emsley, 2758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5516 Ramachandran restraints generated. 2758 Oldfield, 0 Emsley, 2758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 511 time to evaluate : 3.888 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 outliers start: 2 outliers final: 2 residues processed: 512 average time/residue: 0.8746 time to fit residues: 659.8987 Evaluate side-chains 503 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 501 time to evaluate : 3.674 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.4419 time to fit residues: 6.2309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 86 optimal weight: 1.9990 chunk 231 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 257 optimal weight: 1.9990 chunk 213 optimal weight: 0.9980 chunk 119 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 ASN ** E 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 41 ASN H 193 ASN ** L 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9073 moved from start: 0.4363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.043 22162 Z= 0.355 Angle : 0.525 5.671 29862 Z= 0.280 Chirality : 0.042 0.139 3388 Planarity : 0.004 0.057 3892 Dihedral : 4.640 25.585 3052 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer Outliers : 0.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.16), residues: 2758 helix: 2.41 (0.14), residues: 1372 sheet: 1.29 (0.27), residues: 336 loop : -1.33 (0.16), residues: 1050 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5516 Ramachandran restraints generated. 2758 Oldfield, 0 Emsley, 2758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5516 Ramachandran restraints generated. 2758 Oldfield, 0 Emsley, 2758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 515 time to evaluate : 4.084 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 outliers start: 8 outliers final: 7 residues processed: 518 average time/residue: 0.8579 time to fit residues: 656.0573 Evaluate side-chains 510 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 503 time to evaluate : 3.713 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.5619 time to fit residues: 11.2619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 248 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 chunk 187 optimal weight: 0.8980 chunk 145 optimal weight: 0.7980 chunk 216 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 256 optimal weight: 3.9990 chunk 160 optimal weight: 1.9990 chunk 156 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 ASN ** E 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 193 ASN ** L 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 193 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9062 moved from start: 0.4429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 22162 Z= 0.267 Angle : 0.499 5.607 29862 Z= 0.263 Chirality : 0.041 0.142 3388 Planarity : 0.003 0.042 3892 Dihedral : 4.525 23.720 3052 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer Outliers : 0.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.16), residues: 2758 helix: 2.54 (0.14), residues: 1372 sheet: 0.44 (0.22), residues: 532 loop : -1.22 (0.19), residues: 854 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5516 Ramachandran restraints generated. 2758 Oldfield, 0 Emsley, 2758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5516 Ramachandran restraints generated. 2758 Oldfield, 0 Emsley, 2758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 518 time to evaluate : 3.987 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 outliers start: 6 outliers final: 5 residues processed: 518 average time/residue: 0.8831 time to fit residues: 676.4166 Evaluate side-chains 512 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 507 time to evaluate : 4.212 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.4930 time to fit residues: 9.8251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 158 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 162 optimal weight: 0.9980 chunk 174 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 201 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 ASN ** E 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 193 ASN ** L 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9061 moved from start: 0.4494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 22162 Z= 0.275 Angle : 0.506 5.551 29862 Z= 0.267 Chirality : 0.041 0.138 3388 Planarity : 0.003 0.048 3892 Dihedral : 4.516 24.263 3052 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer Outliers : 0.04 % 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: 1.54 (0.16), residues: 2758 helix: 2.56 (0.14), residues: 1372 sheet: 0.44 (0.22), residues: 532 loop : -1.22 (0.19), residues: 854 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5516 Ramachandran restraints generated. 2758 Oldfield, 0 Emsley, 2758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5516 Ramachandran restraints generated. 2758 Oldfield, 0 Emsley, 2758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 512 time to evaluate : 3.828 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 outliers start: 1 outliers final: 1 residues processed: 512 average time/residue: 0.8663 time to fit residues: 660.2271 Evaluate side-chains 509 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 508 time to evaluate : 3.770 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4771 time to fit residues: 5.4197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 233 optimal weight: 0.7980 chunk 245 optimal weight: 1.9990 chunk 224 optimal weight: 2.9990 chunk 238 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 187 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 chunk 215 optimal weight: 1.9990 chunk 225 optimal weight: 0.9990 chunk 156 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 ASN ** E 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 193 ASN ** L 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9058 moved from start: 0.4533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 22162 Z= 0.264 Angle : 0.505 5.576 29862 Z= 0.267 Chirality : 0.041 0.137 3388 Planarity : 0.003 0.044 3892 Dihedral : 4.477 22.691 3052 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer Outliers : 0.09 % 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: 1.58 (0.16), residues: 2758 helix: 2.59 (0.14), residues: 1372 sheet: 0.45 (0.22), residues: 532 loop : -1.21 (0.19), residues: 854 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5516 Ramachandran restraints generated. 2758 Oldfield, 0 Emsley, 2758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5516 Ramachandran restraints generated. 2758 Oldfield, 0 Emsley, 2758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 511 time to evaluate : 3.554 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 outliers start: 2 outliers final: 1 residues processed: 512 average time/residue: 0.8565 time to fit residues: 652.8080 Evaluate side-chains 513 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 512 time to evaluate : 3.649 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.5058 time to fit residues: 5.4060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 252 optimal weight: 0.4980 chunk 154 optimal weight: 0.6980 chunk 119 optimal weight: 0.9980 chunk 175 optimal weight: 1.9990 chunk 265 optimal weight: 2.9990 chunk 243 optimal weight: 1.9990 chunk 211 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 163 optimal weight: 0.9980 chunk 129 optimal weight: 0.0970 chunk 167 optimal weight: 2.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 ASN ** E 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 193 ASN ** L 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9038 moved from start: 0.4582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 22162 Z= 0.172 Angle : 0.483 5.366 29862 Z= 0.252 Chirality : 0.040 0.134 3388 Planarity : 0.003 0.044 3892 Dihedral : 4.277 22.118 3052 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % 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: 1.77 (0.16), residues: 2758 helix: 2.77 (0.14), residues: 1372 sheet: 0.37 (0.23), residues: 504 loop : -0.98 (0.19), residues: 882 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5516 Ramachandran restraints generated. 2758 Oldfield, 0 Emsley, 2758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5516 Ramachandran restraints generated. 2758 Oldfield, 0 Emsley, 2758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 525 time to evaluate : 3.868 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 outliers start: 0 outliers final: 0 residues processed: 525 average time/residue: 0.8868 time to fit residues: 684.2281 Evaluate side-chains 515 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 515 time to evaluate : 3.630 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.4423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 224 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 194 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 211 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 217 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 185 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 ASN ** D 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 ASN ** E 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 193 ASN ** L 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.099461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.084230 restraints weight = 83189.945| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 2.07 r_work: 0.2882 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 1.81 restraints_weight: 0.2500 r_work: 0.2842 rms_B_bonded: 1.89 restraints_weight: 0.1250 r_work: 0.2820 rms_B_bonded: 2.05 restraints_weight: 0.0625 r_work: 0.2795 rms_B_bonded: 2.27 restraints_weight: 0.0312 r_work: 0.2767 rms_B_bonded: 2.56 restraints_weight: 0.0156 r_work: 0.2734 rms_B_bonded: 2.94 restraints_weight: 0.0078 r_work: 0.2697 rms_B_bonded: 3.42 restraints_weight: 0.0039 r_work: 0.2654 rms_B_bonded: 4.01 restraints_weight: 0.0020 r_work: 0.2604 rms_B_bonded: 4.73 restraints_weight: 0.0010 r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.4614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 22162 Z= 0.242 Angle : 0.501 5.470 29862 Z= 0.264 Chirality : 0.041 0.136 3388 Planarity : 0.003 0.041 3892 Dihedral : 4.308 21.992 3052 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer Outliers : 0.09 % 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: 1.73 (0.16), residues: 2758 helix: 2.73 (0.14), residues: 1372 sheet: 0.52 (0.22), residues: 532 loop : -1.14 (0.19), residues: 854 =============================================================================== Job complete usr+sys time: 11459.66 seconds wall clock time: 202 minutes 22.71 seconds (12142.71 seconds total)