Starting phenix.real_space_refine (version: dev) on Sat Feb 25 19:29:15 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7peo_13355/02_2023/7peo_13355_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7peo_13355/02_2023/7peo_13355.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7peo_13355/02_2023/7peo_13355_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7peo_13355/02_2023/7peo_13355_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7peo_13355/02_2023/7peo_13355_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7peo_13355/02_2023/7peo_13355.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7peo_13355/02_2023/7peo_13355.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7peo_13355/02_2023/7peo_13355_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7peo_13355/02_2023/7peo_13355_updated.pdb" } resolution = 4.37 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 79": "OD1" <-> "OD2" Residue "A PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 90": "OD1" <-> "OD2" Residue "A TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 165": "NH1" <-> "NH2" Residue "A ARG 177": "NH1" <-> "NH2" Residue "C TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 79": "OD1" <-> "OD2" Residue "C PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 90": "OD1" <-> "OD2" Residue "C TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 165": "NH1" <-> "NH2" Residue "C ARG 177": "NH1" <-> "NH2" Residue "E TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 79": "OD1" <-> "OD2" Residue "E PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 90": "OD1" <-> "OD2" Residue "E TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 165": "NH1" <-> "NH2" Residue "E ARG 177": "NH1" <-> "NH2" Residue "G TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 79": "OD1" <-> "OD2" Residue "G PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 90": "OD1" <-> "OD2" Residue "G TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 165": "NH1" <-> "NH2" Residue "G ARG 177": "NH1" <-> "NH2" Residue "I TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 79": "OD1" <-> "OD2" Residue "I PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 90": "OD1" <-> "OD2" Residue "I TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 165": "NH1" <-> "NH2" Residue "I ARG 177": "NH1" <-> "NH2" Residue "K TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 79": "OD1" <-> "OD2" Residue "K PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 90": "OD1" <-> "OD2" Residue "K TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 165": "NH1" <-> "NH2" Residue "K ARG 177": "NH1" <-> "NH2" Residue "M TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 79": "OD1" <-> "OD2" Residue "M PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 90": "OD1" <-> "OD2" Residue "M TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 165": "NH1" <-> "NH2" Residue "M ARG 177": "NH1" <-> "NH2" Residue "O TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 79": "OD1" <-> "OD2" Residue "O PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 90": "OD1" <-> "OD2" Residue "O TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 165": "NH1" <-> "NH2" Residue "O ARG 177": "NH1" <-> "NH2" Residue "Q TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 79": "OD1" <-> "OD2" Residue "Q PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 90": "OD1" <-> "OD2" Residue "Q TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 165": "NH1" <-> "NH2" Residue "Q ARG 177": "NH1" <-> "NH2" Residue "S TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 79": "OD1" <-> "OD2" Residue "S PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 90": "OD1" <-> "OD2" Residue "S TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 165": "NH1" <-> "NH2" Residue "S ARG 177": "NH1" <-> "NH2" Residue "U TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 79": "OD1" <-> "OD2" Residue "U PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 90": "OD1" <-> "OD2" Residue "U TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 165": "NH1" <-> "NH2" Residue "U ARG 177": "NH1" <-> "NH2" Residue "W TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 79": "OD1" <-> "OD2" Residue "W PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 90": "OD1" <-> "OD2" Residue "W TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 165": "NH1" <-> "NH2" Residue "W ARG 177": "NH1" <-> "NH2" Residue "Y TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 79": "OD1" <-> "OD2" Residue "Y PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 90": "OD1" <-> "OD2" Residue "Y TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 165": "NH1" <-> "NH2" Residue "Y ARG 177": "NH1" <-> "NH2" Residue "0 TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 ASP 79": "OD1" <-> "OD2" Residue "0 PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 ASP 90": "OD1" <-> "OD2" Residue "0 TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 ARG 165": "NH1" <-> "NH2" Residue "0 ARG 177": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 26278 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1726 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 4, 'TRANS': 237} Chain: "B" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 148 Unusual residues: {'BMA': 4, 'MRH': 8} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 12 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' HO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1726 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 4, 'TRANS': 237} Chain: "D" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 148 Unusual residues: {'BMA': 4, 'MRH': 8} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 12 Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' HO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1726 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 4, 'TRANS': 237} Chain: "F" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 148 Unusual residues: {'BMA': 4, 'MRH': 8} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 12 Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' HO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1726 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 4, 'TRANS': 237} Chain: "H" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 148 Unusual residues: {'BMA': 4, 'MRH': 8} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 12 Chain: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' HO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1726 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 4, 'TRANS': 237} Chain: "J" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 148 Unusual residues: {'BMA': 4, 'MRH': 8} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 12 Chain: "I" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' HO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "K" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1726 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 4, 'TRANS': 237} Chain: "L" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 148 Unusual residues: {'BMA': 4, 'MRH': 8} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 12 Chain: "K" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' HO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "M" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1726 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 4, 'TRANS': 237} Chain: "N" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 148 Unusual residues: {'BMA': 4, 'MRH': 8} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 12 Chain: "M" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' HO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "O" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1726 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 4, 'TRANS': 237} Chain: "P" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 148 Unusual residues: {'BMA': 4, 'MRH': 8} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 12 Chain: "O" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' HO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Q" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1726 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 4, 'TRANS': 237} Chain: "R" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 148 Unusual residues: {'BMA': 4, 'MRH': 8} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 12 Chain: "Q" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' HO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "S" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1726 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 4, 'TRANS': 237} Chain: "T" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 148 Unusual residues: {'BMA': 4, 'MRH': 8} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 12 Chain: "S" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' HO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "U" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1726 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 4, 'TRANS': 237} Chain: "V" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 148 Unusual residues: {'BMA': 4, 'MRH': 8} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 12 Chain: "U" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' HO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "W" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1726 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 4, 'TRANS': 237} Chain: "X" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 148 Unusual residues: {'BMA': 4, 'MRH': 8} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 12 Chain: "W" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' HO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Y" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1726 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 4, 'TRANS': 237} Chain: "Z" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 148 Unusual residues: {'BMA': 4, 'MRH': 8} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 12 Chain: "Y" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' HO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "0" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1726 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 4, 'TRANS': 237} Chain: "1" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 148 Unusual residues: {'BMA': 4, 'MRH': 8} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 12 Chain: "0" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' HO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 14.14, per 1000 atoms: 0.54 Number of scatterers: 26278 At special positions: 0 Unit cell: (159.84, 159.84, 165.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ho 14 66.95 Ca 28 19.99 S 14 16.00 O 5712 8.00 N 4046 7.00 C 16464 6.00 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 Links applied ?1-3 " BMA 1 1 " - " MRH 1 2 " " MRH 1 2 " - " MRH 1 3 " " BMA 1 4 " - " MRH 1 5 " " MRH 1 5 " - " MRH 1 6 " " BMA 1 7 " - " MRH 1 8 " " MRH 1 8 " - " MRH 1 9 " " BMA 1 10 " - " MRH 1 11 " " MRH 1 11 " - " MRH 1 12 " " BMA B 1 " - " MRH B 2 " " MRH B 2 " - " MRH B 3 " " BMA B 4 " - " MRH B 5 " " MRH B 5 " - " MRH B 6 " " BMA B 7 " - " MRH B 8 " " MRH B 8 " - " MRH B 9 " " BMA B 10 " - " MRH B 11 " " MRH B 11 " - " MRH B 12 " " BMA D 1 " - " MRH D 2 " " MRH D 2 " - " MRH D 3 " " BMA D 4 " - " MRH D 5 " " MRH D 5 " - " MRH D 6 " " BMA D 7 " - " MRH D 8 " " MRH D 8 " - " MRH D 9 " " BMA D 10 " - " MRH D 11 " " MRH D 11 " - " MRH D 12 " " BMA F 1 " - " MRH F 2 " " MRH F 2 " - " MRH F 3 " " BMA F 4 " - " MRH F 5 " " MRH F 5 " - " MRH F 6 " " BMA F 7 " - " MRH F 8 " " MRH F 8 " - " MRH F 9 " " BMA F 10 " - " MRH F 11 " " MRH F 11 " - " MRH F 12 " " BMA H 1 " - " MRH H 2 " " MRH H 2 " - " MRH H 3 " " BMA H 4 " - " MRH H 5 " " MRH H 5 " - " MRH H 6 " " BMA H 7 " - " MRH H 8 " " MRH H 8 " - " MRH H 9 " " BMA H 10 " - " MRH H 11 " " MRH H 11 " - " MRH H 12 " " BMA J 1 " - " MRH J 2 " " MRH J 2 " - " MRH J 3 " " BMA J 4 " - " MRH J 5 " " MRH J 5 " - " MRH J 6 " " BMA J 7 " - " MRH J 8 " " MRH J 8 " - " MRH J 9 " " BMA J 10 " - " MRH J 11 " " MRH J 11 " - " MRH J 12 " " BMA L 1 " - " MRH L 2 " " MRH L 2 " - " MRH L 3 " " BMA L 4 " - " MRH L 5 " " MRH L 5 " - " MRH L 6 " " BMA L 7 " - " MRH L 8 " " MRH L 8 " - " MRH L 9 " " BMA L 10 " - " MRH L 11 " " MRH L 11 " - " MRH L 12 " " BMA N 1 " - " MRH N 2 " " MRH N 2 " - " MRH N 3 " " BMA N 4 " - " MRH N 5 " " MRH N 5 " - " MRH N 6 " " BMA N 7 " - " MRH N 8 " " MRH N 8 " - " MRH N 9 " " BMA N 10 " - " MRH N 11 " " MRH N 11 " - " MRH N 12 " " BMA P 1 " - " MRH P 2 " " MRH P 2 " - " MRH P 3 " " BMA P 4 " - " MRH P 5 " " MRH P 5 " - " MRH P 6 " " BMA P 7 " - " MRH P 8 " " MRH P 8 " - " MRH P 9 " " BMA P 10 " - " MRH P 11 " " MRH P 11 " - " MRH P 12 " " BMA R 1 " - " MRH R 2 " " MRH R 2 " - " MRH R 3 " " BMA R 4 " - " MRH R 5 " " MRH R 5 " - " MRH R 6 " " BMA R 7 " - " MRH R 8 " " MRH R 8 " - " MRH R 9 " " BMA R 10 " - " MRH R 11 " " MRH R 11 " - " MRH R 12 " " BMA T 1 " - " MRH T 2 " " MRH T 2 " - " MRH T 3 " " BMA T 4 " - " MRH T 5 " " MRH T 5 " - " MRH T 6 " " BMA T 7 " - " MRH T 8 " " MRH T 8 " - " MRH T 9 " " BMA T 10 " - " MRH T 11 " " MRH T 11 " - " MRH T 12 " " BMA V 1 " - " MRH V 2 " " MRH V 2 " - " MRH V 3 " " BMA V 4 " - " MRH V 5 " " MRH V 5 " - " MRH V 6 " " BMA V 7 " - " MRH V 8 " " MRH V 8 " - " MRH V 9 " " BMA V 10 " - " MRH V 11 " " MRH V 11 " - " MRH V 12 " " BMA X 1 " - " MRH X 2 " " MRH X 2 " - " MRH X 3 " " BMA X 4 " - " MRH X 5 " " MRH X 5 " - " MRH X 6 " " BMA X 7 " - " MRH X 8 " " MRH X 8 " - " MRH X 9 " " BMA X 10 " - " MRH X 11 " " MRH X 11 " - " MRH X 12 " " BMA Z 1 " - " MRH Z 2 " " MRH Z 2 " - " MRH Z 3 " " BMA Z 4 " - " MRH Z 5 " " MRH Z 5 " - " MRH Z 6 " " BMA Z 7 " - " MRH Z 8 " " MRH Z 8 " - " MRH Z 9 " " BMA Z 10 " - " MRH Z 11 " " MRH Z 11 " - " MRH Z 12 " BETA1-3 " MRH 1 3 " - " BMA 1 4 " " MRH 1 6 " - " BMA 1 7 " " MRH 1 9 " - " BMA 1 10 " " MRH B 3 " - " BMA B 4 " " MRH B 6 " - " BMA B 7 " " MRH B 9 " - " BMA B 10 " " MRH D 3 " - " BMA D 4 " " MRH D 6 " - " BMA D 7 " " MRH D 9 " - " BMA D 10 " " MRH F 3 " - " BMA F 4 " " MRH F 6 " - " BMA F 7 " " MRH F 9 " - " BMA F 10 " " MRH H 3 " - " BMA H 4 " " MRH H 6 " - " BMA H 7 " " MRH H 9 " - " BMA H 10 " " MRH J 3 " - " BMA J 4 " " MRH J 6 " - " BMA J 7 " " MRH J 9 " - " BMA J 10 " " MRH L 3 " - " BMA L 4 " " MRH L 6 " - " BMA L 7 " " MRH L 9 " - " BMA L 10 " " MRH N 3 " - " BMA N 4 " " MRH N 6 " - " BMA N 7 " " MRH N 9 " - " BMA N 10 " " MRH P 3 " - " BMA P 4 " " MRH P 6 " - " BMA P 7 " " MRH P 9 " - " BMA P 10 " " MRH R 3 " - " BMA R 4 " " MRH R 6 " - " BMA R 7 " " MRH R 9 " - " BMA R 10 " " MRH T 3 " - " BMA T 4 " " MRH T 6 " - " BMA T 7 " " MRH T 9 " - " BMA T 10 " " MRH V 3 " - " BMA V 4 " " MRH V 6 " - " BMA V 7 " " MRH V 9 " - " BMA V 10 " " MRH X 3 " - " BMA X 4 " " MRH X 6 " - " BMA X 7 " " MRH X 9 " - " BMA X 10 " " MRH Z 3 " - " BMA Z 4 " " MRH Z 6 " - " BMA Z 7 " " MRH Z 9 " - " BMA Z 10 " Time building additional restraints: 14.40 Conformation dependent library (CDL) restraints added in 3.9 seconds 6720 Ramachandran restraints generated. 3360 Oldfield, 0 Emsley, 3360 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6300 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 210 helices and 0 sheets defined 66.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.59 Creating SS restraints... Processing helix chain 'A' and resid 5 through 15 removed outlier: 3.566A pdb=" N VAL A 9 " --> pdb=" O THR A 5 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR A 10 " --> pdb=" O ALA A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 37 removed outlier: 3.515A pdb=" N LEU A 27 " --> pdb=" O ALA A 23 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR A 36 " --> pdb=" O TYR A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 54 removed outlier: 3.542A pdb=" N LEU A 53 " --> pdb=" O ASN A 49 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N VAL A 54 " --> pdb=" O THR A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 69 removed outlier: 3.551A pdb=" N THR A 64 " --> pdb=" O VAL A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 82 Processing helix chain 'A' and resid 94 through 96 No H-bonds generated for 'chain 'A' and resid 94 through 96' Processing helix chain 'A' and resid 101 through 114 Processing helix chain 'A' and resid 120 through 126 removed outlier: 3.525A pdb=" N ALA A 125 " --> pdb=" O THR A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 144 Processing helix chain 'A' and resid 147 through 152 Processing helix chain 'A' and resid 156 through 164 Processing helix chain 'A' and resid 166 through 179 Processing helix chain 'A' and resid 185 through 205 removed outlier: 3.560A pdb=" N ASP A 189 " --> pdb=" O ALA A 185 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS A 193 " --> pdb=" O ASP A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 222 Processing helix chain 'A' and resid 238 through 241 No H-bonds generated for 'chain 'A' and resid 238 through 241' Processing helix chain 'C' and resid 5 through 15 removed outlier: 3.566A pdb=" N VAL C 9 " --> pdb=" O THR C 5 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR C 10 " --> pdb=" O ALA C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 37 removed outlier: 3.516A pdb=" N LEU C 27 " --> pdb=" O ALA C 23 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR C 36 " --> pdb=" O TYR C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 54 removed outlier: 3.543A pdb=" N LEU C 53 " --> pdb=" O ASN C 49 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N VAL C 54 " --> pdb=" O THR C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 69 removed outlier: 3.551A pdb=" N THR C 64 " --> pdb=" O VAL C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 82 Processing helix chain 'C' and resid 94 through 96 No H-bonds generated for 'chain 'C' and resid 94 through 96' Processing helix chain 'C' and resid 101 through 114 Processing helix chain 'C' and resid 120 through 126 removed outlier: 3.525A pdb=" N ALA C 125 " --> pdb=" O THR C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 144 Processing helix chain 'C' and resid 147 through 152 Processing helix chain 'C' and resid 156 through 164 Processing helix chain 'C' and resid 166 through 179 Processing helix chain 'C' and resid 185 through 205 removed outlier: 3.559A pdb=" N ASP C 189 " --> pdb=" O ALA C 185 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS C 193 " --> pdb=" O ASP C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 222 Processing helix chain 'C' and resid 238 through 241 No H-bonds generated for 'chain 'C' and resid 238 through 241' Processing helix chain 'E' and resid 5 through 15 removed outlier: 3.566A pdb=" N VAL E 9 " --> pdb=" O THR E 5 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR E 10 " --> pdb=" O ALA E 6 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 37 removed outlier: 3.515A pdb=" N LEU E 27 " --> pdb=" O ALA E 23 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR E 36 " --> pdb=" O TYR E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 54 removed outlier: 3.543A pdb=" N LEU E 53 " --> pdb=" O ASN E 49 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N VAL E 54 " --> pdb=" O THR E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 69 removed outlier: 3.551A pdb=" N THR E 64 " --> pdb=" O VAL E 60 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 82 Processing helix chain 'E' and resid 94 through 96 No H-bonds generated for 'chain 'E' and resid 94 through 96' Processing helix chain 'E' and resid 101 through 114 Processing helix chain 'E' and resid 120 through 126 removed outlier: 3.525A pdb=" N ALA E 125 " --> pdb=" O THR E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 144 Processing helix chain 'E' and resid 147 through 152 Processing helix chain 'E' and resid 156 through 164 Processing helix chain 'E' and resid 166 through 179 Processing helix chain 'E' and resid 185 through 205 removed outlier: 3.560A pdb=" N ASP E 189 " --> pdb=" O ALA E 185 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS E 193 " --> pdb=" O ASP E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 211 through 222 Processing helix chain 'E' and resid 238 through 241 No H-bonds generated for 'chain 'E' and resid 238 through 241' Processing helix chain 'G' and resid 5 through 15 removed outlier: 3.566A pdb=" N VAL G 9 " --> pdb=" O THR G 5 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR G 10 " --> pdb=" O ALA G 6 " (cutoff:3.500A) Processing helix chain 'G' and resid 23 through 37 removed outlier: 3.515A pdb=" N LEU G 27 " --> pdb=" O ALA G 23 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR G 36 " --> pdb=" O TYR G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 43 through 54 removed outlier: 3.542A pdb=" N LEU G 53 " --> pdb=" O ASN G 49 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N VAL G 54 " --> pdb=" O THR G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 69 removed outlier: 3.551A pdb=" N THR G 64 " --> pdb=" O VAL G 60 " (cutoff:3.500A) Processing helix chain 'G' and resid 75 through 82 Processing helix chain 'G' and resid 94 through 96 No H-bonds generated for 'chain 'G' and resid 94 through 96' Processing helix chain 'G' and resid 101 through 114 Processing helix chain 'G' and resid 120 through 126 removed outlier: 3.524A pdb=" N ALA G 125 " --> pdb=" O THR G 121 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 144 Processing helix chain 'G' and resid 147 through 152 Processing helix chain 'G' and resid 156 through 164 Processing helix chain 'G' and resid 166 through 179 Processing helix chain 'G' and resid 185 through 205 removed outlier: 3.560A pdb=" N ASP G 189 " --> pdb=" O ALA G 185 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS G 193 " --> pdb=" O ASP G 189 " (cutoff:3.500A) Processing helix chain 'G' and resid 211 through 222 Processing helix chain 'G' and resid 238 through 241 No H-bonds generated for 'chain 'G' and resid 238 through 241' Processing helix chain 'I' and resid 5 through 15 removed outlier: 3.566A pdb=" N VAL I 9 " --> pdb=" O THR I 5 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N THR I 10 " --> pdb=" O ALA I 6 " (cutoff:3.500A) Processing helix chain 'I' and resid 23 through 37 removed outlier: 3.515A pdb=" N LEU I 27 " --> pdb=" O ALA I 23 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR I 36 " --> pdb=" O TYR I 32 " (cutoff:3.500A) Processing helix chain 'I' and resid 43 through 54 removed outlier: 3.542A pdb=" N LEU I 53 " --> pdb=" O ASN I 49 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N VAL I 54 " --> pdb=" O THR I 50 " (cutoff:3.500A) Processing helix chain 'I' and resid 59 through 69 removed outlier: 3.551A pdb=" N THR I 64 " --> pdb=" O VAL I 60 " (cutoff:3.500A) Processing helix chain 'I' and resid 75 through 82 Processing helix chain 'I' and resid 94 through 96 No H-bonds generated for 'chain 'I' and resid 94 through 96' Processing helix chain 'I' and resid 101 through 114 Processing helix chain 'I' and resid 120 through 126 removed outlier: 3.524A pdb=" N ALA I 125 " --> pdb=" O THR I 121 " (cutoff:3.500A) Processing helix chain 'I' and resid 132 through 144 Processing helix chain 'I' and resid 147 through 152 Processing helix chain 'I' and resid 156 through 164 Processing helix chain 'I' and resid 166 through 179 Processing helix chain 'I' and resid 185 through 205 removed outlier: 3.559A pdb=" N ASP I 189 " --> pdb=" O ALA I 185 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS I 193 " --> pdb=" O ASP I 189 " (cutoff:3.500A) Processing helix chain 'I' and resid 211 through 222 Processing helix chain 'I' and resid 238 through 241 No H-bonds generated for 'chain 'I' and resid 238 through 241' Processing helix chain 'K' and resid 5 through 15 removed outlier: 3.567A pdb=" N VAL K 9 " --> pdb=" O THR K 5 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N THR K 10 " --> pdb=" O ALA K 6 " (cutoff:3.500A) Processing helix chain 'K' and resid 23 through 37 removed outlier: 3.516A pdb=" N LEU K 27 " --> pdb=" O ALA K 23 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR K 36 " --> pdb=" O TYR K 32 " (cutoff:3.500A) Processing helix chain 'K' and resid 43 through 54 removed outlier: 3.542A pdb=" N LEU K 53 " --> pdb=" O ASN K 49 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N VAL K 54 " --> pdb=" O THR K 50 " (cutoff:3.500A) Processing helix chain 'K' and resid 59 through 69 removed outlier: 3.551A pdb=" N THR K 64 " --> pdb=" O VAL K 60 " (cutoff:3.500A) Processing helix chain 'K' and resid 75 through 82 Processing helix chain 'K' and resid 94 through 96 No H-bonds generated for 'chain 'K' and resid 94 through 96' Processing helix chain 'K' and resid 101 through 114 Processing helix chain 'K' and resid 120 through 126 removed outlier: 3.525A pdb=" N ALA K 125 " --> pdb=" O THR K 121 " (cutoff:3.500A) Processing helix chain 'K' and resid 132 through 144 Processing helix chain 'K' and resid 147 through 152 Processing helix chain 'K' and resid 156 through 164 Processing helix chain 'K' and resid 166 through 179 Processing helix chain 'K' and resid 185 through 205 removed outlier: 3.560A pdb=" N ASP K 189 " --> pdb=" O ALA K 185 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS K 193 " --> pdb=" O ASP K 189 " (cutoff:3.500A) Processing helix chain 'K' and resid 211 through 222 Processing helix chain 'K' and resid 238 through 241 No H-bonds generated for 'chain 'K' and resid 238 through 241' Processing helix chain 'M' and resid 5 through 15 removed outlier: 3.566A pdb=" N VAL M 9 " --> pdb=" O THR M 5 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR M 10 " --> pdb=" O ALA M 6 " (cutoff:3.500A) Processing helix chain 'M' and resid 23 through 37 removed outlier: 3.516A pdb=" N LEU M 27 " --> pdb=" O ALA M 23 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR M 36 " --> pdb=" O TYR M 32 " (cutoff:3.500A) Processing helix chain 'M' and resid 43 through 54 removed outlier: 3.543A pdb=" N LEU M 53 " --> pdb=" O ASN M 49 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N VAL M 54 " --> pdb=" O THR M 50 " (cutoff:3.500A) Processing helix chain 'M' and resid 59 through 69 removed outlier: 3.551A pdb=" N THR M 64 " --> pdb=" O VAL M 60 " (cutoff:3.500A) Processing helix chain 'M' and resid 75 through 82 Processing helix chain 'M' and resid 94 through 96 No H-bonds generated for 'chain 'M' and resid 94 through 96' Processing helix chain 'M' and resid 101 through 114 Processing helix chain 'M' and resid 120 through 126 removed outlier: 3.525A pdb=" N ALA M 125 " --> pdb=" O THR M 121 " (cutoff:3.500A) Processing helix chain 'M' and resid 132 through 144 Processing helix chain 'M' and resid 147 through 152 Processing helix chain 'M' and resid 156 through 164 Processing helix chain 'M' and resid 166 through 179 Processing helix chain 'M' and resid 185 through 205 removed outlier: 3.559A pdb=" N ASP M 189 " --> pdb=" O ALA M 185 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS M 193 " --> pdb=" O ASP M 189 " (cutoff:3.500A) Processing helix chain 'M' and resid 211 through 222 Processing helix chain 'M' and resid 238 through 241 No H-bonds generated for 'chain 'M' and resid 238 through 241' Processing helix chain 'O' and resid 5 through 15 removed outlier: 3.566A pdb=" N VAL O 9 " --> pdb=" O THR O 5 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR O 10 " --> pdb=" O ALA O 6 " (cutoff:3.500A) Processing helix chain 'O' and resid 23 through 37 removed outlier: 3.515A pdb=" N LEU O 27 " --> pdb=" O ALA O 23 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR O 36 " --> pdb=" O TYR O 32 " (cutoff:3.500A) Processing helix chain 'O' and resid 43 through 54 removed outlier: 3.542A pdb=" N LEU O 53 " --> pdb=" O ASN O 49 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N VAL O 54 " --> pdb=" O THR O 50 " (cutoff:3.500A) Processing helix chain 'O' and resid 59 through 69 removed outlier: 3.551A pdb=" N THR O 64 " --> pdb=" O VAL O 60 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 82 Processing helix chain 'O' and resid 94 through 96 No H-bonds generated for 'chain 'O' and resid 94 through 96' Processing helix chain 'O' and resid 101 through 114 Processing helix chain 'O' and resid 120 through 126 removed outlier: 3.524A pdb=" N ALA O 125 " --> pdb=" O THR O 121 " (cutoff:3.500A) Processing helix chain 'O' and resid 132 through 144 Processing helix chain 'O' and resid 147 through 152 Processing helix chain 'O' and resid 156 through 164 Processing helix chain 'O' and resid 166 through 179 Processing helix chain 'O' and resid 185 through 205 removed outlier: 3.559A pdb=" N ASP O 189 " --> pdb=" O ALA O 185 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS O 193 " --> pdb=" O ASP O 189 " (cutoff:3.500A) Processing helix chain 'O' and resid 211 through 222 Processing helix chain 'O' and resid 238 through 241 No H-bonds generated for 'chain 'O' and resid 238 through 241' Processing helix chain 'Q' and resid 5 through 15 removed outlier: 3.565A pdb=" N VAL Q 9 " --> pdb=" O THR Q 5 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N THR Q 10 " --> pdb=" O ALA Q 6 " (cutoff:3.500A) Processing helix chain 'Q' and resid 23 through 37 removed outlier: 3.516A pdb=" N LEU Q 27 " --> pdb=" O ALA Q 23 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR Q 36 " --> pdb=" O TYR Q 32 " (cutoff:3.500A) Processing helix chain 'Q' and resid 43 through 54 removed outlier: 3.543A pdb=" N LEU Q 53 " --> pdb=" O ASN Q 49 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N VAL Q 54 " --> pdb=" O THR Q 50 " (cutoff:3.500A) Processing helix chain 'Q' and resid 59 through 69 removed outlier: 3.551A pdb=" N THR Q 64 " --> pdb=" O VAL Q 60 " (cutoff:3.500A) Processing helix chain 'Q' and resid 75 through 82 Processing helix chain 'Q' and resid 94 through 96 No H-bonds generated for 'chain 'Q' and resid 94 through 96' Processing helix chain 'Q' and resid 101 through 114 Processing helix chain 'Q' and resid 120 through 126 removed outlier: 3.525A pdb=" N ALA Q 125 " --> pdb=" O THR Q 121 " (cutoff:3.500A) Processing helix chain 'Q' and resid 132 through 144 Processing helix chain 'Q' and resid 147 through 152 Processing helix chain 'Q' and resid 156 through 164 Processing helix chain 'Q' and resid 166 through 179 Processing helix chain 'Q' and resid 185 through 205 removed outlier: 3.559A pdb=" N ASP Q 189 " --> pdb=" O ALA Q 185 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS Q 193 " --> pdb=" O ASP Q 189 " (cutoff:3.500A) Processing helix chain 'Q' and resid 211 through 222 Processing helix chain 'Q' and resid 238 through 241 No H-bonds generated for 'chain 'Q' and resid 238 through 241' Processing helix chain 'S' and resid 5 through 15 removed outlier: 3.566A pdb=" N VAL S 9 " --> pdb=" O THR S 5 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N THR S 10 " --> pdb=" O ALA S 6 " (cutoff:3.500A) Processing helix chain 'S' and resid 23 through 37 removed outlier: 3.515A pdb=" N LEU S 27 " --> pdb=" O ALA S 23 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR S 36 " --> pdb=" O TYR S 32 " (cutoff:3.500A) Processing helix chain 'S' and resid 43 through 54 removed outlier: 3.542A pdb=" N LEU S 53 " --> pdb=" O ASN S 49 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N VAL S 54 " --> pdb=" O THR S 50 " (cutoff:3.500A) Processing helix chain 'S' and resid 59 through 69 removed outlier: 3.550A pdb=" N THR S 64 " --> pdb=" O VAL S 60 " (cutoff:3.500A) Processing helix chain 'S' and resid 75 through 82 Processing helix chain 'S' and resid 94 through 96 No H-bonds generated for 'chain 'S' and resid 94 through 96' Processing helix chain 'S' and resid 101 through 114 Processing helix chain 'S' and resid 120 through 126 removed outlier: 3.525A pdb=" N ALA S 125 " --> pdb=" O THR S 121 " (cutoff:3.500A) Processing helix chain 'S' and resid 132 through 144 Processing helix chain 'S' and resid 147 through 152 Processing helix chain 'S' and resid 156 through 164 Processing helix chain 'S' and resid 166 through 179 Processing helix chain 'S' and resid 185 through 205 removed outlier: 3.560A pdb=" N ASP S 189 " --> pdb=" O ALA S 185 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS S 193 " --> pdb=" O ASP S 189 " (cutoff:3.500A) Processing helix chain 'S' and resid 211 through 222 Processing helix chain 'S' and resid 238 through 241 No H-bonds generated for 'chain 'S' and resid 238 through 241' Processing helix chain 'U' and resid 5 through 15 removed outlier: 3.566A pdb=" N VAL U 9 " --> pdb=" O THR U 5 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR U 10 " --> pdb=" O ALA U 6 " (cutoff:3.500A) Processing helix chain 'U' and resid 23 through 37 removed outlier: 3.516A pdb=" N LEU U 27 " --> pdb=" O ALA U 23 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR U 36 " --> pdb=" O TYR U 32 " (cutoff:3.500A) Processing helix chain 'U' and resid 43 through 54 removed outlier: 3.542A pdb=" N LEU U 53 " --> pdb=" O ASN U 49 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N VAL U 54 " --> pdb=" O THR U 50 " (cutoff:3.500A) Processing helix chain 'U' and resid 59 through 69 removed outlier: 3.551A pdb=" N THR U 64 " --> pdb=" O VAL U 60 " (cutoff:3.500A) Processing helix chain 'U' and resid 75 through 82 Processing helix chain 'U' and resid 94 through 96 No H-bonds generated for 'chain 'U' and resid 94 through 96' Processing helix chain 'U' and resid 101 through 114 Processing helix chain 'U' and resid 120 through 126 removed outlier: 3.525A pdb=" N ALA U 125 " --> pdb=" O THR U 121 " (cutoff:3.500A) Processing helix chain 'U' and resid 132 through 144 Processing helix chain 'U' and resid 147 through 152 Processing helix chain 'U' and resid 156 through 164 Processing helix chain 'U' and resid 166 through 179 Processing helix chain 'U' and resid 185 through 205 removed outlier: 3.559A pdb=" N ASP U 189 " --> pdb=" O ALA U 185 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS U 193 " --> pdb=" O ASP U 189 " (cutoff:3.500A) Processing helix chain 'U' and resid 211 through 222 Processing helix chain 'U' and resid 238 through 241 No H-bonds generated for 'chain 'U' and resid 238 through 241' Processing helix chain 'W' and resid 5 through 15 removed outlier: 3.566A pdb=" N VAL W 9 " --> pdb=" O THR W 5 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR W 10 " --> pdb=" O ALA W 6 " (cutoff:3.500A) Processing helix chain 'W' and resid 23 through 37 removed outlier: 3.516A pdb=" N LEU W 27 " --> pdb=" O ALA W 23 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR W 36 " --> pdb=" O TYR W 32 " (cutoff:3.500A) Processing helix chain 'W' and resid 43 through 54 removed outlier: 3.542A pdb=" N LEU W 53 " --> pdb=" O ASN W 49 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N VAL W 54 " --> pdb=" O THR W 50 " (cutoff:3.500A) Processing helix chain 'W' and resid 59 through 69 removed outlier: 3.551A pdb=" N THR W 64 " --> pdb=" O VAL W 60 " (cutoff:3.500A) Processing helix chain 'W' and resid 75 through 82 Processing helix chain 'W' and resid 94 through 96 No H-bonds generated for 'chain 'W' and resid 94 through 96' Processing helix chain 'W' and resid 101 through 114 Processing helix chain 'W' and resid 120 through 126 removed outlier: 3.525A pdb=" N ALA W 125 " --> pdb=" O THR W 121 " (cutoff:3.500A) Processing helix chain 'W' and resid 132 through 144 Processing helix chain 'W' and resid 147 through 152 Processing helix chain 'W' and resid 156 through 164 Processing helix chain 'W' and resid 166 through 179 Processing helix chain 'W' and resid 185 through 205 removed outlier: 3.559A pdb=" N ASP W 189 " --> pdb=" O ALA W 185 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS W 193 " --> pdb=" O ASP W 189 " (cutoff:3.500A) Processing helix chain 'W' and resid 211 through 222 Processing helix chain 'W' and resid 238 through 241 No H-bonds generated for 'chain 'W' and resid 238 through 241' Processing helix chain 'Y' and resid 5 through 15 removed outlier: 3.566A pdb=" N VAL Y 9 " --> pdb=" O THR Y 5 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR Y 10 " --> pdb=" O ALA Y 6 " (cutoff:3.500A) Processing helix chain 'Y' and resid 23 through 37 removed outlier: 3.515A pdb=" N LEU Y 27 " --> pdb=" O ALA Y 23 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR Y 36 " --> pdb=" O TYR Y 32 " (cutoff:3.500A) Processing helix chain 'Y' and resid 43 through 54 removed outlier: 3.542A pdb=" N LEU Y 53 " --> pdb=" O ASN Y 49 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N VAL Y 54 " --> pdb=" O THR Y 50 " (cutoff:3.500A) Processing helix chain 'Y' and resid 59 through 69 removed outlier: 3.551A pdb=" N THR Y 64 " --> pdb=" O VAL Y 60 " (cutoff:3.500A) Processing helix chain 'Y' and resid 75 through 82 Processing helix chain 'Y' and resid 94 through 96 No H-bonds generated for 'chain 'Y' and resid 94 through 96' Processing helix chain 'Y' and resid 101 through 114 Processing helix chain 'Y' and resid 120 through 126 removed outlier: 3.525A pdb=" N ALA Y 125 " --> pdb=" O THR Y 121 " (cutoff:3.500A) Processing helix chain 'Y' and resid 132 through 144 Processing helix chain 'Y' and resid 147 through 152 Processing helix chain 'Y' and resid 156 through 164 Processing helix chain 'Y' and resid 166 through 179 Processing helix chain 'Y' and resid 185 through 205 removed outlier: 3.560A pdb=" N ASP Y 189 " --> pdb=" O ALA Y 185 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS Y 193 " --> pdb=" O ASP Y 189 " (cutoff:3.500A) Processing helix chain 'Y' and resid 211 through 222 Processing helix chain 'Y' and resid 238 through 241 No H-bonds generated for 'chain 'Y' and resid 238 through 241' Processing helix chain '0' and resid 5 through 15 removed outlier: 3.566A pdb=" N VAL 0 9 " --> pdb=" O THR 0 5 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR 0 10 " --> pdb=" O ALA 0 6 " (cutoff:3.500A) Processing helix chain '0' and resid 23 through 37 removed outlier: 3.515A pdb=" N LEU 0 27 " --> pdb=" O ALA 0 23 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR 0 36 " --> pdb=" O TYR 0 32 " (cutoff:3.500A) Processing helix chain '0' and resid 43 through 54 removed outlier: 3.542A pdb=" N LEU 0 53 " --> pdb=" O ASN 0 49 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N VAL 0 54 " --> pdb=" O THR 0 50 " (cutoff:3.500A) Processing helix chain '0' and resid 59 through 69 removed outlier: 3.551A pdb=" N THR 0 64 " --> pdb=" O VAL 0 60 " (cutoff:3.500A) Processing helix chain '0' and resid 75 through 82 Processing helix chain '0' and resid 94 through 96 No H-bonds generated for 'chain '0' and resid 94 through 96' Processing helix chain '0' and resid 101 through 114 Processing helix chain '0' and resid 120 through 126 removed outlier: 3.524A pdb=" N ALA 0 125 " --> pdb=" O THR 0 121 " (cutoff:3.500A) Processing helix chain '0' and resid 132 through 144 Processing helix chain '0' and resid 147 through 152 Processing helix chain '0' and resid 156 through 164 Processing helix chain '0' and resid 166 through 179 Processing helix chain '0' and resid 185 through 205 removed outlier: 3.560A pdb=" N ASP 0 189 " --> pdb=" O ALA 0 185 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS 0 193 " --> pdb=" O ASP 0 189 " (cutoff:3.500A) Processing helix chain '0' and resid 211 through 222 Processing helix chain '0' and resid 238 through 241 No H-bonds generated for 'chain '0' and resid 238 through 241' 1274 hydrogen bonds defined for protein. 3822 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: 7.62 Time building geometry restraints manager: 15.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6930 1.34 - 1.46: 7670 1.46 - 1.57: 11972 1.57 - 1.69: 0 1.69 - 1.81: 28 Bond restraints: 26600 Sorted by residual: bond pdb=" C7 MRH X 8 " pdb=" N4 MRH X 8 " ideal model delta sigma weight residual 1.461 1.331 0.130 2.00e-02 2.50e+03 4.23e+01 bond pdb=" C7 MRH J 8 " pdb=" N4 MRH J 8 " ideal model delta sigma weight residual 1.461 1.331 0.130 2.00e-02 2.50e+03 4.23e+01 bond pdb=" C7 MRH F 8 " pdb=" N4 MRH F 8 " ideal model delta sigma weight residual 1.461 1.331 0.130 2.00e-02 2.50e+03 4.22e+01 bond pdb=" C7 MRH L 8 " pdb=" N4 MRH L 8 " ideal model delta sigma weight residual 1.461 1.331 0.130 2.00e-02 2.50e+03 4.21e+01 bond pdb=" C7 MRH B 8 " pdb=" N4 MRH B 8 " ideal model delta sigma weight residual 1.461 1.331 0.130 2.00e-02 2.50e+03 4.21e+01 ... (remaining 26595 not shown) Histogram of bond angle deviations from ideal: 99.89 - 105.38: 237 105.38 - 110.86: 6853 110.86 - 116.34: 12164 116.34 - 121.82: 10222 121.82 - 127.31: 7078 Bond angle restraints: 36554 Sorted by residual: angle pdb=" CA ASP G 93 " pdb=" CB ASP G 93 " pdb=" CG ASP G 93 " ideal model delta sigma weight residual 112.60 118.04 -5.44 1.00e+00 1.00e+00 2.96e+01 angle pdb=" CA ASP U 93 " pdb=" CB ASP U 93 " pdb=" CG ASP U 93 " ideal model delta sigma weight residual 112.60 118.03 -5.43 1.00e+00 1.00e+00 2.95e+01 angle pdb=" CA ASP M 93 " pdb=" CB ASP M 93 " pdb=" CG ASP M 93 " ideal model delta sigma weight residual 112.60 118.02 -5.42 1.00e+00 1.00e+00 2.93e+01 angle pdb=" CA ASP K 93 " pdb=" CB ASP K 93 " pdb=" CG ASP K 93 " ideal model delta sigma weight residual 112.60 118.01 -5.41 1.00e+00 1.00e+00 2.93e+01 angle pdb=" CA ASP 0 93 " pdb=" CB ASP 0 93 " pdb=" CG ASP 0 93 " ideal model delta sigma weight residual 112.60 118.01 -5.41 1.00e+00 1.00e+00 2.92e+01 ... (remaining 36549 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.46: 13276 17.46 - 34.92: 1088 34.92 - 52.37: 280 52.37 - 69.83: 42 69.83 - 87.29: 42 Dihedral angle restraints: 14728 sinusoidal: 4886 harmonic: 9842 Sorted by residual: dihedral pdb=" CA ASP W 93 " pdb=" C ASP W 93 " pdb=" N ALA W 94 " pdb=" CA ALA W 94 " ideal model delta harmonic sigma weight residual 180.00 -160.10 -19.90 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA ASP K 93 " pdb=" C ASP K 93 " pdb=" N ALA K 94 " pdb=" CA ALA K 94 " ideal model delta harmonic sigma weight residual 180.00 -160.11 -19.89 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA ASP U 93 " pdb=" C ASP U 93 " pdb=" N ALA U 94 " pdb=" CA ALA U 94 " ideal model delta harmonic sigma weight residual -180.00 -160.11 -19.89 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 14725 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.164: 4238 0.164 - 0.327: 681 0.327 - 0.491: 18 0.491 - 0.655: 19 0.655 - 0.818: 28 Chirality restraints: 4984 Sorted by residual: chirality pdb=" C1 BMA D 4 " pdb=" O3 MRH D 3 " pdb=" C2 BMA D 4 " pdb=" O5 BMA D 4 " both_signs ideal model delta sigma weight residual False -2.40 -1.58 -0.82 2.00e-02 2.50e+03 1.67e+03 chirality pdb=" C1 BMA F 4 " pdb=" O3 MRH F 3 " pdb=" C2 BMA F 4 " pdb=" O5 BMA F 4 " both_signs ideal model delta sigma weight residual False -2.40 -1.58 -0.82 2.00e-02 2.50e+03 1.67e+03 chirality pdb=" C1 BMA B 4 " pdb=" O3 MRH B 3 " pdb=" C2 BMA B 4 " pdb=" O5 BMA B 4 " both_signs ideal model delta sigma weight residual False -2.40 -1.58 -0.82 2.00e-02 2.50e+03 1.66e+03 ... (remaining 4981 not shown) Planarity restraints: 4480 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C4 MRH V 12 " -0.268 2.00e-02 2.50e+03 2.34e-01 6.86e+02 pdb=" C7 MRH V 12 " 0.040 2.00e-02 2.50e+03 pdb=" C8 MRH V 12 " -0.002 2.00e-02 2.50e+03 pdb=" N4 MRH V 12 " 0.411 2.00e-02 2.50e+03 pdb=" O7 MRH V 12 " -0.180 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C4 MRH F 12 " -0.268 2.00e-02 2.50e+03 2.34e-01 6.86e+02 pdb=" C7 MRH F 12 " 0.040 2.00e-02 2.50e+03 pdb=" C8 MRH F 12 " -0.002 2.00e-02 2.50e+03 pdb=" N4 MRH F 12 " 0.411 2.00e-02 2.50e+03 pdb=" O7 MRH F 12 " -0.180 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C4 MRH N 12 " -0.268 2.00e-02 2.50e+03 2.34e-01 6.86e+02 pdb=" C7 MRH N 12 " 0.040 2.00e-02 2.50e+03 pdb=" C8 MRH N 12 " -0.002 2.00e-02 2.50e+03 pdb=" N4 MRH N 12 " 0.411 2.00e-02 2.50e+03 pdb=" O7 MRH N 12 " -0.180 2.00e-02 2.50e+03 ... (remaining 4477 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 1506 2.74 - 3.28: 28251 3.28 - 3.82: 42822 3.82 - 4.36: 51580 4.36 - 4.90: 84983 Nonbonded interactions: 209142 Sorted by model distance: nonbonded pdb=" O ALA W 124 " pdb=" OG1 THR W 128 " model vdw 2.206 2.440 nonbonded pdb=" O ALA S 124 " pdb=" OG1 THR S 128 " model vdw 2.206 2.440 nonbonded pdb=" O ALA 0 124 " pdb=" OG1 THR 0 128 " model vdw 2.206 2.440 nonbonded pdb=" O ALA I 124 " pdb=" OG1 THR I 128 " model vdw 2.206 2.440 nonbonded pdb=" O ALA K 124 " pdb=" OG1 THR K 128 " model vdw 2.206 2.440 ... (remaining 209137 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 '0' selection = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'W' selection = chain 'Y' } ncs_group { reference = chain '1' selection = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'X' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ho 14 14.37 5 Ca 28 9.91 5 S 14 5.16 5 C 16464 2.51 5 N 4046 2.21 5 O 5712 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 7.870 Check model and map are aligned: 0.390 Process input model: 67.680 Find NCS groups from input model: 1.820 Set up NCS constraints: 0.260 Set refine NCS operators: 0.000 Set scattering table: 0.200 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 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 : 0.015 0.130 26600 Z= 0.972 Angle : 1.721 10.029 36554 Z= 1.093 Chirality : 0.131 0.818 4984 Planarity : 0.018 0.234 4480 Dihedral : 14.961 87.291 8428 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer Outliers : 0.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.12), residues: 3360 helix: -1.38 (0.09), residues: 2394 sheet: None (None), residues: 0 loop : -2.02 (0.17), residues: 966 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6720 Ramachandran restraints generated. 3360 Oldfield, 0 Emsley, 3360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6720 Ramachandran restraints generated. 3360 Oldfield, 0 Emsley, 3360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 329 time to evaluate : 2.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 0 residues processed: 343 average time/residue: 0.4578 time to fit residues: 232.0920 Evaluate side-chains 122 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 2.787 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.3898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 283 optimal weight: 0.9980 chunk 254 optimal weight: 5.9990 chunk 141 optimal weight: 6.9990 chunk 86 optimal weight: 6.9990 chunk 171 optimal weight: 2.9990 chunk 136 optimal weight: 5.9990 chunk 263 optimal weight: 6.9990 chunk 101 optimal weight: 9.9990 chunk 160 optimal weight: 10.0000 chunk 196 optimal weight: 6.9990 chunk 305 optimal weight: 5.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 ASN A 63 GLN ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 111 ASN A 237 ASN C 49 ASN ** C 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 ASN C 179 ASN C 237 ASN E 49 ASN ** E 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 111 ASN E 134 GLN E 179 ASN E 237 ASN G 49 ASN G 63 GLN G 111 ASN G 134 GLN G 179 ASN G 237 ASN I 49 ASN ** I 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 107 ASN I 111 ASN I 134 GLN I 237 ASN K 49 ASN ** K 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 111 ASN K 134 GLN K 179 ASN K 237 ASN M 49 ASN M 63 GLN ** M 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 111 ASN M 134 GLN M 237 ASN O 49 ASN ** O 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 111 ASN O 134 GLN O 237 ASN Q 49 ASN Q 63 GLN ** Q 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 111 ASN Q 134 GLN Q 237 ASN S 49 ASN S 63 GLN ** S 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 111 ASN S 134 GLN S 237 ASN U 49 ASN ** U 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 111 ASN U 179 ASN U 237 ASN W 49 ASN ** W 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 111 ASN ** W 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 179 ASN W 237 ASN Y 49 ASN Y 63 GLN ** Y 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 107 ASN Y 111 ASN Y 134 GLN Y 179 ASN Y 237 ASN 0 49 ASN 0 63 GLN ** 0 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 107 ASN 0 111 ASN 0 134 GLN 0 179 ASN 0 237 ASN Total number of N/Q/H flips: 70 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 26600 Z= 0.274 Angle : 0.731 9.009 36554 Z= 0.359 Chirality : 0.041 0.248 4984 Planarity : 0.004 0.055 4480 Dihedral : 7.417 56.765 4144 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.14), residues: 3360 helix: 0.32 (0.10), residues: 2436 sheet: None (None), residues: 0 loop : -1.16 (0.19), residues: 924 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6720 Ramachandran restraints generated. 3360 Oldfield, 0 Emsley, 3360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6720 Ramachandran restraints generated. 3360 Oldfield, 0 Emsley, 3360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 179 time to evaluate : 2.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 180 average time/residue: 0.4851 time to fit residues: 128.9121 Evaluate side-chains 84 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 83 time to evaluate : 2.499 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2103 time to fit residues: 3.4958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 169 optimal weight: 0.8980 chunk 94 optimal weight: 7.9990 chunk 253 optimal weight: 4.9990 chunk 207 optimal weight: 0.9980 chunk 84 optimal weight: 10.0000 chunk 305 optimal weight: 8.9990 chunk 330 optimal weight: 0.0040 chunk 272 optimal weight: 2.9990 chunk 303 optimal weight: 4.9990 chunk 104 optimal weight: 9.9990 chunk 245 optimal weight: 0.4980 overall best weight: 1.0794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 ASN ** E 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 ASN G 107 ASN ** G 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 63 GLN ** M 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.3460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 26600 Z= 0.146 Angle : 0.501 7.852 36554 Z= 0.257 Chirality : 0.034 0.200 4984 Planarity : 0.002 0.030 4480 Dihedral : 6.785 59.213 4144 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.15), residues: 3360 helix: 1.26 (0.11), residues: 2408 sheet: None (None), residues: 0 loop : -0.93 (0.21), residues: 952 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6720 Ramachandran restraints generated. 3360 Oldfield, 0 Emsley, 3360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6720 Ramachandran restraints generated. 3360 Oldfield, 0 Emsley, 3360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 2.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 143 average time/residue: 0.4902 time to fit residues: 103.6004 Evaluate side-chains 79 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 2.480 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 302 optimal weight: 9.9990 chunk 229 optimal weight: 20.0000 chunk 158 optimal weight: 20.0000 chunk 33 optimal weight: 10.0000 chunk 145 optimal weight: 1.9990 chunk 205 optimal weight: 10.0000 chunk 306 optimal weight: 2.9990 chunk 324 optimal weight: 9.9990 chunk 160 optimal weight: 10.0000 chunk 290 optimal weight: 5.9990 chunk 87 optimal weight: 0.6980 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 ASN E 107 ASN G 107 ASN G 179 ASN ** I 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 237 ASN ** U 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 107 ASN 0 107 ASN ** 0 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.4262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 26600 Z= 0.244 Angle : 0.602 8.019 36554 Z= 0.304 Chirality : 0.036 0.194 4984 Planarity : 0.003 0.041 4480 Dihedral : 6.378 59.331 4144 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.15), residues: 3360 helix: 1.61 (0.11), residues: 2394 sheet: None (None), residues: 0 loop : -0.90 (0.20), residues: 966 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6720 Ramachandran restraints generated. 3360 Oldfield, 0 Emsley, 3360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6720 Ramachandran restraints generated. 3360 Oldfield, 0 Emsley, 3360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 3.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.5021 time to fit residues: 85.9041 Evaluate side-chains 60 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 2.590 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 270 optimal weight: 0.8980 chunk 184 optimal weight: 8.9990 chunk 4 optimal weight: 5.9990 chunk 241 optimal weight: 2.9990 chunk 134 optimal weight: 6.9990 chunk 277 optimal weight: 8.9990 chunk 224 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 165 optimal weight: 10.0000 chunk 291 optimal weight: 20.0000 chunk 81 optimal weight: 8.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 ASN C 7 GLN G 237 ASN I 107 ASN ** I 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 237 ASN S 237 ASN ** W 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8871 moved from start: 0.4933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 26600 Z= 0.268 Angle : 0.593 10.911 36554 Z= 0.305 Chirality : 0.035 0.198 4984 Planarity : 0.003 0.031 4480 Dihedral : 6.182 59.923 4144 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.15), residues: 3360 helix: 1.63 (0.11), residues: 2408 sheet: None (None), residues: 0 loop : -0.83 (0.20), residues: 952 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6720 Ramachandran restraints generated. 3360 Oldfield, 0 Emsley, 3360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6720 Ramachandran restraints generated. 3360 Oldfield, 0 Emsley, 3360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 2.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.5153 time to fit residues: 76.8041 Evaluate side-chains 54 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 2.823 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.4998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 109 optimal weight: 8.9990 chunk 292 optimal weight: 6.9990 chunk 64 optimal weight: 6.9990 chunk 190 optimal weight: 2.9990 chunk 80 optimal weight: 8.9990 chunk 325 optimal weight: 10.0000 chunk 269 optimal weight: 8.9990 chunk 150 optimal weight: 0.8980 chunk 27 optimal weight: 9.9990 chunk 107 optimal weight: 7.9990 chunk 170 optimal weight: 0.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 ASN G 237 ASN ** I 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 237 ASN ** M 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 101 GLN O 237 ASN ** Q 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 101 GLN Q 237 ASN S 237 ASN ** W 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 moved from start: 0.5222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.061 26600 Z= 0.207 Angle : 0.537 8.696 36554 Z= 0.272 Chirality : 0.034 0.193 4984 Planarity : 0.002 0.033 4480 Dihedral : 5.814 59.536 4144 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.15), residues: 3360 helix: 1.71 (0.11), residues: 2422 sheet: None (None), residues: 0 loop : -0.69 (0.20), residues: 938 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6720 Ramachandran restraints generated. 3360 Oldfield, 0 Emsley, 3360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6720 Ramachandran restraints generated. 3360 Oldfield, 0 Emsley, 3360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 2.760 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 outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.5522 time to fit residues: 73.2560 Evaluate side-chains 53 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 2.657 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 313 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 chunk 185 optimal weight: 0.4980 chunk 237 optimal weight: 0.8980 chunk 183 optimal weight: 8.9990 chunk 273 optimal weight: 10.0000 chunk 181 optimal weight: 1.9990 chunk 323 optimal weight: 30.0000 chunk 202 optimal weight: 8.9990 chunk 197 optimal weight: 5.9990 chunk 149 optimal weight: 0.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 ASN G 237 ASN ** I 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 237 ASN ** K 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 237 ASN ** Q 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 237 ASN S 237 ASN U 92 ASN ** W 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8863 moved from start: 0.5327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 26600 Z= 0.136 Angle : 0.486 9.578 36554 Z= 0.245 Chirality : 0.034 0.196 4984 Planarity : 0.002 0.031 4480 Dihedral : 5.364 59.374 4144 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.15), residues: 3360 helix: 1.89 (0.11), residues: 2408 sheet: None (None), residues: 0 loop : -0.69 (0.20), residues: 952 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6720 Ramachandran restraints generated. 3360 Oldfield, 0 Emsley, 3360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6720 Ramachandran restraints generated. 3360 Oldfield, 0 Emsley, 3360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 104 time to evaluate : 2.723 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 outliers start: 1 outliers final: 0 residues processed: 105 average time/residue: 0.4916 time to fit residues: 78.2260 Evaluate side-chains 53 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 2.653 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 200 optimal weight: 0.5980 chunk 129 optimal weight: 0.0470 chunk 193 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 63 optimal weight: 7.9990 chunk 62 optimal weight: 5.9990 chunk 205 optimal weight: 7.9990 chunk 220 optimal weight: 10.0000 chunk 160 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 254 optimal weight: 7.9990 overall best weight: 1.5284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 ASN ** E 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 237 ASN ** I 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 146 ASN I 237 ASN ** M 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 237 ASN ** Q 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 237 ASN S 237 ASN ** W 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8866 moved from start: 0.5454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.047 26600 Z= 0.134 Angle : 0.478 9.024 36554 Z= 0.242 Chirality : 0.033 0.193 4984 Planarity : 0.002 0.030 4480 Dihedral : 5.069 59.104 4144 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.15), residues: 3360 helix: 1.91 (0.11), residues: 2408 sheet: None (None), residues: 0 loop : -0.69 (0.20), residues: 952 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6720 Ramachandran restraints generated. 3360 Oldfield, 0 Emsley, 3360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6720 Ramachandran restraints generated. 3360 Oldfield, 0 Emsley, 3360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 2.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.5465 time to fit residues: 67.0749 Evaluate side-chains 57 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 2.732 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.5040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 294 optimal weight: 1.9990 chunk 310 optimal weight: 7.9990 chunk 283 optimal weight: 0.8980 chunk 301 optimal weight: 0.1980 chunk 181 optimal weight: 9.9990 chunk 131 optimal weight: 1.9990 chunk 236 optimal weight: 0.0570 chunk 92 optimal weight: 10.0000 chunk 272 optimal weight: 9.9990 chunk 285 optimal weight: 8.9990 chunk 300 optimal weight: 0.9990 overall best weight: 0.8302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 ASN C 7 GLN ** C 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 ASN G 237 ASN ** I 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 237 ASN ** K 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 237 ASN ** Q 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 101 GLN Q 237 ASN S 237 ASN ** W 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 146 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.5553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 26600 Z= 0.118 Angle : 0.457 8.085 36554 Z= 0.232 Chirality : 0.033 0.193 4984 Planarity : 0.002 0.030 4480 Dihedral : 4.580 58.756 4144 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.15), residues: 3360 helix: 1.94 (0.11), residues: 2408 sheet: None (None), residues: 0 loop : -0.64 (0.20), residues: 952 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6720 Ramachandran restraints generated. 3360 Oldfield, 0 Emsley, 3360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6720 Ramachandran restraints generated. 3360 Oldfield, 0 Emsley, 3360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 2.817 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 outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.4999 time to fit residues: 71.5764 Evaluate side-chains 60 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 2.720 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 198 optimal weight: 7.9990 chunk 319 optimal weight: 3.9990 chunk 194 optimal weight: 7.9990 chunk 151 optimal weight: 9.9990 chunk 221 optimal weight: 10.0000 chunk 334 optimal weight: 7.9990 chunk 308 optimal weight: 10.0000 chunk 266 optimal weight: 0.0870 chunk 27 optimal weight: 7.9990 chunk 205 optimal weight: 5.9990 chunk 163 optimal weight: 5.9990 overall best weight: 4.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 ASN C 7 GLN ** E 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 237 ASN I 237 ASN O 7 GLN ** O 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 237 ASN ** Q 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 237 ASN S 237 ASN ** W 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 63 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8927 moved from start: 0.5931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 26600 Z= 0.254 Angle : 0.579 8.945 36554 Z= 0.294 Chirality : 0.035 0.235 4984 Planarity : 0.003 0.032 4480 Dihedral : 4.788 58.197 4144 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.15), residues: 3360 helix: 1.98 (0.11), residues: 2394 sheet: None (None), residues: 0 loop : -0.74 (0.20), residues: 966 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6720 Ramachandran restraints generated. 3360 Oldfield, 0 Emsley, 3360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6720 Ramachandran restraints generated. 3360 Oldfield, 0 Emsley, 3360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 2.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.5463 time to fit residues: 68.6477 Evaluate side-chains 49 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 2.614 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 211 optimal weight: 8.9990 chunk 283 optimal weight: 0.8980 chunk 81 optimal weight: 8.9990 chunk 245 optimal weight: 9.9990 chunk 39 optimal weight: 20.0000 chunk 74 optimal weight: 1.9990 chunk 266 optimal weight: 0.9990 chunk 111 optimal weight: 3.9990 chunk 274 optimal weight: 1.9990 chunk 33 optimal weight: 9.9990 chunk 49 optimal weight: 6.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 ASN G 237 ASN I 237 ASN ** K 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 134 GLN ** M 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 237 ASN ** Q 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 237 ASN S 237 ASN ** W 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2348 r_free = 0.2348 target = 0.019846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2059 r_free = 0.2059 target = 0.013977 restraints weight = 315607.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2079 r_free = 0.2079 target = 0.014346 restraints weight = 233578.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2095 r_free = 0.2095 target = 0.014649 restraints weight = 187602.788| |-----------------------------------------------------------------------------| r_work (final): 0.2088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8894 moved from start: 0.5970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 26600 Z= 0.136 Angle : 0.473 8.102 36554 Z= 0.240 Chirality : 0.033 0.193 4984 Planarity : 0.002 0.031 4480 Dihedral : 4.543 59.250 4144 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.15), residues: 3360 helix: 1.98 (0.11), residues: 2422 sheet: None (None), residues: 0 loop : -0.48 (0.20), residues: 938 =============================================================================== Job complete usr+sys time: 3439.63 seconds wall clock time: 66 minutes 33.49 seconds (3993.49 seconds total)