Starting phenix.real_space_refine on Tue Feb 20 00:27:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7peo_13355/02_2024/7peo_13355_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7peo_13355/02_2024/7peo_13355.map 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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7peo_13355/02_2024/7peo_13355.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7peo_13355/02_2024/7peo_13355.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7peo_13355/02_2024/7peo_13355_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7peo_13355/02_2024/7peo_13355_updated.pdb" } resolution = 4.37 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 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 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. 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-5238/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: 36 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: 36 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: 36 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: 36 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: 36 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: 36 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: 36 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: 36 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: 36 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: 36 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: 36 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: 36 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: 36 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: 36 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: 13.48, per 1000 atoms: 0.51 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: 14.01 Conformation dependent library (CDL) restraints added in 5.0 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: 4.65 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: 7.33 Time building geometry restraints manager: 14.69 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=" C ASP S 83 " pdb=" O ASP S 83 " ideal model delta sigma weight residual 1.233 1.278 -0.045 1.12e-02 7.97e+03 1.64e+01 bond pdb=" C ASP M 83 " pdb=" O ASP M 83 " ideal model delta sigma weight residual 1.233 1.278 -0.045 1.12e-02 7.97e+03 1.63e+01 bond pdb=" C ASP K 83 " pdb=" O ASP K 83 " ideal model delta sigma weight residual 1.233 1.278 -0.045 1.12e-02 7.97e+03 1.61e+01 bond pdb=" C ASP 0 83 " pdb=" O ASP 0 83 " ideal model delta sigma weight residual 1.233 1.278 -0.045 1.12e-02 7.97e+03 1.61e+01 bond pdb=" C ASP E 83 " pdb=" O ASP E 83 " ideal model delta sigma weight residual 1.233 1.278 -0.045 1.12e-02 7.97e+03 1.61e+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 - 20.88: 15610 20.88 - 41.76: 994 41.76 - 62.64: 230 62.64 - 83.53: 316 83.53 - 104.41: 210 Dihedral angle restraints: 17360 sinusoidal: 7518 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 17357 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.164: 4238 0.164 - 0.327: 681 0.327 - 0.491: 32 0.491 - 0.655: 5 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 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: 1.390 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: 7.030 Check model and map are aligned: 0.370 Set scattering table: 0.240 Process input model: 69.990 Find NCS groups from input model: 1.990 Set up NCS constraints: 0.270 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 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 : 0.009 0.053 26600 Z= 0.581 Angle : 1.634 10.029 36554 Z= 1.072 Chirality : 0.129 0.818 4984 Planarity : 0.018 0.234 4480 Dihedral : 22.193 104.407 11060 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 % Allowed : 10.71 % Favored : 88.69 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.012 0.003 PHE U 80 TYR 0.014 0.004 TYR G 171 ARG 0.004 0.002 ARG K 165 *********************** 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 : 2.755 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 REVERT: A 165 ARG cc_start: 0.9710 (OUTLIER) cc_final: 0.9170 (ptt90) REVERT: C 62 ILE cc_start: 0.9770 (mt) cc_final: 0.9473 (mp) REVERT: C 143 ILE cc_start: 0.9569 (mt) cc_final: 0.9219 (tt) REVERT: C 165 ARG cc_start: 0.9504 (OUTLIER) cc_final: 0.9182 (ptt90) REVERT: E 63 GLN cc_start: 0.9592 (mt0) cc_final: 0.9368 (mm-40) REVERT: E 165 ARG cc_start: 0.9700 (OUTLIER) cc_final: 0.9119 (ptt90) REVERT: E 166 GLN cc_start: 0.9734 (tp40) cc_final: 0.9406 (tp-100) REVERT: G 62 ILE cc_start: 0.9809 (mt) cc_final: 0.9454 (tt) REVERT: G 165 ARG cc_start: 0.9510 (OUTLIER) cc_final: 0.9029 (ptt90) REVERT: G 166 GLN cc_start: 0.9652 (tp40) cc_final: 0.9141 (tp-100) REVERT: G 220 ILE cc_start: 0.9524 (mt) cc_final: 0.9242 (mt) REVERT: G 223 LEU cc_start: 0.9761 (tp) cc_final: 0.9489 (tt) REVERT: I 127 TYR cc_start: 0.9190 (m-80) cc_final: 0.8752 (m-80) REVERT: I 166 GLN cc_start: 0.9571 (tp40) cc_final: 0.8993 (tp-100) REVERT: I 170 ASP cc_start: 0.9641 (m-30) cc_final: 0.9387 (m-30) REVERT: I 223 LEU cc_start: 0.9698 (tp) cc_final: 0.9425 (tt) REVERT: K 63 GLN cc_start: 0.9438 (mt0) cc_final: 0.9194 (mt0) REVERT: K 127 TYR cc_start: 0.8867 (m-80) cc_final: 0.8598 (m-80) REVERT: K 177 ARG cc_start: 0.9663 (ttm110) cc_final: 0.9404 (tpm170) REVERT: K 197 ILE cc_start: 0.9764 (mt) cc_final: 0.9544 (tp) REVERT: K 223 LEU cc_start: 0.9734 (tp) cc_final: 0.9335 (tt) REVERT: M 78 LEU cc_start: 0.9595 (mt) cc_final: 0.9373 (mt) REVERT: M 223 LEU cc_start: 0.9792 (tp) cc_final: 0.9554 (tt) REVERT: O 200 ILE cc_start: 0.9561 (mt) cc_final: 0.9260 (tt) REVERT: Q 62 ILE cc_start: 0.9826 (mt) cc_final: 0.9599 (mp) REVERT: S 166 GLN cc_start: 0.9644 (tp40) cc_final: 0.9224 (tp-100) REVERT: U 63 GLN cc_start: 0.9795 (mt0) cc_final: 0.9221 (mm-40) REVERT: U 78 LEU cc_start: 0.9867 (mt) cc_final: 0.9659 (mt) REVERT: U 143 ILE cc_start: 0.9754 (mt) cc_final: 0.9464 (tt) REVERT: U 165 ARG cc_start: 0.9744 (OUTLIER) cc_final: 0.9272 (ptt90) REVERT: U 200 ILE cc_start: 0.9865 (mt) cc_final: 0.9619 (tt) REVERT: U 219 MET cc_start: 0.9635 (ttt) cc_final: 0.9181 (tpp) REVERT: U 223 LEU cc_start: 0.9608 (tp) cc_final: 0.9392 (tp) REVERT: W 63 GLN cc_start: 0.9742 (mt0) cc_final: 0.9236 (mm110) REVERT: W 78 LEU cc_start: 0.9871 (mt) cc_final: 0.9622 (mt) REVERT: W 165 ARG cc_start: 0.9657 (OUTLIER) cc_final: 0.9219 (ptt90) REVERT: W 177 ARG cc_start: 0.9788 (ttm110) cc_final: 0.9428 (tpm170) REVERT: Y 196 LEU cc_start: 0.9510 (mt) cc_final: 0.9293 (mt) REVERT: 0 165 ARG cc_start: 0.9498 (OUTLIER) cc_final: 0.9273 (ptt90) REVERT: 0 166 GLN cc_start: 0.9187 (tp40) cc_final: 0.8514 (tp40) outliers start: 14 outliers final: 0 residues processed: 343 average time/residue: 0.4415 time to fit residues: 223.9854 Evaluate side-chains 143 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 136 time to evaluate : 2.557 ------------------------------------------------------------------------------- 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: 8.9990 chunk 141 optimal weight: 0.9990 chunk 86 optimal weight: 6.9990 chunk 171 optimal weight: 2.9990 chunk 136 optimal weight: 5.9990 chunk 263 optimal weight: 5.9990 chunk 101 optimal weight: 9.9990 chunk 160 optimal weight: 10.0000 chunk 196 optimal weight: 6.9990 chunk 305 optimal weight: 8.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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 237 ASN C 49 ASN ** C 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 ASN C 111 ASN C 179 ASN C 237 ASN E 49 ASN E 63 GLN ** E 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 ASN E 111 ASN E 134 GLN E 179 ASN E 237 ASN G 49 ASN G 63 GLN G 107 ASN G 111 ASN G 134 GLN 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 63 GLN ** K 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 107 ASN K 111 ASN K 134 GLN 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 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 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 179 ASN U 237 ASN W 49 ASN W 63 GLN ** W 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 71 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 26600 Z= 0.239 Angle : 0.740 8.945 36554 Z= 0.347 Chirality : 0.048 0.254 4984 Planarity : 0.003 0.033 4480 Dihedral : 13.524 59.775 6776 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 0.04 % Allowed : 1.74 % Favored : 98.21 % 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: -0.08 (0.14), residues: 3360 helix: 0.45 (0.10), residues: 2436 sheet: None (None), residues: 0 loop : -1.20 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.022 0.002 PHE O 108 TYR 0.029 0.002 TYR Y 65 ARG 0.008 0.001 ARG M 165 *********************** 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 197 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 196 time to evaluate : 2.574 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: A 219 MET cc_start: 0.9727 (ttm) cc_final: 0.9151 (ppp) REVERT: E 166 GLN cc_start: 0.9601 (tp40) cc_final: 0.9138 (tp-100) REVERT: G 99 PHE cc_start: 0.9519 (m-80) cc_final: 0.9051 (m-80) REVERT: G 166 GLN cc_start: 0.9455 (tp40) cc_final: 0.9165 (tp-100) REVERT: G 219 MET cc_start: 0.8999 (tmm) cc_final: 0.8662 (ppp) REVERT: I 127 TYR cc_start: 0.9179 (m-80) cc_final: 0.8707 (m-80) REVERT: K 127 TYR cc_start: 0.8971 (m-80) cc_final: 0.8641 (m-80) REVERT: O 197 ILE cc_start: 0.9477 (tp) cc_final: 0.9267 (tp) REVERT: Q 231 ASP cc_start: 0.9018 (t0) cc_final: 0.8197 (p0) REVERT: U 63 GLN cc_start: 0.9710 (mt0) cc_final: 0.9216 (mm-40) REVERT: U 219 MET cc_start: 0.9614 (ttt) cc_final: 0.9373 (tpp) REVERT: U 223 LEU cc_start: 0.9651 (tp) cc_final: 0.9326 (tt) REVERT: W 63 GLN cc_start: 0.9723 (mt0) cc_final: 0.9384 (mm110) REVERT: W 177 ARG cc_start: 0.9818 (ttm110) cc_final: 0.9484 (tpm170) REVERT: W 223 LEU cc_start: 0.9710 (tp) cc_final: 0.9496 (tt) REVERT: Y 63 GLN cc_start: 0.9457 (mt0) cc_final: 0.9100 (mm110) REVERT: Y 196 LEU cc_start: 0.9540 (mt) cc_final: 0.9266 (mt) REVERT: 0 166 GLN cc_start: 0.9001 (tp40) cc_final: 0.8393 (tp-100) REVERT: 0 170 ASP cc_start: 0.9591 (m-30) cc_final: 0.9293 (m-30) REVERT: 0 223 LEU cc_start: 0.9088 (tt) cc_final: 0.8623 (pp) outliers start: 1 outliers final: 1 residues processed: 196 average time/residue: 0.4664 time to fit residues: 134.6769 Evaluate side-chains 92 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 91 time to evaluate : 2.655 ------------------------------------------------------------------------------- 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: 9.9990 chunk 253 optimal weight: 7.9990 chunk 207 optimal weight: 0.3980 chunk 84 optimal weight: 9.9990 chunk 305 optimal weight: 10.0000 chunk 330 optimal weight: 2.9990 chunk 272 optimal weight: 3.9990 chunk 303 optimal weight: 3.9990 chunk 104 optimal weight: 6.9990 chunk 245 optimal weight: 5.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 ASN ** C 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 ASN ** 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** ** Q 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 111 ASN ** S 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 63 GLN ** U 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 111 ASN W 111 ASN ** W 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.3663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 26600 Z= 0.171 Angle : 0.577 9.534 36554 Z= 0.278 Chirality : 0.038 0.237 4984 Planarity : 0.002 0.035 4480 Dihedral : 9.184 52.832 6776 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.15), residues: 3360 helix: 1.38 (0.11), residues: 2408 sheet: None (None), residues: 0 loop : -0.95 (0.20), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.014 0.002 PHE E 175 TYR 0.017 0.001 TYR Y 65 ARG 0.017 0.001 ARG E 177 *********************** 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 144 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 2.655 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: A 219 MET cc_start: 0.9745 (ttt) cc_final: 0.9447 (ppp) REVERT: G 99 PHE cc_start: 0.9558 (m-80) cc_final: 0.9054 (m-80) REVERT: G 166 GLN cc_start: 0.9428 (tp40) cc_final: 0.9177 (tp-100) REVERT: G 219 MET cc_start: 0.9148 (tmm) cc_final: 0.8705 (ppp) REVERT: I 127 TYR cc_start: 0.9171 (m-80) cc_final: 0.8795 (m-80) REVERT: I 140 TYR cc_start: 0.9649 (t80) cc_final: 0.9339 (t80) REVERT: K 63 GLN cc_start: 0.9514 (pt0) cc_final: 0.9304 (pt0) REVERT: K 127 TYR cc_start: 0.9017 (m-80) cc_final: 0.8763 (m-80) REVERT: Q 231 ASP cc_start: 0.9074 (t0) cc_final: 0.8231 (p0) REVERT: U 223 LEU cc_start: 0.9686 (tp) cc_final: 0.9382 (tt) REVERT: W 63 GLN cc_start: 0.9707 (mt0) cc_final: 0.9429 (mm110) REVERT: W 177 ARG cc_start: 0.9810 (ttm110) cc_final: 0.9542 (tpm170) REVERT: W 219 MET cc_start: 0.9373 (ppp) cc_final: 0.8977 (ppp) REVERT: Y 196 LEU cc_start: 0.9547 (mt) cc_final: 0.9273 (mt) REVERT: 0 166 GLN cc_start: 0.9000 (tp40) cc_final: 0.8597 (tp40) REVERT: 0 170 ASP cc_start: 0.9554 (m-30) cc_final: 0.9346 (m-30) outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.5074 time to fit residues: 106.5228 Evaluate side-chains 86 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 2.460 ------------------------------------------------------------------------------- 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: 5.9990 chunk 229 optimal weight: 20.0000 chunk 158 optimal weight: 4.9990 chunk 33 optimal weight: 9.9990 chunk 145 optimal weight: 0.9990 chunk 205 optimal weight: 10.0000 chunk 306 optimal weight: 5.9990 chunk 324 optimal weight: 10.0000 chunk 160 optimal weight: 9.9990 chunk 290 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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** ** 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 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8900 moved from start: 0.4267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 26600 Z= 0.206 Angle : 0.593 9.582 36554 Z= 0.285 Chirality : 0.040 0.240 4984 Planarity : 0.003 0.047 4480 Dihedral : 7.544 52.559 6776 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % 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: 1.49 (0.15), residues: 3360 helix: 1.68 (0.11), residues: 2408 sheet: None (None), residues: 0 loop : -0.79 (0.20), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.018 0.002 PHE E 239 TYR 0.014 0.001 TYR E 212 ARG 0.009 0.001 ARG E 177 *********************** 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 121 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 2.088 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: A 219 MET cc_start: 0.9732 (ttt) cc_final: 0.9438 (ppp) REVERT: G 99 PHE cc_start: 0.9529 (m-80) cc_final: 0.9046 (m-80) REVERT: G 219 MET cc_start: 0.9188 (tmm) cc_final: 0.8661 (ppp) REVERT: M 127 TYR cc_start: 0.9146 (m-80) cc_final: 0.8935 (m-80) REVERT: Q 231 ASP cc_start: 0.9140 (t0) cc_final: 0.8344 (p0) REVERT: U 30 ASP cc_start: 0.9718 (m-30) cc_final: 0.9500 (m-30) REVERT: U 63 GLN cc_start: 0.9688 (mt0) cc_final: 0.9267 (mm-40) REVERT: U 219 MET cc_start: 0.9245 (ppp) cc_final: 0.9006 (ppp) REVERT: U 223 LEU cc_start: 0.9744 (tp) cc_final: 0.9392 (pp) REVERT: W 63 GLN cc_start: 0.9727 (mt0) cc_final: 0.9449 (mm110) REVERT: W 142 LYS cc_start: 0.9643 (ttmm) cc_final: 0.9400 (ttmm) REVERT: W 177 ARG cc_start: 0.9811 (ttm110) cc_final: 0.9517 (tpm170) REVERT: W 219 MET cc_start: 0.9450 (ppp) cc_final: 0.9058 (ppp) REVERT: W 223 LEU cc_start: 0.9700 (tt) cc_final: 0.9490 (pp) REVERT: 0 166 GLN cc_start: 0.8988 (tp40) cc_final: 0.8415 (tp-100) REVERT: 0 170 ASP cc_start: 0.9547 (m-30) cc_final: 0.9258 (m-30) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.4352 time to fit residues: 77.3205 Evaluate side-chains 72 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 1.924 ------------------------------------------------------------------------------- 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: 1.9990 chunk 184 optimal weight: 7.9990 chunk 4 optimal weight: 5.9990 chunk 241 optimal weight: 0.9990 chunk 134 optimal weight: 6.9990 chunk 277 optimal weight: 8.9990 chunk 224 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 165 optimal weight: 5.9990 chunk 291 optimal weight: 20.0000 chunk 81 optimal weight: 8.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 107 ASN G 237 ASN ** I 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 101 GLN O 237 ASN ** Q 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 237 ASN ** U 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8951 moved from start: 0.4794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 26600 Z= 0.227 Angle : 0.609 9.636 36554 Z= 0.295 Chirality : 0.039 0.240 4984 Planarity : 0.003 0.030 4480 Dihedral : 7.309 54.403 6776 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.04 % Allowed : 2.89 % Favored : 97.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.15), residues: 3360 helix: 1.75 (0.11), residues: 2422 sheet: None (None), residues: 0 loop : -0.82 (0.20), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.018 0.002 PHE Y 239 TYR 0.027 0.002 TYR C 32 ARG 0.005 0.001 ARG E 177 *********************** 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 112 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 111 time to evaluate : 2.644 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: A 219 MET cc_start: 0.9732 (ttt) cc_final: 0.9435 (ppp) REVERT: E 219 MET cc_start: 0.9430 (ppp) cc_final: 0.9165 (ppp) REVERT: G 99 PHE cc_start: 0.9503 (m-80) cc_final: 0.9002 (m-80) REVERT: G 219 MET cc_start: 0.9241 (tmm) cc_final: 0.8695 (ppp) REVERT: I 201 LEU cc_start: 0.9859 (mt) cc_final: 0.9516 (tp) REVERT: K 127 TYR cc_start: 0.9255 (m-80) cc_final: 0.8963 (m-80) REVERT: Q 231 ASP cc_start: 0.9041 (t0) cc_final: 0.8172 (p0) REVERT: U 30 ASP cc_start: 0.9767 (m-30) cc_final: 0.9547 (m-30) REVERT: U 219 MET cc_start: 0.9292 (ppp) cc_final: 0.9020 (ppp) REVERT: W 63 GLN cc_start: 0.9740 (mt0) cc_final: 0.9458 (mm110) REVERT: W 142 LYS cc_start: 0.9679 (ttmm) cc_final: 0.9417 (ttmm) REVERT: W 177 ARG cc_start: 0.9821 (ttm110) cc_final: 0.9508 (tpm170) REVERT: W 219 MET cc_start: 0.9532 (ppp) cc_final: 0.9134 (ppp) REVERT: Y 196 LEU cc_start: 0.9567 (mt) cc_final: 0.9334 (mt) REVERT: 0 166 GLN cc_start: 0.8945 (tp40) cc_final: 0.8609 (tp40) REVERT: 0 219 MET cc_start: 0.9603 (ttm) cc_final: 0.9351 (ppp) outliers start: 1 outliers final: 1 residues processed: 112 average time/residue: 0.5021 time to fit residues: 83.1127 Evaluate side-chains 67 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 66 time to evaluate : 2.741 ------------------------------------------------------------------------------- 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: 10.0000 chunk 292 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 190 optimal weight: 5.9990 chunk 80 optimal weight: 20.0000 chunk 325 optimal weight: 10.0000 chunk 269 optimal weight: 8.9990 chunk 150 optimal weight: 1.9990 chunk 27 optimal weight: 9.9990 chunk 107 optimal weight: 20.0000 chunk 170 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 63 GLN K 107 ASN K 237 ASN ** M 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** U 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8993 moved from start: 0.5270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 26600 Z= 0.241 Angle : 0.628 9.640 36554 Z= 0.302 Chirality : 0.039 0.241 4984 Planarity : 0.003 0.032 4480 Dihedral : 7.119 54.343 6776 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.15), residues: 3360 helix: 1.77 (0.11), residues: 2408 sheet: None (None), residues: 0 loop : -0.70 (0.20), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.025 0.002 PHE I 105 TYR 0.014 0.002 TYR E 212 ARG 0.004 0.001 ARG S 165 *********************** 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 96 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 2.683 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: E 219 MET cc_start: 0.9496 (ppp) cc_final: 0.9212 (ppp) REVERT: I 201 LEU cc_start: 0.9854 (mt) cc_final: 0.9561 (tp) REVERT: K 127 TYR cc_start: 0.9281 (m-80) cc_final: 0.9025 (m-80) REVERT: M 63 GLN cc_start: 0.9571 (mt0) cc_final: 0.9315 (mp10) REVERT: M 196 LEU cc_start: 0.9476 (mt) cc_final: 0.9247 (mt) REVERT: Q 219 MET cc_start: 0.9303 (ppp) cc_final: 0.9098 (ppp) REVERT: U 30 ASP cc_start: 0.9758 (m-30) cc_final: 0.9530 (m-30) REVERT: U 219 MET cc_start: 0.9349 (ppp) cc_final: 0.9121 (ppp) REVERT: W 63 GLN cc_start: 0.9753 (mt0) cc_final: 0.9462 (mm110) REVERT: W 142 LYS cc_start: 0.9691 (ttmm) cc_final: 0.9425 (ttmm) REVERT: W 177 ARG cc_start: 0.9819 (ttm110) cc_final: 0.9608 (mmm-85) REVERT: W 219 MET cc_start: 0.9523 (ppp) cc_final: 0.9130 (ppp) REVERT: Y 196 LEU cc_start: 0.9588 (mt) cc_final: 0.9355 (mt) REVERT: 0 166 GLN cc_start: 0.9050 (tp40) cc_final: 0.8454 (tp-100) REVERT: 0 170 ASP cc_start: 0.9577 (m-30) cc_final: 0.9325 (m-30) REVERT: 0 219 MET cc_start: 0.9668 (ttm) cc_final: 0.9229 (ppp) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.5411 time to fit residues: 75.7121 Evaluate side-chains 63 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 2.661 ------------------------------------------------------------------------------- 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: 5.9990 chunk 185 optimal weight: 5.9990 chunk 237 optimal weight: 20.0000 chunk 183 optimal weight: 7.9990 chunk 273 optimal weight: 7.9990 chunk 181 optimal weight: 5.9990 chunk 323 optimal weight: 30.0000 chunk 202 optimal weight: 5.9990 chunk 197 optimal weight: 5.9990 chunk 149 optimal weight: 3.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 ASN C 101 GLN C 107 ASN E 101 GLN E 107 ASN ** G 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 237 ASN ** I 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 7 GLN ** O 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 237 ASN ** U 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 63 GLN ** 0 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9026 moved from start: 0.5795 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= 0.275 Angle : 0.679 11.105 36554 Z= 0.330 Chirality : 0.040 0.242 4984 Planarity : 0.003 0.069 4480 Dihedral : 7.227 55.758 6776 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.15), residues: 3360 helix: 1.65 (0.10), residues: 2394 sheet: None (None), residues: 0 loop : -0.57 (0.21), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.025 0.002 PHE E 239 TYR 0.022 0.002 TYR A 242 ARG 0.010 0.001 ARG U 177 *********************** 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 90 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 2.765 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: E 219 MET cc_start: 0.9558 (ppp) cc_final: 0.9290 (ppp) REVERT: G 99 PHE cc_start: 0.9424 (m-80) cc_final: 0.8954 (m-80) REVERT: I 146 ASN cc_start: 0.9666 (t0) cc_final: 0.9428 (m-40) REVERT: I 201 LEU cc_start: 0.9859 (mt) cc_final: 0.9608 (tp) REVERT: K 63 GLN cc_start: 0.9492 (mt0) cc_final: 0.9287 (mt0) REVERT: K 127 TYR cc_start: 0.9369 (m-80) cc_final: 0.9156 (m-80) REVERT: M 196 LEU cc_start: 0.9507 (mt) cc_final: 0.9269 (mt) REVERT: Q 142 LYS cc_start: 0.9549 (ttmm) cc_final: 0.9282 (mttm) REVERT: Q 219 MET cc_start: 0.9334 (ppp) cc_final: 0.9125 (ppp) REVERT: Q 231 ASP cc_start: 0.9236 (t0) cc_final: 0.8461 (p0) REVERT: U 30 ASP cc_start: 0.9782 (m-30) cc_final: 0.9567 (m-30) REVERT: U 219 MET cc_start: 0.9361 (ppp) cc_final: 0.9130 (ppp) REVERT: W 63 GLN cc_start: 0.9731 (mt0) cc_final: 0.9423 (mm110) REVERT: W 142 LYS cc_start: 0.9704 (ttmm) cc_final: 0.9434 (ttmm) REVERT: W 177 ARG cc_start: 0.9826 (ttm110) cc_final: 0.9616 (mmm160) REVERT: W 219 MET cc_start: 0.9520 (ppp) cc_final: 0.9166 (ppp) REVERT: 0 166 GLN cc_start: 0.9066 (tp40) cc_final: 0.8798 (tp-100) REVERT: 0 219 MET cc_start: 0.9667 (ttm) cc_final: 0.9384 (ppp) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.5037 time to fit residues: 66.9848 Evaluate side-chains 58 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 2.414 ------------------------------------------------------------------------------- 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: 9.9990 chunk 129 optimal weight: 7.9990 chunk 193 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 205 optimal weight: 6.9990 chunk 220 optimal weight: 0.0040 chunk 160 optimal weight: 30.0000 chunk 30 optimal weight: 0.8980 chunk 254 optimal weight: 10.0000 overall best weight: 1.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 ASN C 101 GLN C 107 ASN ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 GLN G 166 GLN G 179 ASN G 237 ASN I 237 ASN K 237 ASN M 63 GLN ** M 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 237 ASN S 237 ASN ** U 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8997 moved from start: 0.5773 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= 0.132 Angle : 0.544 9.662 36554 Z= 0.259 Chirality : 0.037 0.240 4984 Planarity : 0.002 0.030 4480 Dihedral : 6.747 54.870 6776 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.15), residues: 3360 helix: 1.97 (0.11), residues: 2394 sheet: None (None), residues: 0 loop : -0.54 (0.21), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.026 0.001 PHE Y 105 TYR 0.029 0.001 TYR W 140 ARG 0.005 0.000 ARG U 177 *********************** 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 93 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 2.587 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: C 219 MET cc_start: 0.9686 (ttp) cc_final: 0.9453 (tmm) REVERT: E 142 LYS cc_start: 0.9245 (tmtt) cc_final: 0.9033 (tptp) REVERT: E 219 MET cc_start: 0.9548 (ppp) cc_final: 0.9265 (ppp) REVERT: I 127 TYR cc_start: 0.9242 (m-80) cc_final: 0.8887 (m-80) REVERT: I 201 LEU cc_start: 0.9852 (mt) cc_final: 0.9570 (tp) REVERT: K 127 TYR cc_start: 0.9324 (m-80) cc_final: 0.9046 (m-80) REVERT: M 63 GLN cc_start: 0.9567 (mt0) cc_final: 0.9353 (mp10) REVERT: Q 219 MET cc_start: 0.9255 (ppp) cc_final: 0.9020 (ppp) REVERT: Q 231 ASP cc_start: 0.9188 (t0) cc_final: 0.8394 (p0) REVERT: U 30 ASP cc_start: 0.9769 (m-30) cc_final: 0.9542 (m-30) REVERT: U 219 MET cc_start: 0.9288 (ppp) cc_final: 0.9071 (ppp) REVERT: W 63 GLN cc_start: 0.9722 (mt0) cc_final: 0.9392 (mm110) REVERT: W 142 LYS cc_start: 0.9688 (ttmm) cc_final: 0.9424 (ttmm) REVERT: W 146 ASN cc_start: 0.9449 (t0) cc_final: 0.9169 (m-40) REVERT: W 177 ARG cc_start: 0.9820 (ttm110) cc_final: 0.9506 (tpm170) REVERT: W 219 MET cc_start: 0.9456 (ppp) cc_final: 0.9063 (ppp) REVERT: 0 166 GLN cc_start: 0.8956 (tp40) cc_final: 0.8587 (tp-100) REVERT: 0 219 MET cc_start: 0.9639 (ttm) cc_final: 0.9237 (ppp) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.5087 time to fit residues: 69.6319 Evaluate side-chains 61 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 2.522 ------------------------------------------------------------------------------- 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: 2.9990 chunk 310 optimal weight: 10.0000 chunk 283 optimal weight: 4.9990 chunk 301 optimal weight: 10.0000 chunk 181 optimal weight: 10.0000 chunk 131 optimal weight: 0.2980 chunk 236 optimal weight: 10.0000 chunk 92 optimal weight: 4.9990 chunk 272 optimal weight: 0.8980 chunk 285 optimal weight: 10.0000 chunk 300 optimal weight: 10.0000 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 ASN ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 237 ASN I 146 ASN I 237 ASN K 237 ASN ** O 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 237 ASN ** U 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9012 moved from start: 0.5986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 26600 Z= 0.166 Angle : 0.556 9.645 36554 Z= 0.266 Chirality : 0.037 0.242 4984 Planarity : 0.002 0.029 4480 Dihedral : 6.414 53.813 6776 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % 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: 1.97 (0.15), residues: 3360 helix: 2.02 (0.11), residues: 2380 sheet: None (None), residues: 0 loop : -0.44 (0.21), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.016 0.002 PHE Y 105 TYR 0.014 0.001 TYR I 140 ARG 0.005 0.000 ARG U 177 *********************** 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 93 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 2.628 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: E 142 LYS cc_start: 0.9258 (tmtt) cc_final: 0.9043 (tptp) REVERT: E 219 MET cc_start: 0.9571 (ppp) cc_final: 0.9288 (ppp) REVERT: G 99 PHE cc_start: 0.9412 (m-10) cc_final: 0.8960 (m-80) REVERT: I 127 TYR cc_start: 0.9265 (m-80) cc_final: 0.8899 (m-80) REVERT: I 201 LEU cc_start: 0.9854 (mt) cc_final: 0.9583 (tp) REVERT: K 127 TYR cc_start: 0.9325 (m-80) cc_final: 0.9060 (m-80) REVERT: M 63 GLN cc_start: 0.9557 (mt0) cc_final: 0.9351 (mp10) REVERT: Q 142 LYS cc_start: 0.9552 (ttmm) cc_final: 0.9270 (mttm) REVERT: Q 219 MET cc_start: 0.9310 (ppp) cc_final: 0.9074 (ppp) REVERT: Q 231 ASP cc_start: 0.9083 (t0) cc_final: 0.8213 (p0) REVERT: U 30 ASP cc_start: 0.9770 (m-30) cc_final: 0.9543 (m-30) REVERT: U 219 MET cc_start: 0.9336 (ppp) cc_final: 0.9115 (ppp) REVERT: W 63 GLN cc_start: 0.9712 (mt0) cc_final: 0.9412 (mm110) REVERT: W 142 LYS cc_start: 0.9697 (ttmm) cc_final: 0.9425 (ttmm) REVERT: W 146 ASN cc_start: 0.9452 (t0) cc_final: 0.9177 (m-40) REVERT: W 219 MET cc_start: 0.9506 (ppp) cc_final: 0.9107 (ppp) REVERT: 0 166 GLN cc_start: 0.9017 (tp40) cc_final: 0.8668 (tp-100) REVERT: 0 219 MET cc_start: 0.9657 (ttm) cc_final: 0.9376 (ppp) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.5247 time to fit residues: 71.7201 Evaluate side-chains 59 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 2.504 ------------------------------------------------------------------------------- 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: 1.9990 chunk 319 optimal weight: 5.9990 chunk 194 optimal weight: 7.9990 chunk 151 optimal weight: 7.9990 chunk 221 optimal weight: 4.9990 chunk 334 optimal weight: 8.9990 chunk 308 optimal weight: 4.9990 chunk 266 optimal weight: 10.0000 chunk 27 optimal weight: 4.9990 chunk 205 optimal weight: 9.9990 chunk 163 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 ASN ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 89 ASN ** G 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 237 ASN I 237 ASN K 237 ASN O 101 GLN ** O 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 237 ASN ** U 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 89 ASN ** W 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9043 moved from start: 0.6367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 26600 Z= 0.235 Angle : 0.618 9.664 36554 Z= 0.300 Chirality : 0.038 0.241 4984 Planarity : 0.003 0.051 4480 Dihedral : 6.687 55.593 6776 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.09 % Allowed : 0.55 % Favored : 99.36 % 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: 1.78 (0.15), residues: 3360 helix: 1.86 (0.11), residues: 2380 sheet: None (None), residues: 0 loop : -0.49 (0.21), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.020 0.002 PHE E 239 TYR 0.025 0.002 TYR O 140 ARG 0.009 0.001 ARG W 177 ********************** 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 82 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 80 time to evaluate : 2.514 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: E 89 ASN cc_start: 0.9408 (OUTLIER) cc_final: 0.9066 (p0) REVERT: E 142 LYS cc_start: 0.9337 (tmtt) cc_final: 0.9135 (tptp) REVERT: E 219 MET cc_start: 0.9576 (ppp) cc_final: 0.9281 (ppp) REVERT: I 201 LEU cc_start: 0.9859 (mt) cc_final: 0.9593 (tp) REVERT: K 63 GLN cc_start: 0.9522 (mt0) cc_final: 0.9306 (mt0) REVERT: K 127 TYR cc_start: 0.9390 (m-80) cc_final: 0.9177 (m-80) REVERT: Q 142 LYS cc_start: 0.9548 (ttmm) cc_final: 0.9273 (mttm) REVERT: Q 219 MET cc_start: 0.9322 (ppp) cc_final: 0.9073 (ppp) REVERT: U 30 ASP cc_start: 0.9779 (m-30) cc_final: 0.9557 (m-30) REVERT: U 89 ASN cc_start: 0.9620 (OUTLIER) cc_final: 0.9389 (p0) REVERT: U 219 MET cc_start: 0.9353 (ppp) cc_final: 0.9147 (ppp) REVERT: W 63 GLN cc_start: 0.9734 (mt0) cc_final: 0.9426 (mm110) REVERT: W 142 LYS cc_start: 0.9704 (ttmm) cc_final: 0.9435 (ttmm) REVERT: W 146 ASN cc_start: 0.9500 (t0) cc_final: 0.9167 (m-40) REVERT: W 219 MET cc_start: 0.9313 (ppp) cc_final: 0.9066 (ppp) REVERT: 0 166 GLN cc_start: 0.9053 (tp40) cc_final: 0.8726 (tp-100) REVERT: 0 219 MET cc_start: 0.9679 (ttm) cc_final: 0.9417 (ppp) outliers start: 2 outliers final: 0 residues processed: 82 average time/residue: 0.5135 time to fit residues: 62.3109 Evaluate side-chains 58 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 56 time to evaluate : 2.546 ------------------------------------------------------------------------------- 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: 0.9980 chunk 283 optimal weight: 5.9990 chunk 81 optimal weight: 7.9990 chunk 245 optimal weight: 8.9990 chunk 39 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 266 optimal weight: 7.9990 chunk 111 optimal weight: 6.9990 chunk 274 optimal weight: 0.0970 chunk 33 optimal weight: 20.0000 chunk 49 optimal weight: 0.8980 overall best weight: 1.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 ASN ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 89 ASN G 237 ASN I 237 ASN K 237 ASN O 101 GLN ** O 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 237 ASN ** U 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 89 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2340 r_free = 0.2340 target = 0.019417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2048 r_free = 0.2048 target = 0.013543 restraints weight = 319774.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2068 r_free = 0.2068 target = 0.013912 restraints weight = 235250.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2084 r_free = 0.2084 target = 0.014210 restraints weight = 188363.152| |-----------------------------------------------------------------------------| r_work (final): 0.2077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9076 moved from start: 0.6340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 26600 Z= 0.126 Angle : 0.524 9.645 36554 Z= 0.250 Chirality : 0.036 0.255 4984 Planarity : 0.002 0.030 4480 Dihedral : 6.294 54.244 6776 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.09 % Allowed : 0.60 % Favored : 99.32 % 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: 1.94 (0.15), residues: 3360 helix: 2.00 (0.11), residues: 2394 sheet: None (None), residues: 0 loop : -0.51 (0.21), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.019 0.001 PHE 0 123 TYR 0.012 0.001 TYR I 65 ARG 0.005 0.000 ARG U 177 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3616.43 seconds wall clock time: 72 minutes 8.51 seconds (4328.51 seconds total)