Starting phenix.real_space_refine on Sat Feb 24 11:30:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ppe_20434/02_2024/6ppe_20434.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ppe_20434/02_2024/6ppe_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_20434/02_2024/6ppe_20434.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ppe_20434/02_2024/6ppe_20434.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ppe_20434/02_2024/6ppe_20434.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ppe_20434/02_2024/6ppe_20434.pdb" } resolution = 3.19 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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. 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-5238/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: 19.05, per 1000 atoms: 0.44 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: 34.53 Conformation dependent library (CDL) restraints added in 4.3 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: 3.81 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: 18.97 Time building geometry restraints manager: 35.66 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: 18565 15.41 - 30.83: 1366 30.83 - 46.24: 327 46.24 - 61.66: 294 61.66 - 77.07: 14 Dihedral angle restraints: 20566 sinusoidal: 11466 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 20563 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 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: 1.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.720 Extract box with map and model: 8.000 Check model and map are aligned: 0.680 Set scattering table: 0.420 Process input model: 136.630 Find NCS groups from input model: 2.170 Set up NCS constraints: 0.480 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 153.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8916 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 % Allowed : 1.80 % Favored : 98.20 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS L 122 PHE 0.013 0.002 PHE I 17 TYR 0.008 0.002 TYR J 182 ARG 0.003 0.001 ARG G 27 *********************** 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 : 3.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 ASP cc_start: 0.9366 (m-30) cc_final: 0.9098 (m-30) REVERT: A 186 ASP cc_start: 0.9386 (m-30) cc_final: 0.9065 (m-30) REVERT: C 186 ASP cc_start: 0.9358 (m-30) cc_final: 0.9121 (m-30) REVERT: D 20 TYR cc_start: 0.9498 (m-80) cc_final: 0.9225 (m-10) REVERT: E 15 ARG cc_start: 0.8905 (ttm170) cc_final: 0.8600 (ttm-80) REVERT: E 41 ASN cc_start: 0.9286 (t0) cc_final: 0.8731 (t0) REVERT: E 186 ASP cc_start: 0.9379 (m-30) cc_final: 0.9120 (m-30) REVERT: H 118 ARG cc_start: 0.8451 (mtt-85) cc_final: 0.8074 (ptt180) REVERT: I 186 ASP cc_start: 0.9260 (m-30) cc_final: 0.9020 (m-30) REVERT: J 41 ASN cc_start: 0.9380 (t0) cc_final: 0.9038 (t0) REVERT: J 175 SER cc_start: 0.9212 (p) cc_final: 0.8922 (p) REVERT: J 178 GLU cc_start: 0.9259 (mt-10) cc_final: 0.9038 (mt-10) REVERT: J 186 ASP cc_start: 0.9284 (m-30) cc_final: 0.9037 (m-30) REVERT: K 20 TYR cc_start: 0.9469 (m-80) cc_final: 0.9250 (m-10) REVERT: K 80 MET cc_start: 0.8887 (mtp) cc_final: 0.8624 (mtp) REVERT: N 41 ASN cc_start: 0.9150 (t0) cc_final: 0.8921 (t0) REVERT: Y 273 THR cc_start: 0.9144 (t) cc_final: 0.8820 (p) outliers start: 0 outliers final: 0 residues processed: 758 average time/residue: 1.0093 time to fit residues: 1088.3450 Evaluate side-chains 488 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 488 time to evaluate : 3.481 ------------------------------------------------------------------------------- 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: 1.9990 chunk 111 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 135 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 208 optimal weight: 0.5980 chunk 80 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 241 optimal weight: 1.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 ASN E 41 ASN E 193 ASN ** F 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 193 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 Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9006 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 22162 Z= 0.313 Angle : 0.556 6.173 29862 Z= 0.300 Chirality : 0.043 0.147 3388 Planarity : 0.004 0.036 3892 Dihedral : 4.678 27.666 3052 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.11 % Allowed : 8.17 % Favored : 90.72 % 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: 0.00 (0.15), residues: 2758 helix: 1.00 (0.14), residues: 1372 sheet: 0.72 (0.28), residues: 308 loop : -1.54 (0.16), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 122 PHE 0.010 0.001 PHE K 17 TYR 0.009 0.001 TYR M 182 ARG 0.006 0.000 ARG J 118 *********************** 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 559 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 533 time to evaluate : 3.401 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: B 120 MET cc_start: 0.9444 (ttp) cc_final: 0.9203 (ttt) REVERT: D 15 ARG cc_start: 0.8811 (ttp-170) cc_final: 0.8528 (ttp-170) REVERT: E 74 MET cc_start: 0.9086 (mmm) cc_final: 0.8878 (mmt) REVERT: G 41 ASN cc_start: 0.9285 (t0) cc_final: 0.8921 (t0) REVERT: H 141 GLU cc_start: 0.9196 (tp30) cc_final: 0.8930 (tp30) REVERT: J 41 ASN cc_start: 0.9269 (t0) cc_final: 0.8958 (t0) REVERT: K 74 MET cc_start: 0.9137 (tpp) cc_final: 0.8826 (mmt) REVERT: M 20 TYR cc_start: 0.9475 (m-10) cc_final: 0.9242 (m-10) REVERT: M 74 MET cc_start: 0.9175 (mmt) cc_final: 0.8827 (mmt) outliers start: 26 outliers final: 21 residues processed: 553 average time/residue: 0.9358 time to fit residues: 758.5548 Evaluate side-chains 516 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 495 time to evaluate : 3.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain G residue 36 GLU Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain H residue 41 ASN Chi-restraints excluded: chain H residue 191 HIS Chi-restraints excluded: chain I residue 41 ASN Chi-restraints excluded: chain I residue 175 SER Chi-restraints excluded: chain J residue 16 SER Chi-restraints excluded: chain K residue 16 SER Chi-restraints excluded: chain K residue 36 GLU Chi-restraints excluded: chain K residue 41 ASN Chi-restraints excluded: chain L residue 36 GLU Chi-restraints excluded: chain L residue 113 CYS Chi-restraints excluded: chain M residue 36 GLU Chi-restraints excluded: chain M residue 41 ASN Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain N residue 36 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 134 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 201 optimal weight: 2.9990 chunk 164 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 241 optimal weight: 1.9990 chunk 261 optimal weight: 0.6980 chunk 215 optimal weight: 1.9990 chunk 239 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 194 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 ASN ** E 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 41 ASN G 41 ASN H 41 ASN H 193 ASN I 41 ASN J 41 ASN K 41 ASN L 64 ASN L 193 ASN N 41 ASN N 193 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9029 moved from start: 0.3611 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= 0.306 Angle : 0.516 5.682 29862 Z= 0.276 Chirality : 0.042 0.143 3388 Planarity : 0.004 0.038 3892 Dihedral : 4.564 23.318 3052 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 0.98 % Allowed : 8.17 % Favored : 90.85 % 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: 0.89 (0.16), residues: 2758 helix: 1.95 (0.14), residues: 1372 sheet: 0.89 (0.28), residues: 308 loop : -1.37 (0.16), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS B 122 PHE 0.011 0.001 PHE E 17 TYR 0.006 0.001 TYR M 182 ARG 0.003 0.000 ARG M 15 *********************** 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 537 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 514 time to evaluate : 3.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 MET cc_start: 0.9087 (ppp) cc_final: 0.8710 (ptm) REVERT: B 120 MET cc_start: 0.9458 (ttp) cc_final: 0.9233 (ttt) REVERT: D 15 ARG cc_start: 0.8867 (ttp-170) cc_final: 0.8597 (ttp-170) REVERT: E 172 ARG cc_start: 0.9181 (ttt90) cc_final: 0.8976 (ttt-90) REVERT: G 41 ASN cc_start: 0.9299 (t0) cc_final: 0.8908 (t0) REVERT: G 78 ASP cc_start: 0.9213 (m-30) cc_final: 0.8972 (m-30) REVERT: H 141 GLU cc_start: 0.9410 (tp30) cc_final: 0.9138 (tp30) REVERT: J 41 ASN cc_start: 0.9320 (t0) cc_final: 0.8936 (t0) REVERT: K 74 MET cc_start: 0.9151 (tpp) cc_final: 0.8862 (mmt) REVERT: M 9 GLN cc_start: 0.9137 (mm-40) cc_final: 0.8936 (mm-40) REVERT: N 15 ARG cc_start: 0.9106 (ttp-170) cc_final: 0.8882 (ttm-80) outliers start: 23 outliers final: 20 residues processed: 528 average time/residue: 0.9237 time to fit residues: 705.7679 Evaluate side-chains 519 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 499 time to evaluate : 3.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ASP Chi-restraints excluded: chain B residue 41 ASN Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain F residue 41 ASN Chi-restraints excluded: chain F residue 97 SER Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 190 THR Chi-restraints excluded: chain H residue 149 MET Chi-restraints excluded: chain H residue 191 HIS Chi-restraints excluded: chain J residue 16 SER Chi-restraints excluded: chain J residue 18 ASP Chi-restraints excluded: chain K residue 16 SER Chi-restraints excluded: chain L residue 36 GLU Chi-restraints excluded: chain L residue 113 CYS Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain N residue 36 GLU Chi-restraints excluded: chain N residue 117 SER 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: 1.9990 chunk 242 optimal weight: 1.9990 chunk 257 optimal weight: 0.9980 chunk 126 optimal weight: 1.9990 chunk 230 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** K 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 64 ASN N 123 GLN N 193 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9042 moved from start: 0.3980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 22162 Z= 0.356 Angle : 0.526 6.247 29862 Z= 0.282 Chirality : 0.043 0.147 3388 Planarity : 0.004 0.039 3892 Dihedral : 4.669 26.356 3052 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.11 % Allowed : 9.11 % Favored : 89.78 % 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: 1.12 (0.16), residues: 2758 helix: 2.15 (0.14), residues: 1372 sheet: 1.15 (0.26), residues: 336 loop : -1.39 (0.17), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS B 122 PHE 0.010 0.001 PHE J 30 TYR 0.007 0.001 TYR H 62 ARG 0.002 0.000 ARG E 118 *********************** 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 536 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 510 time to evaluate : 3.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 MET cc_start: 0.9117 (ppp) cc_final: 0.8739 (ptm) REVERT: B 120 MET cc_start: 0.9466 (ttp) cc_final: 0.9237 (ttt) REVERT: D 15 ARG cc_start: 0.8917 (ttp-170) cc_final: 0.8654 (ttp-170) REVERT: E 74 MET cc_start: 0.8977 (mmt) cc_final: 0.8763 (mmt) REVERT: F 15 ARG cc_start: 0.9142 (ttp-170) cc_final: 0.8899 (ttm-80) REVERT: G 41 ASN cc_start: 0.9335 (t0) cc_final: 0.8908 (t0) REVERT: G 78 ASP cc_start: 0.9171 (m-30) cc_final: 0.8957 (m-30) REVERT: I 118 ARG cc_start: 0.8954 (ptt180) cc_final: 0.8116 (mtp85) REVERT: K 74 MET cc_start: 0.9120 (tpp) cc_final: 0.8774 (mmt) REVERT: L 80 MET cc_start: 0.9391 (mtp) cc_final: 0.9189 (mtp) REVERT: N 15 ARG cc_start: 0.9079 (ttp-170) cc_final: 0.8863 (ttm-80) outliers start: 26 outliers final: 24 residues processed: 524 average time/residue: 0.9964 time to fit residues: 772.8515 Evaluate side-chains 513 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 489 time to evaluate : 3.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 ASN Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain F residue 97 SER Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain G residue 36 GLU Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 144 LYS Chi-restraints excluded: chain G residue 190 THR Chi-restraints excluded: chain H residue 41 ASN Chi-restraints excluded: chain H residue 149 MET Chi-restraints excluded: chain I residue 41 ASN Chi-restraints excluded: chain I residue 190 THR Chi-restraints excluded: chain J residue 16 SER Chi-restraints excluded: chain J residue 18 ASP Chi-restraints excluded: chain K residue 16 SER Chi-restraints excluded: chain K residue 36 GLU Chi-restraints excluded: chain L residue 16 SER Chi-restraints excluded: chain L residue 36 GLU Chi-restraints excluded: chain L residue 113 CYS Chi-restraints excluded: chain M residue 41 ASN Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain N residue 36 GLU Chi-restraints excluded: chain N residue 117 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 214 optimal weight: 0.3980 chunk 145 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 191 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 219 optimal weight: 1.9990 chunk 177 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 230 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 ASN E 41 ASN ** F 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 193 ASN ** K 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9028 moved from start: 0.4161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 22162 Z= 0.256 Angle : 0.484 5.596 29862 Z= 0.257 Chirality : 0.041 0.140 3388 Planarity : 0.004 0.039 3892 Dihedral : 4.490 23.184 3052 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.81 % Allowed : 9.88 % Favored : 89.31 % 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: 1.41 (0.16), residues: 2758 helix: 2.42 (0.14), residues: 1372 sheet: 1.21 (0.26), residues: 336 loop : -1.27 (0.17), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS B 122 PHE 0.009 0.001 PHE K 17 TYR 0.011 0.001 TYR G 62 ARG 0.002 0.000 ARG K 15 *********************** 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 523 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 504 time to evaluate : 3.952 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: A 39 MET cc_start: 0.9062 (ppp) cc_final: 0.8701 (ptm) REVERT: B 120 MET cc_start: 0.9463 (ttp) cc_final: 0.9237 (ttt) REVERT: D 15 ARG cc_start: 0.8918 (ttp-170) cc_final: 0.8685 (ttp-170) REVERT: E 74 MET cc_start: 0.8811 (mmt) cc_final: 0.8549 (mmt) REVERT: F 15 ARG cc_start: 0.9051 (ttp-170) cc_final: 0.8825 (ttm-80) REVERT: G 41 ASN cc_start: 0.9299 (t0) cc_final: 0.8842 (t0) REVERT: G 78 ASP cc_start: 0.9177 (m-30) cc_final: 0.8969 (m-30) REVERT: K 74 MET cc_start: 0.9103 (tpp) cc_final: 0.8703 (mmt) REVERT: L 80 MET cc_start: 0.9386 (mtp) cc_final: 0.9181 (mtp) REVERT: M 9 GLN cc_start: 0.9191 (mm-40) cc_final: 0.8968 (mm-40) outliers start: 19 outliers final: 16 residues processed: 512 average time/residue: 0.8966 time to fit residues: 671.2978 Evaluate side-chains 510 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 494 time to evaluate : 3.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ASP Chi-restraints excluded: chain B residue 41 ASN Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain F residue 97 SER Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain G residue 36 GLU Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain H residue 41 ASN Chi-restraints excluded: chain H residue 191 HIS Chi-restraints excluded: chain I residue 175 SER Chi-restraints excluded: chain I residue 190 THR Chi-restraints excluded: chain J residue 18 ASP Chi-restraints excluded: chain K residue 16 SER Chi-restraints excluded: chain L residue 113 CYS Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain N residue 18 ASP 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: 0.8980 chunk 150 optimal weight: 0.9980 chunk 63 optimal weight: 0.6980 chunk 257 optimal weight: 1.9990 chunk 213 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 135 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 ASN ** F 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 41 ASN H 193 ASN ** K 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9015 moved from start: 0.4261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 22162 Z= 0.201 Angle : 0.465 5.409 29862 Z= 0.245 Chirality : 0.040 0.137 3388 Planarity : 0.003 0.038 3892 Dihedral : 4.344 22.863 3052 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.73 % Allowed : 10.22 % Favored : 89.05 % 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: 1.62 (0.16), residues: 2758 helix: 2.61 (0.14), residues: 1372 sheet: 1.29 (0.26), residues: 336 loop : -1.20 (0.17), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS B 122 PHE 0.008 0.001 PHE B 17 TYR 0.011 0.001 TYR M 62 ARG 0.001 0.000 ARG E 118 *********************** 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 529 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 512 time to evaluate : 3.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 MET cc_start: 0.9022 (ppp) cc_final: 0.8673 (ptm) REVERT: D 15 ARG cc_start: 0.8921 (ttp-170) cc_final: 0.8711 (ttp-170) REVERT: F 15 ARG cc_start: 0.9032 (ttp-170) cc_final: 0.8828 (ttm-80) REVERT: H 20 TYR cc_start: 0.9423 (m-10) cc_final: 0.9221 (m-10) REVERT: K 74 MET cc_start: 0.9035 (tpp) cc_final: 0.8622 (mmt) REVERT: L 80 MET cc_start: 0.9400 (mtp) cc_final: 0.9170 (mtp) REVERT: M 9 GLN cc_start: 0.9177 (mm-40) cc_final: 0.8958 (mm-40) outliers start: 17 outliers final: 16 residues processed: 521 average time/residue: 0.9206 time to fit residues: 707.1102 Evaluate side-chains 518 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 502 time to evaluate : 3.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ASP Chi-restraints excluded: chain B residue 41 ASN Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain F residue 97 SER Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 190 THR Chi-restraints excluded: chain H residue 41 ASN Chi-restraints excluded: chain H residue 191 HIS Chi-restraints excluded: chain I residue 41 ASN Chi-restraints excluded: chain J residue 16 SER Chi-restraints excluded: chain J residue 18 ASP Chi-restraints excluded: chain L residue 36 GLU Chi-restraints excluded: chain L residue 113 CYS Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain N residue 117 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 248 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 chunk 187 optimal weight: 2.9990 chunk 145 optimal weight: 0.3980 chunk 216 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 256 optimal weight: 2.9990 chunk 160 optimal weight: 1.9990 chunk 156 optimal weight: 0.9980 chunk 118 optimal weight: 0.9980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 ASN ** F 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 41 ASN H 193 ASN ** K 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9026 moved from start: 0.4331 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= 0.263 Angle : 0.485 5.471 29862 Z= 0.257 Chirality : 0.041 0.136 3388 Planarity : 0.004 0.037 3892 Dihedral : 4.353 21.855 3052 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.20 % Allowed : 10.44 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.16), residues: 2758 helix: 2.60 (0.14), residues: 1372 sheet: 0.48 (0.22), residues: 532 loop : -1.03 (0.19), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS B 122 PHE 0.008 0.001 PHE H 17 TYR 0.008 0.001 TYR M 62 ARG 0.002 0.000 ARG E 118 *********************** 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 539 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 511 time to evaluate : 3.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 MET cc_start: 0.9088 (ppp) cc_final: 0.8718 (ptm) REVERT: B 120 MET cc_start: 0.9467 (ttp) cc_final: 0.9241 (ttt) REVERT: D 15 ARG cc_start: 0.8920 (ttp-170) cc_final: 0.8706 (ttp-170) REVERT: E 74 MET cc_start: 0.8801 (mmt) cc_final: 0.8554 (mmt) REVERT: H 20 TYR cc_start: 0.9440 (m-10) cc_final: 0.9235 (m-10) REVERT: K 74 MET cc_start: 0.8999 (tpp) cc_final: 0.8578 (mmt) REVERT: L 80 MET cc_start: 0.9411 (mtp) cc_final: 0.9170 (mtp) REVERT: M 9 GLN cc_start: 0.9196 (mm-40) cc_final: 0.8981 (mm-40) outliers start: 28 outliers final: 23 residues processed: 527 average time/residue: 0.8988 time to fit residues: 694.7153 Evaluate side-chains 525 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 502 time to evaluate : 3.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ASP Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain B residue 41 ASN Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain F residue 97 SER Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 144 LYS Chi-restraints excluded: chain G residue 190 THR Chi-restraints excluded: chain H residue 41 ASN Chi-restraints excluded: chain H residue 191 HIS Chi-restraints excluded: chain I residue 41 ASN Chi-restraints excluded: chain I residue 175 SER Chi-restraints excluded: chain I residue 190 THR Chi-restraints excluded: chain J residue 16 SER Chi-restraints excluded: chain J residue 18 ASP Chi-restraints excluded: chain L residue 16 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 113 CYS Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain N residue 117 SER 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: 0.9980 chunk 49 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 chunk 174 optimal weight: 2.9990 chunk 126 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 201 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 ASN ** F 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 193 ASN ** K 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9028 moved from start: 0.4397 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= 0.278 Angle : 0.493 5.537 29862 Z= 0.262 Chirality : 0.041 0.136 3388 Planarity : 0.004 0.037 3892 Dihedral : 4.424 23.945 3052 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.11 % Allowed : 10.78 % Favored : 88.11 % 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: 1.67 (0.16), residues: 2758 helix: 2.59 (0.14), residues: 1372 sheet: 0.49 (0.22), residues: 532 loop : -1.02 (0.20), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS J 122 PHE 0.009 0.001 PHE F 17 TYR 0.007 0.001 TYR M 62 ARG 0.002 0.000 ARG N 15 *********************** 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 535 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 509 time to evaluate : 3.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 MET cc_start: 0.9106 (ppp) cc_final: 0.8734 (ptm) REVERT: B 39 MET cc_start: 0.9085 (ppp) cc_final: 0.8864 (ttp) REVERT: B 120 MET cc_start: 0.9458 (ttp) cc_final: 0.9240 (ttt) REVERT: D 15 ARG cc_start: 0.8908 (ttp-170) cc_final: 0.8682 (ttp-170) REVERT: E 74 MET cc_start: 0.8893 (mmt) cc_final: 0.8642 (mmt) REVERT: K 74 MET cc_start: 0.8997 (tpp) cc_final: 0.8570 (mmt) REVERT: L 80 MET cc_start: 0.9415 (mtp) cc_final: 0.9156 (mtp) REVERT: M 9 GLN cc_start: 0.9193 (mm-40) cc_final: 0.8984 (mm-40) REVERT: Q 273 THR cc_start: 0.9307 (t) cc_final: 0.8897 (p) outliers start: 26 outliers final: 24 residues processed: 523 average time/residue: 0.9152 time to fit residues: 705.2709 Evaluate side-chains 530 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 506 time to evaluate : 3.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ASP Chi-restraints excluded: chain B residue 41 ASN Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain F residue 97 SER Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain G residue 36 GLU Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 144 LYS Chi-restraints excluded: chain G residue 190 THR Chi-restraints excluded: chain H residue 41 ASN Chi-restraints excluded: chain H residue 191 HIS Chi-restraints excluded: chain I residue 41 ASN Chi-restraints excluded: chain I residue 175 SER Chi-restraints excluded: chain I residue 190 THR Chi-restraints excluded: chain J residue 16 SER Chi-restraints excluded: chain J residue 18 ASP Chi-restraints excluded: chain L residue 16 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 113 CYS Chi-restraints excluded: chain M residue 41 ASN Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain N residue 117 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 233 optimal weight: 0.6980 chunk 245 optimal weight: 1.9990 chunk 224 optimal weight: 2.9990 chunk 238 optimal weight: 0.8980 chunk 143 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 187 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 215 optimal weight: 1.9990 chunk 225 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 ASN ** F 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 193 ASN ** K 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9034 moved from start: 0.4433 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= 0.303 Angle : 0.503 5.562 29862 Z= 0.268 Chirality : 0.042 0.136 3388 Planarity : 0.004 0.037 3892 Dihedral : 4.477 23.271 3052 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.07 % Allowed : 10.78 % Favored : 88.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.16), residues: 2758 helix: 2.57 (0.14), residues: 1372 sheet: 0.44 (0.22), residues: 532 loop : -1.03 (0.20), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS B 122 PHE 0.008 0.001 PHE G 17 TYR 0.007 0.001 TYR M 62 ARG 0.002 0.000 ARG N 15 *********************** 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 538 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 513 time to evaluate : 3.569 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: A 39 MET cc_start: 0.9122 (ppp) cc_final: 0.8745 (ptm) REVERT: A 163 GLN cc_start: 0.8889 (tp40) cc_final: 0.8685 (tp40) REVERT: B 120 MET cc_start: 0.9460 (ttp) cc_final: 0.9237 (ttt) REVERT: D 15 ARG cc_start: 0.8903 (ttp-170) cc_final: 0.8690 (ttp-110) REVERT: E 74 MET cc_start: 0.8913 (mmt) cc_final: 0.8635 (mmt) REVERT: K 15 ARG cc_start: 0.8926 (ttm-80) cc_final: 0.8669 (ttp-110) REVERT: K 74 MET cc_start: 0.8996 (tpp) cc_final: 0.8562 (mmt) REVERT: L 80 MET cc_start: 0.9419 (mtp) cc_final: 0.9155 (mtp) REVERT: Q 273 THR cc_start: 0.9298 (t) cc_final: 0.8884 (p) REVERT: X 273 THR cc_start: 0.9414 (t) cc_final: 0.9013 (p) outliers start: 25 outliers final: 25 residues processed: 527 average time/residue: 0.9112 time to fit residues: 711.0475 Evaluate side-chains 535 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 510 time to evaluate : 3.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain B residue 41 ASN Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain F residue 97 SER Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain G residue 36 GLU Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 144 LYS Chi-restraints excluded: chain G residue 190 THR Chi-restraints excluded: chain H residue 41 ASN Chi-restraints excluded: chain H residue 191 HIS Chi-restraints excluded: chain I residue 41 ASN Chi-restraints excluded: chain I residue 175 SER Chi-restraints excluded: chain I residue 190 THR Chi-restraints excluded: chain J residue 16 SER Chi-restraints excluded: chain J residue 18 ASP Chi-restraints excluded: chain L residue 16 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 113 CYS Chi-restraints excluded: chain M residue 41 ASN Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain N residue 117 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 252 optimal weight: 0.6980 chunk 154 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 chunk 175 optimal weight: 1.9990 chunk 265 optimal weight: 2.9990 chunk 243 optimal weight: 2.9990 chunk 211 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 163 optimal weight: 0.8980 chunk 129 optimal weight: 0.8980 chunk 167 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 ASN ** F 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 193 ASN ** K 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 193 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9014 moved from start: 0.4471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 22162 Z= 0.206 Angle : 0.478 5.414 29862 Z= 0.252 Chirality : 0.040 0.134 3388 Planarity : 0.003 0.037 3892 Dihedral : 4.320 22.401 3052 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.81 % Allowed : 11.08 % Favored : 88.11 % 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: 2.72 (0.14), residues: 1372 sheet: 0.47 (0.22), residues: 532 loop : -1.00 (0.20), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS J 122 PHE 0.007 0.001 PHE F 17 TYR 0.007 0.001 TYR M 62 ARG 0.001 0.000 ARG N 15 ********************** 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 531 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 512 time to evaluate : 3.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 MET cc_start: 0.9025 (ppp) cc_final: 0.8677 (ptm) REVERT: E 74 MET cc_start: 0.8830 (mmt) cc_final: 0.8576 (mmt) REVERT: H 20 TYR cc_start: 0.9430 (m-10) cc_final: 0.9218 (m-10) REVERT: K 15 ARG cc_start: 0.8927 (ttm-80) cc_final: 0.8670 (ttp-110) REVERT: K 74 MET cc_start: 0.8968 (tpp) cc_final: 0.8574 (mmt) REVERT: L 80 MET cc_start: 0.9393 (mtp) cc_final: 0.9132 (mtp) REVERT: Q 273 THR cc_start: 0.9278 (t) cc_final: 0.8866 (p) REVERT: X 273 THR cc_start: 0.9321 (t) cc_final: 0.8913 (p) outliers start: 19 outliers final: 17 residues processed: 522 average time/residue: 0.9007 time to fit residues: 688.0842 Evaluate side-chains 526 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 509 time to evaluate : 3.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ASP Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain B residue 41 ASN Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain F residue 97 SER Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 144 LYS Chi-restraints excluded: chain H residue 41 ASN Chi-restraints excluded: chain H residue 191 HIS Chi-restraints excluded: chain I residue 41 ASN Chi-restraints excluded: chain J residue 16 SER Chi-restraints excluded: chain J residue 18 ASP Chi-restraints excluded: chain L residue 113 CYS Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain N residue 117 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 224 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 194 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 58 optimal weight: 0.4980 chunk 211 optimal weight: 0.9990 chunk 88 optimal weight: 0.6980 chunk 217 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 185 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 ASN ** F 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 193 ASN ** K 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 193 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.098423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.083854 restraints weight = 82115.207| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 1.93 r_work: 0.2806 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2646 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.4504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 22162 Z= 0.192 Angle : 0.472 5.338 29862 Z= 0.248 Chirality : 0.040 0.134 3388 Planarity : 0.003 0.038 3892 Dihedral : 4.192 20.628 3052 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.68 % Allowed : 11.21 % Favored : 88.11 % 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: 1.86 (0.16), residues: 2758 helix: 2.79 (0.14), residues: 1372 sheet: 0.51 (0.22), residues: 532 loop : -0.96 (0.20), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS J 122 PHE 0.007 0.001 PHE A 17 TYR 0.006 0.001 TYR M 62 ARG 0.002 0.000 ARG K 166 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12767.68 seconds wall clock time: 225 minutes 53.26 seconds (13553.26 seconds total)