Starting phenix.real_space_refine on Wed Mar 20 04:09:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t72_10389/03_2024/6t72_10389_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t72_10389/03_2024/6t72_10389.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t72_10389/03_2024/6t72_10389.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t72_10389/03_2024/6t72_10389.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t72_10389/03_2024/6t72_10389_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t72_10389/03_2024/6t72_10389_updated.pdb" } resolution = 3.7 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 42 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: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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': 3} 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': 3} 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': 3} 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': 3} 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': 3} 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': 3} 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': 3} 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': 3} 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': 3} 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': 3} 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': 3} 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': 3} 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': 3} 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': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 14.30, per 1000 atoms: 0.54 Number of scatterers: 26278 At special positions: 0 Unit cell: (156.6, 157.68, 157.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 42 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: 14.05 Conformation dependent library (CDL) restraints added in 4.7 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 67.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.39 Creating SS restraints... Processing helix chain 'A' and resid 5 through 15 removed outlier: 3.559A pdb=" N VAL A 9 " --> pdb=" O THR A 5 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THR A 10 " --> pdb=" O ALA A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 37 removed outlier: 3.569A pdb=" N THR A 36 " --> pdb=" O TYR A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 54 removed outlier: 3.507A pdb=" N LEU A 53 " --> pdb=" O ASN A 49 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N VAL A 54 " --> pdb=" O THR A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 69 removed outlier: 3.591A 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: 3.523A 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: 3.599A pdb=" N ASP A 189 " --> pdb=" O ALA A 185 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS A 193 " --> pdb=" O ASP A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 225 removed outlier: 4.377A pdb=" N ASP A 225 " --> pdb=" O ASN A 221 " (cutoff:3.500A) 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: 3.558A pdb=" N VAL C 9 " --> pdb=" O THR C 5 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR C 10 " --> pdb=" O ALA C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 37 removed outlier: 3.569A pdb=" N THR C 36 " --> pdb=" O TYR C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 54 removed outlier: 3.506A pdb=" N LEU C 53 " --> pdb=" O ASN C 49 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N VAL C 54 " --> pdb=" O THR C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 69 removed outlier: 3.591A 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: 3.523A 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: 3.599A pdb=" N ASP C 189 " --> pdb=" O ALA C 185 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS C 193 " --> pdb=" O ASP C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 225 removed outlier: 4.377A pdb=" N ASP C 225 " --> pdb=" O ASN C 221 " (cutoff:3.500A) 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: 3.559A pdb=" N VAL E 9 " --> pdb=" O THR E 5 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THR E 10 " --> pdb=" O ALA E 6 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 37 removed outlier: 3.569A pdb=" N THR E 36 " --> pdb=" O TYR E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 54 removed outlier: 3.507A pdb=" N LEU E 53 " --> pdb=" O ASN E 49 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N VAL E 54 " --> pdb=" O THR E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 69 removed outlier: 3.591A 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: 3.523A 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: 3.599A pdb=" N ASP E 189 " --> pdb=" O ALA E 185 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS E 193 " --> pdb=" O ASP E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 211 through 225 removed outlier: 4.378A pdb=" N ASP E 225 " --> pdb=" O ASN E 221 " (cutoff:3.500A) 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: 3.559A pdb=" N VAL G 9 " --> pdb=" O THR G 5 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THR G 10 " --> pdb=" O ALA G 6 " (cutoff:3.500A) Processing helix chain 'G' and resid 23 through 37 removed outlier: 3.570A pdb=" N THR G 36 " --> pdb=" O TYR G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 43 through 54 removed outlier: 3.506A pdb=" N LEU G 53 " --> pdb=" O ASN G 49 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N VAL G 54 " --> pdb=" O THR G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 69 removed outlier: 3.590A 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: 3.523A 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: 3.599A pdb=" N ASP G 189 " --> pdb=" O ALA G 185 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS G 193 " --> pdb=" O ASP G 189 " (cutoff:3.500A) Processing helix chain 'G' and resid 211 through 225 removed outlier: 4.377A pdb=" N ASP G 225 " --> pdb=" O ASN G 221 " (cutoff:3.500A) 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: 3.558A pdb=" N VAL I 9 " --> pdb=" O THR I 5 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THR I 10 " --> pdb=" O ALA I 6 " (cutoff:3.500A) Processing helix chain 'I' and resid 23 through 37 removed outlier: 3.569A pdb=" N THR I 36 " --> pdb=" O TYR I 32 " (cutoff:3.500A) Processing helix chain 'I' and resid 43 through 54 removed outlier: 3.506A pdb=" N LEU I 53 " --> pdb=" O ASN I 49 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N VAL I 54 " --> pdb=" O THR I 50 " (cutoff:3.500A) Processing helix chain 'I' and resid 59 through 69 removed outlier: 3.591A 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: 3.523A 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: 3.599A pdb=" N ASP I 189 " --> pdb=" O ALA I 185 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS I 193 " --> pdb=" O ASP I 189 " (cutoff:3.500A) Processing helix chain 'I' and resid 211 through 225 removed outlier: 4.378A pdb=" N ASP I 225 " --> pdb=" O ASN I 221 " (cutoff:3.500A) 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: 3.559A pdb=" N VAL K 9 " --> pdb=" O THR K 5 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR K 10 " --> pdb=" O ALA K 6 " (cutoff:3.500A) Processing helix chain 'K' and resid 23 through 37 removed outlier: 3.570A pdb=" N THR K 36 " --> pdb=" O TYR K 32 " (cutoff:3.500A) Processing helix chain 'K' and resid 43 through 54 removed outlier: 3.507A pdb=" N LEU K 53 " --> pdb=" O ASN K 49 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N VAL K 54 " --> pdb=" O THR K 50 " (cutoff:3.500A) Processing helix chain 'K' and resid 59 through 69 removed outlier: 3.590A 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: 3.523A 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: 3.599A pdb=" N ASP K 189 " --> pdb=" O ALA K 185 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS K 193 " --> pdb=" O ASP K 189 " (cutoff:3.500A) Processing helix chain 'K' and resid 211 through 225 removed outlier: 4.378A pdb=" N ASP K 225 " --> pdb=" O ASN K 221 " (cutoff:3.500A) 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: 3.559A pdb=" N VAL M 9 " --> pdb=" O THR M 5 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR M 10 " --> pdb=" O ALA M 6 " (cutoff:3.500A) Processing helix chain 'M' and resid 23 through 37 removed outlier: 3.569A pdb=" N THR M 36 " --> pdb=" O TYR M 32 " (cutoff:3.500A) Processing helix chain 'M' and resid 43 through 54 removed outlier: 3.506A pdb=" N LEU M 53 " --> pdb=" O ASN M 49 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N VAL M 54 " --> pdb=" O THR M 50 " (cutoff:3.500A) Processing helix chain 'M' and resid 59 through 69 removed outlier: 3.591A 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: 3.522A 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: 3.599A pdb=" N ASP M 189 " --> pdb=" O ALA M 185 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS M 193 " --> pdb=" O ASP M 189 " (cutoff:3.500A) Processing helix chain 'M' and resid 211 through 225 removed outlier: 4.377A pdb=" N ASP M 225 " --> pdb=" O ASN M 221 " (cutoff:3.500A) 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: 3.558A pdb=" N VAL O 9 " --> pdb=" O THR O 5 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR O 10 " --> pdb=" O ALA O 6 " (cutoff:3.500A) Processing helix chain 'O' and resid 23 through 37 removed outlier: 3.569A pdb=" N THR O 36 " --> pdb=" O TYR O 32 " (cutoff:3.500A) Processing helix chain 'O' and resid 43 through 54 removed outlier: 3.507A pdb=" N LEU O 53 " --> pdb=" O ASN O 49 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N VAL O 54 " --> pdb=" O THR O 50 " (cutoff:3.500A) Processing helix chain 'O' and resid 59 through 69 removed outlier: 3.591A 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: 3.523A 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: 3.599A pdb=" N ASP O 189 " --> pdb=" O ALA O 185 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS O 193 " --> pdb=" O ASP O 189 " (cutoff:3.500A) Processing helix chain 'O' and resid 211 through 225 removed outlier: 4.378A pdb=" N ASP O 225 " --> pdb=" O ASN O 221 " (cutoff:3.500A) 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: 3.558A pdb=" N VAL Q 9 " --> pdb=" O THR Q 5 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THR Q 10 " --> pdb=" O ALA Q 6 " (cutoff:3.500A) Processing helix chain 'Q' and resid 23 through 37 removed outlier: 3.569A pdb=" N THR Q 36 " --> pdb=" O TYR Q 32 " (cutoff:3.500A) Processing helix chain 'Q' and resid 43 through 54 removed outlier: 3.507A pdb=" N LEU Q 53 " --> pdb=" O ASN Q 49 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N VAL Q 54 " --> pdb=" O THR Q 50 " (cutoff:3.500A) Processing helix chain 'Q' and resid 59 through 69 removed outlier: 3.591A 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: 3.523A 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: 3.599A pdb=" N ASP Q 189 " --> pdb=" O ALA Q 185 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS Q 193 " --> pdb=" O ASP Q 189 " (cutoff:3.500A) Processing helix chain 'Q' and resid 211 through 225 removed outlier: 4.378A pdb=" N ASP Q 225 " --> pdb=" O ASN Q 221 " (cutoff:3.500A) 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: 3.559A pdb=" N VAL S 9 " --> pdb=" O THR S 5 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR S 10 " --> pdb=" O ALA S 6 " (cutoff:3.500A) Processing helix chain 'S' and resid 23 through 37 removed outlier: 3.570A pdb=" N THR S 36 " --> pdb=" O TYR S 32 " (cutoff:3.500A) Processing helix chain 'S' and resid 43 through 54 removed outlier: 3.506A pdb=" N LEU S 53 " --> pdb=" O ASN S 49 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N VAL S 54 " --> pdb=" O THR S 50 " (cutoff:3.500A) Processing helix chain 'S' and resid 59 through 69 removed outlier: 3.591A 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: 3.523A 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: 3.599A pdb=" N ASP S 189 " --> pdb=" O ALA S 185 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS S 193 " --> pdb=" O ASP S 189 " (cutoff:3.500A) Processing helix chain 'S' and resid 211 through 225 removed outlier: 4.377A pdb=" N ASP S 225 " --> pdb=" O ASN S 221 " (cutoff:3.500A) 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: 3.558A pdb=" N VAL U 9 " --> pdb=" O THR U 5 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR U 10 " --> pdb=" O ALA U 6 " (cutoff:3.500A) Processing helix chain 'U' and resid 23 through 37 removed outlier: 3.569A pdb=" N THR U 36 " --> pdb=" O TYR U 32 " (cutoff:3.500A) Processing helix chain 'U' and resid 43 through 54 removed outlier: 3.506A pdb=" N LEU U 53 " --> pdb=" O ASN U 49 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N VAL U 54 " --> pdb=" O THR U 50 " (cutoff:3.500A) Processing helix chain 'U' and resid 59 through 69 removed outlier: 3.591A 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: 3.523A 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: 3.599A pdb=" N ASP U 189 " --> pdb=" O ALA U 185 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS U 193 " --> pdb=" O ASP U 189 " (cutoff:3.500A) Processing helix chain 'U' and resid 211 through 225 removed outlier: 4.377A pdb=" N ASP U 225 " --> pdb=" O ASN U 221 " (cutoff:3.500A) 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: 3.558A pdb=" N VAL W 9 " --> pdb=" O THR W 5 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THR W 10 " --> pdb=" O ALA W 6 " (cutoff:3.500A) Processing helix chain 'W' and resid 23 through 37 removed outlier: 3.569A pdb=" N THR W 36 " --> pdb=" O TYR W 32 " (cutoff:3.500A) Processing helix chain 'W' and resid 43 through 54 removed outlier: 3.506A pdb=" N LEU W 53 " --> pdb=" O ASN W 49 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N VAL W 54 " --> pdb=" O THR W 50 " (cutoff:3.500A) Processing helix chain 'W' and resid 59 through 69 removed outlier: 3.590A 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: 3.522A 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: 3.600A pdb=" N ASP W 189 " --> pdb=" O ALA W 185 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS W 193 " --> pdb=" O ASP W 189 " (cutoff:3.500A) Processing helix chain 'W' and resid 211 through 225 removed outlier: 4.378A pdb=" N ASP W 225 " --> pdb=" O ASN W 221 " (cutoff:3.500A) 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: 3.559A pdb=" N VAL Y 9 " --> pdb=" O THR Y 5 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THR Y 10 " --> pdb=" O ALA Y 6 " (cutoff:3.500A) Processing helix chain 'Y' and resid 23 through 37 removed outlier: 3.570A pdb=" N THR Y 36 " --> pdb=" O TYR Y 32 " (cutoff:3.500A) Processing helix chain 'Y' and resid 43 through 54 removed outlier: 3.507A pdb=" N LEU Y 53 " --> pdb=" O ASN Y 49 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N VAL Y 54 " --> pdb=" O THR Y 50 " (cutoff:3.500A) Processing helix chain 'Y' and resid 59 through 69 removed outlier: 3.591A 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: 3.523A 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: 3.598A pdb=" N ASP Y 189 " --> pdb=" O ALA Y 185 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS Y 193 " --> pdb=" O ASP Y 189 " (cutoff:3.500A) Processing helix chain 'Y' and resid 211 through 225 removed outlier: 4.377A pdb=" N ASP Y 225 " --> pdb=" O ASN Y 221 " (cutoff:3.500A) 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: 3.559A pdb=" N VAL 0 9 " --> pdb=" O THR 0 5 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THR 0 10 " --> pdb=" O ALA 0 6 " (cutoff:3.500A) Processing helix chain '0' and resid 23 through 37 removed outlier: 3.570A pdb=" N THR 0 36 " --> pdb=" O TYR 0 32 " (cutoff:3.500A) Processing helix chain '0' and resid 43 through 54 removed outlier: 3.506A pdb=" N LEU 0 53 " --> pdb=" O ASN 0 49 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N VAL 0 54 " --> pdb=" O THR 0 50 " (cutoff:3.500A) Processing helix chain '0' and resid 59 through 69 removed outlier: 3.590A 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: 3.523A 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: 3.600A pdb=" N ASP 0 189 " --> pdb=" O ALA 0 185 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS 0 193 " --> pdb=" O ASP 0 189 " (cutoff:3.500A) Processing helix chain '0' and resid 211 through 225 removed outlier: 4.377A pdb=" N ASP 0 225 " --> pdb=" O ASN 0 221 " (cutoff:3.500A) Processing helix chain '0' and resid 238 through 241 No H-bonds generated for 'chain '0' and resid 238 through 241' 1316 hydrogen bonds defined for protein. 3948 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: 7.26 Time building geometry restraints manager: 14.79 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: 6293 1.34 - 1.46: 7644 1.46 - 1.57: 12635 1.57 - 1.69: 0 1.69 - 1.80: 28 Bond restraints: 26600 Sorted by residual: bond pdb=" C ALA O 20 " pdb=" N PRO O 21 " ideal model delta sigma weight residual 1.330 1.358 -0.028 1.22e-02 6.72e+03 5.27e+00 bond pdb=" C ALA W 20 " pdb=" N PRO W 21 " ideal model delta sigma weight residual 1.330 1.358 -0.028 1.22e-02 6.72e+03 5.21e+00 bond pdb=" C ALA 0 20 " pdb=" N PRO 0 21 " ideal model delta sigma weight residual 1.330 1.357 -0.027 1.22e-02 6.72e+03 5.05e+00 bond pdb=" C ALA A 20 " pdb=" N PRO A 21 " ideal model delta sigma weight residual 1.330 1.357 -0.027 1.22e-02 6.72e+03 5.02e+00 bond pdb=" C ALA U 20 " pdb=" N PRO U 21 " ideal model delta sigma weight residual 1.330 1.357 -0.027 1.22e-02 6.72e+03 5.01e+00 ... (remaining 26595 not shown) Histogram of bond angle deviations from ideal: 99.92 - 105.28: 238 105.28 - 110.64: 6181 110.64 - 116.01: 12116 116.01 - 121.37: 10541 121.37 - 126.74: 7478 Bond angle restraints: 36554 Sorted by residual: angle pdb=" C ASP U 93 " pdb=" N ALA U 94 " pdb=" CA ALA U 94 " ideal model delta sigma weight residual 120.44 125.91 -5.47 1.30e+00 5.92e-01 1.77e+01 angle pdb=" C ASP G 93 " pdb=" N ALA G 94 " pdb=" CA ALA G 94 " ideal model delta sigma weight residual 120.44 125.90 -5.46 1.30e+00 5.92e-01 1.76e+01 angle pdb=" C ASP Y 93 " pdb=" N ALA Y 94 " pdb=" CA ALA Y 94 " ideal model delta sigma weight residual 120.44 125.89 -5.45 1.30e+00 5.92e-01 1.76e+01 angle pdb=" C ASP I 93 " pdb=" N ALA I 94 " pdb=" CA ALA I 94 " ideal model delta sigma weight residual 120.44 125.89 -5.45 1.30e+00 5.92e-01 1.76e+01 angle pdb=" C ASP S 93 " pdb=" N ALA S 94 " pdb=" CA ALA S 94 " ideal model delta sigma weight residual 120.44 125.89 -5.45 1.30e+00 5.92e-01 1.76e+01 ... (remaining 36549 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.52: 15512 19.52 - 39.03: 1022 39.03 - 58.55: 280 58.55 - 78.06: 350 78.06 - 97.58: 196 Dihedral angle restraints: 17360 sinusoidal: 7518 harmonic: 9842 Sorted by residual: dihedral pdb=" CA ALA M 113 " pdb=" C ALA M 113 " pdb=" N THR M 114 " pdb=" CA THR M 114 " ideal model delta harmonic sigma weight residual -180.00 -160.53 -19.47 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA ALA K 113 " pdb=" C ALA K 113 " pdb=" N THR K 114 " pdb=" CA THR K 114 " ideal model delta harmonic sigma weight residual -180.00 -160.54 -19.46 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA ALA S 113 " pdb=" C ALA S 113 " pdb=" N THR S 114 " pdb=" CA THR S 114 " ideal model delta harmonic sigma weight residual 180.00 -160.55 -19.45 0 5.00e+00 4.00e-02 1.51e+01 ... (remaining 17357 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 2298 0.063 - 0.127: 1626 0.127 - 0.190: 595 0.190 - 0.253: 314 0.253 - 0.316: 151 Chirality restraints: 4984 Sorted by residual: chirality pdb=" C1 BMA T 10 " pdb=" O3 MRH T 9 " pdb=" C2 BMA T 10 " pdb=" O5 BMA T 10 " both_signs ideal model delta sigma weight residual False -2.40 -2.32 -0.08 2.00e-02 2.50e+03 1.54e+01 chirality pdb=" C1 BMA F 10 " pdb=" O3 MRH F 9 " pdb=" C2 BMA F 10 " pdb=" O5 BMA F 10 " both_signs ideal model delta sigma weight residual False -2.40 -2.32 -0.08 2.00e-02 2.50e+03 1.51e+01 chirality pdb=" C1 BMA 1 10 " pdb=" O3 MRH 1 9 " pdb=" C2 BMA 1 10 " pdb=" O5 BMA 1 10 " both_signs ideal model delta sigma weight residual False -2.40 -2.32 -0.08 2.00e-02 2.50e+03 1.48e+01 ... (remaining 4981 not shown) Planarity restraints: 4480 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C4 MRH X 12 " -0.284 2.00e-02 2.50e+03 2.50e-01 7.79e+02 pdb=" C7 MRH X 12 " 0.041 2.00e-02 2.50e+03 pdb=" C8 MRH X 12 " -0.022 2.00e-02 2.50e+03 pdb=" N4 MRH X 12 " 0.443 2.00e-02 2.50e+03 pdb=" O7 MRH X 12 " -0.178 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C4 MRH H 12 " -0.284 2.00e-02 2.50e+03 2.50e-01 7.78e+02 pdb=" C7 MRH H 12 " 0.041 2.00e-02 2.50e+03 pdb=" C8 MRH H 12 " -0.022 2.00e-02 2.50e+03 pdb=" N4 MRH H 12 " 0.443 2.00e-02 2.50e+03 pdb=" O7 MRH H 12 " -0.178 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C4 MRH Z 12 " -0.284 2.00e-02 2.50e+03 2.50e-01 7.78e+02 pdb=" C7 MRH Z 12 " 0.042 2.00e-02 2.50e+03 pdb=" C8 MRH Z 12 " -0.022 2.00e-02 2.50e+03 pdb=" N4 MRH Z 12 " 0.443 2.00e-02 2.50e+03 pdb=" O7 MRH Z 12 " -0.178 2.00e-02 2.50e+03 ... (remaining 4477 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 887 2.71 - 3.26: 27796 3.26 - 3.81: 41175 3.81 - 4.35: 54151 4.35 - 4.90: 85691 Nonbonded interactions: 209700 Sorted by model distance: nonbonded pdb=" O ALA G 124 " pdb=" OG1 THR G 128 " model vdw 2.167 2.440 nonbonded pdb=" O ALA Y 124 " pdb=" OG1 THR Y 128 " model vdw 2.167 2.440 nonbonded pdb=" O ALA W 124 " pdb=" OG1 THR W 128 " model vdw 2.167 2.440 nonbonded pdb=" O ALA Q 124 " pdb=" OG1 THR Q 128 " model vdw 2.167 2.440 nonbonded pdb=" O ALA M 124 " pdb=" OG1 THR M 128 " model vdw 2.167 2.440 ... (remaining 209695 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: 1.500 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: 7.110 Check model and map are aligned: 0.420 Set scattering table: 0.270 Process input model: 71.920 Find NCS groups from input model: 1.870 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: 0.010 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 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 : 0.008 0.042 26600 Z= 0.534 Angle : 1.553 7.550 36554 Z= 1.031 Chirality : 0.108 0.316 4984 Planarity : 0.024 0.250 4480 Dihedral : 21.392 97.577 11060 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % 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: -2.53 (0.12), residues: 3360 helix: -1.41 (0.09), residues: 2408 sheet: None (None), residues: 0 loop : -1.92 (0.17), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.014 0.003 PHE Q 68 TYR 0.014 0.002 TYR E 95 ARG 0.005 0.002 ARG C 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 370 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 370 time to evaluate : 2.868 Fit side-chains REVERT: A 79 ASP cc_start: 0.8537 (t70) cc_final: 0.8295 (t0) REVERT: A 166 GLN cc_start: 0.8605 (tp40) cc_final: 0.7913 (tp40) REVERT: A 170 ASP cc_start: 0.7890 (m-30) cc_final: 0.7683 (m-30) REVERT: C 52 LYS cc_start: 0.8596 (tttt) cc_final: 0.8364 (ttmm) REVERT: C 170 ASP cc_start: 0.8626 (m-30) cc_final: 0.8285 (m-30) REVERT: E 102 GLU cc_start: 0.8473 (tt0) cc_final: 0.8247 (tt0) REVERT: E 166 GLN cc_start: 0.7974 (tp40) cc_final: 0.7616 (tm-30) REVERT: E 212 TYR cc_start: 0.8729 (m-80) cc_final: 0.8520 (m-80) REVERT: G 30 ASP cc_start: 0.8471 (t70) cc_final: 0.8136 (t0) REVERT: G 52 LYS cc_start: 0.8561 (tttt) cc_final: 0.8288 (ttmm) REVERT: G 189 ASP cc_start: 0.8922 (t0) cc_final: 0.7887 (m-30) REVERT: I 95 TYR cc_start: 0.9150 (t80) cc_final: 0.8761 (t80) REVERT: K 162 PHE cc_start: 0.7783 (t80) cc_final: 0.7255 (t80) REVERT: K 171 TYR cc_start: 0.8124 (t80) cc_final: 0.7875 (t80) REVERT: M 155 ASP cc_start: 0.7416 (t70) cc_final: 0.7112 (p0) REVERT: S 114 THR cc_start: 0.9249 (p) cc_final: 0.8966 (t) REVERT: U 87 ASN cc_start: 0.9112 (t0) cc_final: 0.8832 (t0) REVERT: U 93 ASP cc_start: 0.7924 (t70) cc_final: 0.7212 (t0) REVERT: U 134 GLN cc_start: 0.8677 (mt0) cc_final: 0.8352 (mt0) REVERT: U 166 GLN cc_start: 0.8562 (tp40) cc_final: 0.8150 (tp-100) REVERT: U 177 ARG cc_start: 0.8036 (ttm110) cc_final: 0.7783 (ttm-80) REVERT: W 30 ASP cc_start: 0.8039 (t70) cc_final: 0.7753 (t0) REVERT: W 52 LYS cc_start: 0.8784 (tttt) cc_final: 0.8469 (ttmm) REVERT: W 79 ASP cc_start: 0.7906 (t70) cc_final: 0.7570 (t70) REVERT: Y 231 ASP cc_start: 0.8160 (t0) cc_final: 0.7926 (t0) outliers start: 0 outliers final: 0 residues processed: 370 average time/residue: 0.3827 time to fit residues: 218.5098 Evaluate side-chains 171 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 2.573 ------------------------------------------------------------------------------- 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: 0.9990 chunk 254 optimal weight: 0.5980 chunk 141 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 chunk 171 optimal weight: 1.9990 chunk 136 optimal weight: 4.9990 chunk 263 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 chunk 196 optimal weight: 0.9990 chunk 305 optimal weight: 9.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- 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 89 ASN ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 107 ASN A 111 ASN ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 237 ASN C 49 ASN C 63 GLN C 89 ASN ** C 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 ASN C 111 ASN ** C 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 237 ASN E 49 ASN E 63 GLN E 89 ASN E 92 ASN E 107 ASN E 111 ASN E 134 GLN E 237 ASN G 49 ASN G 63 GLN G 89 ASN G 92 ASN G 107 ASN G 111 ASN G 134 GLN ** G 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 237 ASN I 49 ASN I 89 ASN ** I 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 107 ASN I 111 ASN I 134 GLN K 49 ASN K 63 GLN K 107 ASN K 111 ASN K 237 ASN M 49 ASN M 89 ASN M 107 ASN M 134 GLN ** M 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 237 ASN O 49 ASN ** O 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 101 GLN O 107 ASN O 111 ASN O 237 ASN Q 49 ASN Q 63 GLN Q 89 ASN ** Q 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 101 GLN Q 107 ASN Q 111 ASN Q 134 GLN Q 168 ASN ** Q 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 237 ASN S 49 ASN S 63 GLN S 89 ASN ** S 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 107 ASN S 111 ASN S 134 GLN ** S 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 237 ASN U 49 ASN U 63 GLN U 89 ASN U 107 ASN U 111 ASN U 134 GLN ** U 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 237 ASN W 49 ASN W 63 GLN W 89 ASN ** W 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 107 ASN W 111 ASN W 134 GLN ** W 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 237 ASN Y 49 ASN Y 63 GLN Y 107 ASN Y 111 ASN Y 134 GLN ** Y 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 237 ASN 0 49 ASN ** 0 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 89 ASN ** 0 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 101 GLN 0 107 ASN 0 134 GLN 0 237 ASN Total number of N/Q/H flips: 90 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 26600 Z= 0.197 Angle : 0.635 9.303 36554 Z= 0.310 Chirality : 0.043 0.242 4984 Planarity : 0.003 0.039 4480 Dihedral : 14.613 65.114 6776 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 2.64 % Allowed : 12.12 % Favored : 85.25 % 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: 0.28 (0.14), residues: 3360 helix: 0.82 (0.11), residues: 2282 sheet: None (None), residues: 0 loop : -1.10 (0.17), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.016 0.002 PHE Y 175 TYR 0.018 0.001 TYR G 171 ARG 0.007 0.001 ARG I 177 *********************** 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 259 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 197 time to evaluate : 2.645 Fit side-chains revert: symmetry clash REVERT: A 165 ARG cc_start: 0.6863 (OUTLIER) cc_final: 0.6202 (ptt90) REVERT: A 166 GLN cc_start: 0.8343 (tp40) cc_final: 0.7945 (tm-30) REVERT: C 30 ASP cc_start: 0.8629 (t70) cc_final: 0.8245 (t0) REVERT: C 52 LYS cc_start: 0.8785 (tttt) cc_final: 0.8567 (ttmm) REVERT: C 165 ARG cc_start: 0.7534 (OUTLIER) cc_final: 0.7280 (ptt90) REVERT: C 170 ASP cc_start: 0.8775 (m-30) cc_final: 0.8480 (m-30) REVERT: E 57 THR cc_start: 0.9159 (p) cc_final: 0.8953 (p) REVERT: E 89 ASN cc_start: 0.8467 (OUTLIER) cc_final: 0.8179 (p0) REVERT: E 98 LYS cc_start: 0.8531 (mttt) cc_final: 0.8328 (ttmm) REVERT: E 165 ARG cc_start: 0.7965 (OUTLIER) cc_final: 0.6598 (ptp90) REVERT: E 219 MET cc_start: 0.8688 (OUTLIER) cc_final: 0.8479 (ttt) REVERT: G 30 ASP cc_start: 0.8586 (t70) cc_final: 0.8068 (t0) REVERT: G 52 LYS cc_start: 0.8795 (tttt) cc_final: 0.8495 (ttmm) REVERT: G 189 ASP cc_start: 0.8928 (t0) cc_final: 0.8064 (m-30) REVERT: I 89 ASN cc_start: 0.8311 (OUTLIER) cc_final: 0.7718 (p0) REVERT: I 92 ASN cc_start: 0.7761 (p0) cc_final: 0.7467 (p0) REVERT: K 62 ILE cc_start: 0.9125 (mm) cc_final: 0.8804 (mt) REVERT: K 79 ASP cc_start: 0.8361 (OUTLIER) cc_final: 0.7870 (t70) REVERT: K 162 PHE cc_start: 0.7998 (t80) cc_final: 0.6303 (t80) REVERT: K 165 ARG cc_start: 0.7716 (OUTLIER) cc_final: 0.5824 (ptp90) REVERT: M 98 LYS cc_start: 0.9129 (mmtm) cc_final: 0.8816 (mmmt) REVERT: M 111 ASN cc_start: 0.7753 (m-40) cc_final: 0.7552 (m-40) REVERT: S 98 LYS cc_start: 0.8576 (mmtt) cc_final: 0.8085 (mtpp) REVERT: S 165 ARG cc_start: 0.7394 (OUTLIER) cc_final: 0.7025 (ptt-90) REVERT: U 87 ASN cc_start: 0.9210 (t0) cc_final: 0.8680 (t0) REVERT: U 162 PHE cc_start: 0.8669 (t80) cc_final: 0.8135 (t80) REVERT: U 166 GLN cc_start: 0.8431 (tp40) cc_final: 0.8145 (tp-100) REVERT: U 172 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7841 (mm) REVERT: W 30 ASP cc_start: 0.8118 (t70) cc_final: 0.7709 (t0) REVERT: W 52 LYS cc_start: 0.8913 (tttt) cc_final: 0.8627 (ttmm) REVERT: W 83 ASP cc_start: 0.8694 (t0) cc_final: 0.8487 (t0) REVERT: 0 35 GLN cc_start: 0.7915 (mm-40) cc_final: 0.7281 (tm-30) outliers start: 62 outliers final: 32 residues processed: 254 average time/residue: 0.4127 time to fit residues: 158.7405 Evaluate side-chains 170 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 128 time to evaluate : 2.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 165 ARG Chi-restraints excluded: chain C residue 89 ASN Chi-restraints excluded: chain C residue 165 ARG Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 189 ASP Chi-restraints excluded: chain E residue 89 ASN Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 92 ASN Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 165 ARG Chi-restraints excluded: chain E residue 219 MET Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain G residue 155 ASP Chi-restraints excluded: chain G residue 209 ILE Chi-restraints excluded: chain I residue 89 ASN Chi-restraints excluded: chain I residue 230 THR Chi-restraints excluded: chain K residue 27 LEU Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 79 ASP Chi-restraints excluded: chain K residue 165 ARG Chi-restraints excluded: chain M residue 89 ASN Chi-restraints excluded: chain M residue 156 VAL Chi-restraints excluded: chain M residue 187 ASP Chi-restraints excluded: chain O residue 89 ASN Chi-restraints excluded: chain O residue 156 VAL Chi-restraints excluded: chain Q residue 89 ASN Chi-restraints excluded: chain Q residue 236 VAL Chi-restraints excluded: chain S residue 60 VAL Chi-restraints excluded: chain S residue 89 ASN Chi-restraints excluded: chain S residue 121 THR Chi-restraints excluded: chain S residue 165 ARG Chi-restraints excluded: chain U residue 89 ASN Chi-restraints excluded: chain U residue 165 ARG Chi-restraints excluded: chain U residue 172 LEU Chi-restraints excluded: chain W residue 60 VAL Chi-restraints excluded: chain W residue 89 ASN Chi-restraints excluded: chain W residue 230 THR Chi-restraints excluded: chain Y residue 60 VAL Chi-restraints excluded: chain 0 residue 60 VAL Chi-restraints excluded: chain 0 residue 89 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 169 optimal weight: 1.9990 chunk 94 optimal weight: 9.9990 chunk 253 optimal weight: 0.7980 chunk 207 optimal weight: 10.0000 chunk 84 optimal weight: 2.9990 chunk 305 optimal weight: 1.9990 chunk 330 optimal weight: 8.9990 chunk 272 optimal weight: 9.9990 chunk 303 optimal weight: 9.9990 chunk 104 optimal weight: 7.9990 chunk 245 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 ASN ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 92 ASN G 101 GLN ** G 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 179 ASN ** Q 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 166 GLN ** 0 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 111 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 26600 Z= 0.232 Angle : 0.593 9.551 36554 Z= 0.286 Chirality : 0.042 0.256 4984 Planarity : 0.003 0.034 4480 Dihedral : 11.624 58.575 6776 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 2.76 % Allowed : 13.78 % Favored : 83.46 % 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: 0.86 (0.14), residues: 3360 helix: 1.33 (0.11), residues: 2282 sheet: None (None), residues: 0 loop : -1.05 (0.18), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.015 0.002 PHE A 175 TYR 0.019 0.001 TYR Y 171 ARG 0.014 0.001 ARG 0 165 *********************** 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 222 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 157 time to evaluate : 2.577 Fit side-chains revert: symmetry clash REVERT: A 89 ASN cc_start: 0.8551 (OUTLIER) cc_final: 0.8324 (p0) REVERT: A 166 GLN cc_start: 0.8210 (tp40) cc_final: 0.7860 (tp40) REVERT: C 30 ASP cc_start: 0.8666 (t70) cc_final: 0.8336 (t0) REVERT: C 52 LYS cc_start: 0.8890 (tttt) cc_final: 0.8665 (ttmm) REVERT: C 170 ASP cc_start: 0.8762 (m-30) cc_final: 0.8467 (m-30) REVERT: E 57 THR cc_start: 0.9173 (p) cc_final: 0.8971 (p) REVERT: E 89 ASN cc_start: 0.8783 (OUTLIER) cc_final: 0.8486 (p0) REVERT: E 98 LYS cc_start: 0.8538 (mttt) cc_final: 0.8320 (ttmm) REVERT: E 166 GLN cc_start: 0.7872 (tp40) cc_final: 0.7600 (tm-30) REVERT: G 30 ASP cc_start: 0.8579 (t70) cc_final: 0.8071 (t0) REVERT: G 52 LYS cc_start: 0.8898 (tttt) cc_final: 0.8562 (ttmm) REVERT: G 166 GLN cc_start: 0.7786 (tp-100) cc_final: 0.7335 (tp-100) REVERT: I 89 ASN cc_start: 0.8239 (OUTLIER) cc_final: 0.7897 (p0) REVERT: K 62 ILE cc_start: 0.9186 (mm) cc_final: 0.8925 (mt) REVERT: K 79 ASP cc_start: 0.8467 (OUTLIER) cc_final: 0.7941 (t70) REVERT: K 162 PHE cc_start: 0.8072 (t80) cc_final: 0.7489 (t80) REVERT: M 98 LYS cc_start: 0.9182 (mmtm) cc_final: 0.8886 (mmmt) REVERT: S 89 ASN cc_start: 0.8680 (OUTLIER) cc_final: 0.8248 (p0) REVERT: S 98 LYS cc_start: 0.8633 (mmtt) cc_final: 0.8189 (mtpp) REVERT: U 111 ASN cc_start: 0.8107 (m-40) cc_final: 0.7898 (m110) REVERT: U 162 PHE cc_start: 0.8703 (t80) cc_final: 0.8181 (t80) REVERT: U 166 GLN cc_start: 0.8426 (tp40) cc_final: 0.8078 (tp-100) REVERT: W 30 ASP cc_start: 0.8159 (t70) cc_final: 0.7688 (t0) REVERT: W 52 LYS cc_start: 0.8920 (tttt) cc_final: 0.8608 (ttmm) REVERT: Y 231 ASP cc_start: 0.8041 (t0) cc_final: 0.7841 (t0) REVERT: 0 35 GLN cc_start: 0.7925 (mm-40) cc_final: 0.7240 (tm-30) REVERT: 0 89 ASN cc_start: 0.7817 (OUTLIER) cc_final: 0.7553 (p0) outliers start: 65 outliers final: 37 residues processed: 216 average time/residue: 0.3933 time to fit residues: 133.0980 Evaluate side-chains 175 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 132 time to evaluate : 2.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain C residue 89 ASN Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain E residue 89 ASN Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain G residue 89 ASN Chi-restraints excluded: chain G residue 155 ASP Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 209 ILE Chi-restraints excluded: chain I residue 89 ASN Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain I residue 91 LEU Chi-restraints excluded: chain I residue 230 THR Chi-restraints excluded: chain K residue 27 LEU Chi-restraints excluded: chain K residue 52 LYS Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 79 ASP Chi-restraints excluded: chain K residue 197 ILE Chi-restraints excluded: chain M residue 89 ASN Chi-restraints excluded: chain M residue 135 THR Chi-restraints excluded: chain M residue 156 VAL Chi-restraints excluded: chain M residue 187 ASP Chi-restraints excluded: chain O residue 51 LEU Chi-restraints excluded: chain O residue 156 VAL Chi-restraints excluded: chain Q residue 236 VAL Chi-restraints excluded: chain S residue 60 VAL Chi-restraints excluded: chain S residue 89 ASN Chi-restraints excluded: chain S residue 121 THR Chi-restraints excluded: chain S residue 206 VAL Chi-restraints excluded: chain U residue 22 ASP Chi-restraints excluded: chain U residue 206 VAL Chi-restraints excluded: chain W residue 60 VAL Chi-restraints excluded: chain W residue 230 THR Chi-restraints excluded: chain Y residue 60 VAL Chi-restraints excluded: chain Y residue 89 ASN Chi-restraints excluded: chain Y residue 200 ILE Chi-restraints excluded: chain 0 residue 60 VAL Chi-restraints excluded: chain 0 residue 89 ASN Chi-restraints excluded: chain 0 residue 200 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 302 optimal weight: 4.9990 chunk 229 optimal weight: 4.9990 chunk 158 optimal weight: 9.9990 chunk 33 optimal weight: 6.9990 chunk 145 optimal weight: 1.9990 chunk 205 optimal weight: 4.9990 chunk 306 optimal weight: 3.9990 chunk 324 optimal weight: 0.9980 chunk 160 optimal weight: 5.9990 chunk 290 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN A 111 ASN A 179 ASN ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 237 ASN C 89 ASN C 168 ASN E 16 ASN ** E 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 GLN G 92 ASN ** G 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 237 ASN I 89 ASN M 63 GLN ** M 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 89 ASN ** S 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 111 ASN U 89 ASN ** U 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 179 ASN Y 37 GLN 0 179 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 26600 Z= 0.311 Angle : 0.609 9.852 36554 Z= 0.295 Chirality : 0.042 0.260 4984 Planarity : 0.003 0.036 4480 Dihedral : 9.157 57.684 6776 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.66 % Allowed : 14.12 % Favored : 82.23 % 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: 0.74 (0.14), residues: 3360 helix: 1.19 (0.11), residues: 2338 sheet: None (None), residues: 0 loop : -1.09 (0.19), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.022 0.002 PHE A 175 TYR 0.020 0.002 TYR Y 171 ARG 0.005 0.001 ARG I 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 234 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 148 time to evaluate : 2.638 Fit side-chains REVERT: A 83 ASP cc_start: 0.7767 (t0) cc_final: 0.7433 (t70) REVERT: A 166 GLN cc_start: 0.8188 (tp40) cc_final: 0.7935 (tm-30) REVERT: C 30 ASP cc_start: 0.8831 (t70) cc_final: 0.8583 (t0) REVERT: C 52 LYS cc_start: 0.8956 (tttt) cc_final: 0.8690 (ttmm) REVERT: C 162 PHE cc_start: 0.8472 (t80) cc_final: 0.7940 (t80) REVERT: C 170 ASP cc_start: 0.8772 (m-30) cc_final: 0.8513 (m-30) REVERT: E 16 ASN cc_start: 0.8948 (OUTLIER) cc_final: 0.8585 (t0) REVERT: E 98 LYS cc_start: 0.8630 (mttt) cc_final: 0.8404 (ttmm) REVERT: E 166 GLN cc_start: 0.8003 (tp40) cc_final: 0.7467 (tm-30) REVERT: G 30 ASP cc_start: 0.8550 (t70) cc_final: 0.8130 (t0) REVERT: G 52 LYS cc_start: 0.8945 (tttt) cc_final: 0.8610 (ttmm) REVERT: G 166 GLN cc_start: 0.7895 (tp-100) cc_final: 0.7523 (tp-100) REVERT: I 89 ASN cc_start: 0.8378 (OUTLIER) cc_final: 0.7789 (p0) REVERT: K 62 ILE cc_start: 0.9289 (mm) cc_final: 0.9033 (mt) REVERT: K 93 ASP cc_start: 0.8957 (OUTLIER) cc_final: 0.8286 (m-30) REVERT: K 162 PHE cc_start: 0.8110 (t80) cc_final: 0.7573 (t80) REVERT: K 171 TYR cc_start: 0.8160 (t80) cc_final: 0.7812 (t80) REVERT: M 52 LYS cc_start: 0.9075 (ttmm) cc_final: 0.8750 (ttmt) REVERT: M 98 LYS cc_start: 0.9218 (mmtm) cc_final: 0.8931 (mmmt) REVERT: M 111 ASN cc_start: 0.7833 (m-40) cc_final: 0.7560 (m110) REVERT: O 101 GLN cc_start: 0.8418 (tt0) cc_final: 0.8091 (tt0) REVERT: Q 90 ASP cc_start: 0.8666 (OUTLIER) cc_final: 0.8042 (p0) REVERT: S 89 ASN cc_start: 0.8634 (OUTLIER) cc_final: 0.8317 (p0) REVERT: S 98 LYS cc_start: 0.8735 (mmtt) cc_final: 0.8220 (mtpp) REVERT: U 162 PHE cc_start: 0.8647 (t80) cc_final: 0.8122 (t80) REVERT: U 166 GLN cc_start: 0.8396 (tp40) cc_final: 0.7945 (tp-100) REVERT: W 30 ASP cc_start: 0.8129 (t70) cc_final: 0.7679 (t0) REVERT: W 52 LYS cc_start: 0.8924 (tttt) cc_final: 0.8618 (ttmm) REVERT: Y 231 ASP cc_start: 0.8328 (t0) cc_final: 0.8021 (t0) REVERT: 0 35 GLN cc_start: 0.8011 (mm-40) cc_final: 0.7352 (tm-30) outliers start: 86 outliers final: 63 residues processed: 228 average time/residue: 0.3679 time to fit residues: 133.1754 Evaluate side-chains 202 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 134 time to evaluate : 2.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain C residue 89 ASN Chi-restraints excluded: chain C residue 168 ASN Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain E residue 16 ASN Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain G residue 89 ASN Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain G residue 155 ASP Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 209 ILE Chi-restraints excluded: chain I residue 89 ASN Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain I residue 91 LEU Chi-restraints excluded: chain I residue 130 VAL Chi-restraints excluded: chain I residue 206 VAL Chi-restraints excluded: chain I residue 230 THR Chi-restraints excluded: chain I residue 240 THR Chi-restraints excluded: chain K residue 27 LEU Chi-restraints excluded: chain K residue 52 LYS Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 93 ASP Chi-restraints excluded: chain K residue 110 ILE Chi-restraints excluded: chain K residue 130 VAL Chi-restraints excluded: chain K residue 206 VAL Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 130 VAL Chi-restraints excluded: chain M residue 135 THR Chi-restraints excluded: chain M residue 156 VAL Chi-restraints excluded: chain M residue 187 ASP Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain O residue 51 LEU Chi-restraints excluded: chain O residue 89 ASN Chi-restraints excluded: chain O residue 156 VAL Chi-restraints excluded: chain O residue 187 ASP Chi-restraints excluded: chain Q residue 90 ASP Chi-restraints excluded: chain Q residue 236 VAL Chi-restraints excluded: chain S residue 60 VAL Chi-restraints excluded: chain S residue 89 ASN Chi-restraints excluded: chain S residue 121 THR Chi-restraints excluded: chain S residue 156 VAL Chi-restraints excluded: chain S residue 206 VAL Chi-restraints excluded: chain U residue 89 ASN Chi-restraints excluded: chain U residue 93 ASP Chi-restraints excluded: chain U residue 130 VAL Chi-restraints excluded: chain U residue 172 LEU Chi-restraints excluded: chain U residue 206 VAL Chi-restraints excluded: chain W residue 60 VAL Chi-restraints excluded: chain W residue 89 ASN Chi-restraints excluded: chain W residue 164 SER Chi-restraints excluded: chain W residue 206 VAL Chi-restraints excluded: chain W residue 230 THR Chi-restraints excluded: chain Y residue 89 ASN Chi-restraints excluded: chain Y residue 200 ILE Chi-restraints excluded: chain Y residue 220 ILE Chi-restraints excluded: chain 0 residue 91 LEU Chi-restraints excluded: chain 0 residue 114 THR Chi-restraints excluded: chain 0 residue 189 ASP Chi-restraints excluded: chain 0 residue 206 VAL Chi-restraints excluded: chain 0 residue 236 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 270 optimal weight: 0.6980 chunk 184 optimal weight: 6.9990 chunk 4 optimal weight: 0.9990 chunk 241 optimal weight: 4.9990 chunk 134 optimal weight: 5.9990 chunk 277 optimal weight: 2.9990 chunk 224 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 165 optimal weight: 6.9990 chunk 291 optimal weight: 7.9990 chunk 81 optimal weight: 5.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 ASN A 92 ASN C 111 ASN E 92 ASN G 92 ASN ** G 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 111 ASN ** M 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 237 ASN ** S 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 111 ASN U 89 ASN U 111 ASN ** U 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 37 GLN 0 237 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.3298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 26600 Z= 0.317 Angle : 0.600 9.901 36554 Z= 0.290 Chirality : 0.041 0.260 4984 Planarity : 0.003 0.041 4480 Dihedral : 8.662 57.422 6776 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.74 % Allowed : 14.67 % Favored : 81.59 % 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: 0.71 (0.15), residues: 3360 helix: 1.16 (0.11), residues: 2338 sheet: None (None), residues: 0 loop : -1.09 (0.19), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.033 0.002 PHE K 175 TYR 0.019 0.002 TYR 0 171 ARG 0.009 0.001 ARG C 165 *********************** 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 228 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 140 time to evaluate : 2.421 Fit side-chains REVERT: A 83 ASP cc_start: 0.7828 (t0) cc_final: 0.7503 (t70) REVERT: C 52 LYS cc_start: 0.8985 (tttt) cc_final: 0.8724 (ttmm) REVERT: C 170 ASP cc_start: 0.8638 (m-30) cc_final: 0.8381 (m-30) REVERT: E 98 LYS cc_start: 0.8697 (mttt) cc_final: 0.8451 (ttmm) REVERT: E 166 GLN cc_start: 0.8064 (tp40) cc_final: 0.7449 (tm-30) REVERT: G 30 ASP cc_start: 0.8542 (t70) cc_final: 0.8089 (t0) REVERT: G 52 LYS cc_start: 0.9014 (tttt) cc_final: 0.8654 (ttmm) REVERT: G 91 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8422 (mt) REVERT: G 166 GLN cc_start: 0.7888 (tp-100) cc_final: 0.7500 (tp-100) REVERT: I 89 ASN cc_start: 0.8066 (OUTLIER) cc_final: 0.7311 (p0) REVERT: K 62 ILE cc_start: 0.9289 (mm) cc_final: 0.9033 (mt) REVERT: K 93 ASP cc_start: 0.8968 (OUTLIER) cc_final: 0.8372 (m-30) REVERT: K 162 PHE cc_start: 0.8099 (t80) cc_final: 0.7566 (t80) REVERT: K 171 TYR cc_start: 0.8157 (t80) cc_final: 0.7854 (t80) REVERT: M 52 LYS cc_start: 0.9113 (ttmm) cc_final: 0.8795 (ttmt) REVERT: M 98 LYS cc_start: 0.9228 (mmtm) cc_final: 0.8941 (mmmt) REVERT: O 91 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8135 (tt) REVERT: O 101 GLN cc_start: 0.8418 (tt0) cc_final: 0.8047 (tt0) REVERT: Q 19 LYS cc_start: 0.8792 (tptp) cc_final: 0.8523 (tptp) REVERT: Q 90 ASP cc_start: 0.8722 (OUTLIER) cc_final: 0.8135 (p0) REVERT: S 98 LYS cc_start: 0.8758 (mmtt) cc_final: 0.8185 (mtpp) REVERT: U 111 ASN cc_start: 0.8177 (m110) cc_final: 0.7892 (m110) REVERT: U 162 PHE cc_start: 0.8511 (t80) cc_final: 0.8163 (t80) REVERT: U 166 GLN cc_start: 0.8360 (tp40) cc_final: 0.7838 (tp-100) REVERT: W 30 ASP cc_start: 0.8128 (t70) cc_final: 0.7668 (t0) REVERT: W 52 LYS cc_start: 0.8960 (tttt) cc_final: 0.8651 (ttmm) REVERT: Y 231 ASP cc_start: 0.8405 (t0) cc_final: 0.8066 (t0) REVERT: 0 35 GLN cc_start: 0.8118 (mm-40) cc_final: 0.7494 (tm-30) REVERT: 0 89 ASN cc_start: 0.7803 (OUTLIER) cc_final: 0.7476 (p0) outliers start: 88 outliers final: 71 residues processed: 221 average time/residue: 0.3694 time to fit residues: 130.3155 Evaluate side-chains 203 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 126 time to evaluate : 2.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain C residue 89 ASN Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 189 ASP Chi-restraints excluded: chain E residue 90 ASP Chi-restraints excluded: chain E residue 97 SER Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain G residue 34 THR Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain G residue 89 ASN Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 155 ASP Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 209 ILE Chi-restraints excluded: chain I residue 89 ASN Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain I residue 91 LEU Chi-restraints excluded: chain I residue 121 THR Chi-restraints excluded: chain I residue 130 VAL Chi-restraints excluded: chain I residue 230 THR Chi-restraints excluded: chain I residue 240 THR Chi-restraints excluded: chain K residue 27 LEU Chi-restraints excluded: chain K residue 52 LYS Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 93 ASP Chi-restraints excluded: chain K residue 130 VAL Chi-restraints excluded: chain K residue 206 VAL Chi-restraints excluded: chain M residue 4 THR Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 89 ASN Chi-restraints excluded: chain M residue 135 THR Chi-restraints excluded: chain M residue 156 VAL Chi-restraints excluded: chain M residue 187 ASP Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain O residue 51 LEU Chi-restraints excluded: chain O residue 89 ASN Chi-restraints excluded: chain O residue 91 LEU Chi-restraints excluded: chain O residue 156 VAL Chi-restraints excluded: chain O residue 180 THR Chi-restraints excluded: chain Q residue 90 ASP Chi-restraints excluded: chain Q residue 236 VAL Chi-restraints excluded: chain S residue 60 VAL Chi-restraints excluded: chain S residue 65 TYR Chi-restraints excluded: chain S residue 121 THR Chi-restraints excluded: chain S residue 156 VAL Chi-restraints excluded: chain S residue 160 VAL Chi-restraints excluded: chain S residue 206 VAL Chi-restraints excluded: chain U residue 89 ASN Chi-restraints excluded: chain U residue 93 ASP Chi-restraints excluded: chain U residue 130 VAL Chi-restraints excluded: chain U residue 172 LEU Chi-restraints excluded: chain U residue 206 VAL Chi-restraints excluded: chain W residue 60 VAL Chi-restraints excluded: chain W residue 89 ASN Chi-restraints excluded: chain W residue 130 VAL Chi-restraints excluded: chain W residue 206 VAL Chi-restraints excluded: chain W residue 230 THR Chi-restraints excluded: chain Y residue 89 ASN Chi-restraints excluded: chain Y residue 91 LEU Chi-restraints excluded: chain Y residue 200 ILE Chi-restraints excluded: chain Y residue 220 ILE Chi-restraints excluded: chain 0 residue 89 ASN Chi-restraints excluded: chain 0 residue 91 LEU Chi-restraints excluded: chain 0 residue 189 ASP Chi-restraints excluded: chain 0 residue 236 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 109 optimal weight: 4.9990 chunk 292 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 190 optimal weight: 10.0000 chunk 80 optimal weight: 7.9990 chunk 325 optimal weight: 1.9990 chunk 269 optimal weight: 2.9990 chunk 150 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 170 optimal weight: 0.6980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 ASN A 92 ASN C 89 ASN G 92 ASN ** G 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 89 ASN ** M 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 89 ASN ** S 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 89 ASN ** W 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 37 GLN ** 0 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 111 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 26600 Z= 0.188 Angle : 0.528 9.805 36554 Z= 0.253 Chirality : 0.038 0.251 4984 Planarity : 0.002 0.035 4480 Dihedral : 7.874 52.912 6776 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.53 % Allowed : 15.35 % Favored : 81.12 % 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: 1.51 (0.11), residues: 2282 sheet: None (None), residues: 0 loop : -0.99 (0.19), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.015 0.001 PHE M 175 TYR 0.018 0.001 TYR 0 171 ARG 0.005 0.001 ARG 0 165 *********************** 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 231 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 148 time to evaluate : 2.641 Fit side-chains REVERT: A 83 ASP cc_start: 0.7847 (t0) cc_final: 0.7561 (t70) REVERT: A 89 ASN cc_start: 0.8217 (OUTLIER) cc_final: 0.7862 (p0) REVERT: C 30 ASP cc_start: 0.8814 (t70) cc_final: 0.8555 (t0) REVERT: C 170 ASP cc_start: 0.8801 (m-30) cc_final: 0.8525 (m-30) REVERT: E 98 LYS cc_start: 0.8684 (mttt) cc_final: 0.8427 (ttmm) REVERT: E 166 GLN cc_start: 0.7999 (tp40) cc_final: 0.7377 (tm-30) REVERT: G 30 ASP cc_start: 0.8587 (t70) cc_final: 0.8122 (t0) REVERT: G 52 LYS cc_start: 0.9017 (tttt) cc_final: 0.8643 (ttmm) REVERT: G 65 TYR cc_start: 0.9171 (OUTLIER) cc_final: 0.8678 (m-80) REVERT: G 166 GLN cc_start: 0.7890 (tp-100) cc_final: 0.7499 (tp-100) REVERT: I 89 ASN cc_start: 0.8128 (OUTLIER) cc_final: 0.7370 (p0) REVERT: K 62 ILE cc_start: 0.9198 (mm) cc_final: 0.8969 (mt) REVERT: K 93 ASP cc_start: 0.8946 (OUTLIER) cc_final: 0.8438 (m-30) REVERT: K 162 PHE cc_start: 0.8064 (t80) cc_final: 0.7532 (t80) REVERT: K 171 TYR cc_start: 0.8175 (t80) cc_final: 0.7871 (t80) REVERT: M 52 LYS cc_start: 0.9114 (ttmm) cc_final: 0.8790 (ttmt) REVERT: M 98 LYS cc_start: 0.9234 (mmtm) cc_final: 0.8944 (mmmt) REVERT: O 91 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8038 (tt) REVERT: O 101 GLN cc_start: 0.8338 (tt0) cc_final: 0.7968 (tt0) REVERT: Q 90 ASP cc_start: 0.8697 (OUTLIER) cc_final: 0.8066 (p0) REVERT: S 98 LYS cc_start: 0.8758 (mmtt) cc_final: 0.8190 (mtpp) REVERT: U 111 ASN cc_start: 0.8163 (m110) cc_final: 0.7874 (m110) REVERT: U 162 PHE cc_start: 0.8510 (t80) cc_final: 0.8181 (t80) REVERT: U 166 GLN cc_start: 0.8312 (tp40) cc_final: 0.7817 (tp-100) REVERT: W 30 ASP cc_start: 0.8101 (t70) cc_final: 0.7648 (t0) REVERT: W 52 LYS cc_start: 0.8976 (tttt) cc_final: 0.8649 (ttmm) REVERT: Y 231 ASP cc_start: 0.8367 (t0) cc_final: 0.8036 (t0) REVERT: 0 35 GLN cc_start: 0.8104 (mm-40) cc_final: 0.7503 (tm-30) outliers start: 83 outliers final: 60 residues processed: 225 average time/residue: 0.3636 time to fit residues: 130.7673 Evaluate side-chains 195 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 129 time to evaluate : 2.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain C residue 89 ASN Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain G residue 65 TYR Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain G residue 89 ASN Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain G residue 92 ASN Chi-restraints excluded: chain G residue 155 ASP Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 209 ILE Chi-restraints excluded: chain I residue 89 ASN Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain I residue 91 LEU Chi-restraints excluded: chain I residue 130 VAL Chi-restraints excluded: chain I residue 206 VAL Chi-restraints excluded: chain I residue 230 THR Chi-restraints excluded: chain K residue 27 LEU Chi-restraints excluded: chain K residue 52 LYS Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 93 ASP Chi-restraints excluded: chain K residue 110 ILE Chi-restraints excluded: chain K residue 130 VAL Chi-restraints excluded: chain K residue 206 VAL Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 89 ASN Chi-restraints excluded: chain M residue 130 VAL Chi-restraints excluded: chain M residue 135 THR Chi-restraints excluded: chain M residue 156 VAL Chi-restraints excluded: chain M residue 187 ASP Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain O residue 51 LEU Chi-restraints excluded: chain O residue 89 ASN Chi-restraints excluded: chain O residue 91 LEU Chi-restraints excluded: chain O residue 156 VAL Chi-restraints excluded: chain O residue 206 VAL Chi-restraints excluded: chain Q residue 90 ASP Chi-restraints excluded: chain Q residue 236 VAL Chi-restraints excluded: chain S residue 60 VAL Chi-restraints excluded: chain S residue 65 TYR Chi-restraints excluded: chain S residue 89 ASN Chi-restraints excluded: chain S residue 121 THR Chi-restraints excluded: chain S residue 156 VAL Chi-restraints excluded: chain U residue 22 ASP Chi-restraints excluded: chain U residue 89 ASN Chi-restraints excluded: chain U residue 93 ASP Chi-restraints excluded: chain U residue 130 VAL Chi-restraints excluded: chain U residue 172 LEU Chi-restraints excluded: chain U residue 219 MET Chi-restraints excluded: chain W residue 60 VAL Chi-restraints excluded: chain W residue 89 ASN Chi-restraints excluded: chain W residue 164 SER Chi-restraints excluded: chain W residue 206 VAL Chi-restraints excluded: chain W residue 230 THR Chi-restraints excluded: chain Y residue 89 ASN Chi-restraints excluded: chain Y residue 220 ILE Chi-restraints excluded: chain 0 residue 206 VAL Chi-restraints excluded: chain 0 residue 236 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 313 optimal weight: 0.6980 chunk 36 optimal weight: 5.9990 chunk 185 optimal weight: 5.9990 chunk 237 optimal weight: 0.9980 chunk 183 optimal weight: 5.9990 chunk 273 optimal weight: 4.9990 chunk 181 optimal weight: 10.0000 chunk 323 optimal weight: 6.9990 chunk 202 optimal weight: 0.8980 chunk 197 optimal weight: 0.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN ** E 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 92 ASN I 89 ASN K 179 ASN ** M 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 111 ASN O 89 ASN S 89 ASN ** S 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 111 ASN U 89 ASN ** W 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 37 GLN ** 0 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 26600 Z= 0.158 Angle : 0.508 9.794 36554 Z= 0.243 Chirality : 0.037 0.249 4984 Planarity : 0.002 0.038 4480 Dihedral : 7.376 52.566 6776 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.40 % Allowed : 15.43 % Favored : 81.16 % 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: 1.26 (0.15), residues: 3360 helix: 1.66 (0.11), residues: 2282 sheet: None (None), residues: 0 loop : -0.95 (0.19), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.015 0.001 PHE M 175 TYR 0.020 0.001 TYR 0 171 ARG 0.006 0.001 ARG 0 165 *********************** 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 227 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 147 time to evaluate : 2.566 Fit side-chains REVERT: A 83 ASP cc_start: 0.7792 (t0) cc_final: 0.7539 (t70) REVERT: A 89 ASN cc_start: 0.8485 (OUTLIER) cc_final: 0.8092 (p0) REVERT: C 30 ASP cc_start: 0.8819 (t70) cc_final: 0.8561 (t0) REVERT: C 170 ASP cc_start: 0.8800 (m-30) cc_final: 0.8524 (m-30) REVERT: E 98 LYS cc_start: 0.8709 (mttt) cc_final: 0.8447 (ttmm) REVERT: E 166 GLN cc_start: 0.7991 (tp40) cc_final: 0.7360 (tm-30) REVERT: G 30 ASP cc_start: 0.8531 (t70) cc_final: 0.8039 (t0) REVERT: G 52 LYS cc_start: 0.9011 (tttt) cc_final: 0.8643 (ttmm) REVERT: G 65 TYR cc_start: 0.9139 (OUTLIER) cc_final: 0.8671 (m-80) REVERT: G 89 ASN cc_start: 0.8306 (OUTLIER) cc_final: 0.8030 (p0) REVERT: G 166 GLN cc_start: 0.7888 (tp-100) cc_final: 0.7455 (tp-100) REVERT: I 89 ASN cc_start: 0.8232 (OUTLIER) cc_final: 0.7817 (p0) REVERT: K 62 ILE cc_start: 0.9178 (mm) cc_final: 0.8963 (mt) REVERT: K 79 ASP cc_start: 0.8501 (OUTLIER) cc_final: 0.8037 (t70) REVERT: K 93 ASP cc_start: 0.8894 (OUTLIER) cc_final: 0.8509 (m-30) REVERT: K 162 PHE cc_start: 0.8014 (t80) cc_final: 0.7501 (t80) REVERT: K 171 TYR cc_start: 0.8178 (t80) cc_final: 0.7886 (t80) REVERT: M 52 LYS cc_start: 0.9119 (ttmm) cc_final: 0.8803 (ttmt) REVERT: M 98 LYS cc_start: 0.9231 (mmtm) cc_final: 0.8973 (mmmt) REVERT: O 91 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8063 (tt) REVERT: O 101 GLN cc_start: 0.8346 (tt0) cc_final: 0.7976 (tt0) REVERT: Q 90 ASP cc_start: 0.8671 (OUTLIER) cc_final: 0.8047 (p0) REVERT: S 98 LYS cc_start: 0.8783 (mmtt) cc_final: 0.8265 (mtpp) REVERT: U 111 ASN cc_start: 0.8093 (m110) cc_final: 0.7764 (m110) REVERT: U 162 PHE cc_start: 0.8513 (t80) cc_final: 0.8224 (t80) REVERT: U 166 GLN cc_start: 0.8324 (tp40) cc_final: 0.7811 (tp-100) REVERT: W 30 ASP cc_start: 0.8097 (t70) cc_final: 0.7620 (t0) REVERT: W 52 LYS cc_start: 0.8912 (tttt) cc_final: 0.8585 (ttmm) REVERT: Y 231 ASP cc_start: 0.8385 (t0) cc_final: 0.8028 (t0) REVERT: 0 35 GLN cc_start: 0.8122 (mm-40) cc_final: 0.7528 (tm-30) REVERT: 0 89 ASN cc_start: 0.7916 (OUTLIER) cc_final: 0.7616 (p0) outliers start: 80 outliers final: 68 residues processed: 219 average time/residue: 0.3757 time to fit residues: 130.0243 Evaluate side-chains 208 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 131 time to evaluate : 2.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 189 ASP Chi-restraints excluded: chain E residue 65 TYR Chi-restraints excluded: chain E residue 89 ASN Chi-restraints excluded: chain E residue 90 ASP Chi-restraints excluded: chain E residue 97 SER Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain G residue 65 TYR Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain G residue 89 ASN Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain G residue 92 ASN Chi-restraints excluded: chain G residue 155 ASP Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 209 ILE Chi-restraints excluded: chain I residue 89 ASN Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain I residue 91 LEU Chi-restraints excluded: chain I residue 121 THR Chi-restraints excluded: chain I residue 130 VAL Chi-restraints excluded: chain I residue 206 VAL Chi-restraints excluded: chain I residue 230 THR Chi-restraints excluded: chain I residue 240 THR Chi-restraints excluded: chain K residue 27 LEU Chi-restraints excluded: chain K residue 52 LYS Chi-restraints excluded: chain K residue 79 ASP Chi-restraints excluded: chain K residue 93 ASP Chi-restraints excluded: chain K residue 110 ILE Chi-restraints excluded: chain K residue 206 VAL Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 89 ASN Chi-restraints excluded: chain M residue 130 VAL Chi-restraints excluded: chain M residue 135 THR Chi-restraints excluded: chain M residue 156 VAL Chi-restraints excluded: chain M residue 187 ASP Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain O residue 51 LEU Chi-restraints excluded: chain O residue 89 ASN Chi-restraints excluded: chain O residue 91 LEU Chi-restraints excluded: chain O residue 156 VAL Chi-restraints excluded: chain O residue 180 THR Chi-restraints excluded: chain Q residue 90 ASP Chi-restraints excluded: chain Q residue 236 VAL Chi-restraints excluded: chain S residue 60 VAL Chi-restraints excluded: chain S residue 65 TYR Chi-restraints excluded: chain S residue 83 ASP Chi-restraints excluded: chain S residue 89 ASN Chi-restraints excluded: chain S residue 156 VAL Chi-restraints excluded: chain S residue 206 VAL Chi-restraints excluded: chain U residue 22 ASP Chi-restraints excluded: chain U residue 89 ASN Chi-restraints excluded: chain U residue 93 ASP Chi-restraints excluded: chain U residue 130 VAL Chi-restraints excluded: chain U residue 172 LEU Chi-restraints excluded: chain U residue 206 VAL Chi-restraints excluded: chain U residue 219 MET Chi-restraints excluded: chain W residue 60 VAL Chi-restraints excluded: chain W residue 89 ASN Chi-restraints excluded: chain W residue 130 VAL Chi-restraints excluded: chain W residue 206 VAL Chi-restraints excluded: chain W residue 228 LEU Chi-restraints excluded: chain W residue 230 THR Chi-restraints excluded: chain Y residue 89 ASN Chi-restraints excluded: chain Y residue 220 ILE Chi-restraints excluded: chain 0 residue 89 ASN Chi-restraints excluded: chain 0 residue 206 VAL Chi-restraints excluded: chain 0 residue 236 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 200 optimal weight: 10.0000 chunk 129 optimal weight: 0.9990 chunk 193 optimal weight: 0.7980 chunk 97 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 205 optimal weight: 5.9990 chunk 220 optimal weight: 0.5980 chunk 160 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 254 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 ASN A 92 ASN A 237 ASN ** E 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 89 ASN S 89 ASN ** S 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 89 ASN ** W 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 37 GLN ** 0 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.3643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 26600 Z= 0.139 Angle : 0.492 9.782 36554 Z= 0.235 Chirality : 0.037 0.248 4984 Planarity : 0.002 0.042 4480 Dihedral : 6.947 52.365 6776 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.36 % Allowed : 15.31 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.15), residues: 3360 helix: 1.72 (0.11), residues: 2296 sheet: None (None), residues: 0 loop : -0.87 (0.19), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.017 0.001 PHE K 175 TYR 0.021 0.001 TYR 0 171 ARG 0.005 0.001 ARG 0 165 *********************** 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 224 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 145 time to evaluate : 2.718 Fit side-chains REVERT: A 83 ASP cc_start: 0.7840 (t0) cc_final: 0.7580 (t70) REVERT: A 89 ASN cc_start: 0.8557 (OUTLIER) cc_final: 0.8157 (p0) REVERT: C 30 ASP cc_start: 0.8804 (t70) cc_final: 0.8548 (t0) REVERT: C 170 ASP cc_start: 0.8796 (m-30) cc_final: 0.8522 (m-30) REVERT: E 98 LYS cc_start: 0.8708 (mttt) cc_final: 0.8451 (ttmm) REVERT: E 166 GLN cc_start: 0.7969 (tp40) cc_final: 0.7333 (tm-30) REVERT: G 30 ASP cc_start: 0.8534 (t70) cc_final: 0.8029 (t0) REVERT: G 52 LYS cc_start: 0.9013 (tttt) cc_final: 0.8644 (ttmm) REVERT: G 65 TYR cc_start: 0.9118 (OUTLIER) cc_final: 0.8665 (m-80) REVERT: G 89 ASN cc_start: 0.8284 (OUTLIER) cc_final: 0.8008 (p0) REVERT: G 166 GLN cc_start: 0.7874 (tp-100) cc_final: 0.7435 (tp-100) REVERT: I 89 ASN cc_start: 0.7911 (OUTLIER) cc_final: 0.7107 (p0) REVERT: K 62 ILE cc_start: 0.9169 (mm) cc_final: 0.8968 (mt) REVERT: K 79 ASP cc_start: 0.8491 (OUTLIER) cc_final: 0.8035 (t70) REVERT: K 93 ASP cc_start: 0.8888 (OUTLIER) cc_final: 0.8534 (m-30) REVERT: K 162 PHE cc_start: 0.7969 (t80) cc_final: 0.7439 (t80) REVERT: K 171 TYR cc_start: 0.8193 (t80) cc_final: 0.7900 (t80) REVERT: M 35 GLN cc_start: 0.9001 (mm110) cc_final: 0.8472 (mm110) REVERT: M 98 LYS cc_start: 0.9226 (mmtm) cc_final: 0.8975 (mmmt) REVERT: Q 90 ASP cc_start: 0.8653 (OUTLIER) cc_final: 0.8038 (p0) REVERT: S 98 LYS cc_start: 0.8796 (mmtt) cc_final: 0.8311 (mtpp) REVERT: U 111 ASN cc_start: 0.8141 (m110) cc_final: 0.7828 (m110) REVERT: U 162 PHE cc_start: 0.8497 (t80) cc_final: 0.8212 (t80) REVERT: U 166 GLN cc_start: 0.8318 (tp40) cc_final: 0.7879 (tp-100) REVERT: W 30 ASP cc_start: 0.8059 (t70) cc_final: 0.7744 (t0) REVERT: W 52 LYS cc_start: 0.8894 (tttt) cc_final: 0.8576 (ttmm) REVERT: Y 231 ASP cc_start: 0.8356 (t0) cc_final: 0.7991 (t0) REVERT: 0 35 GLN cc_start: 0.8175 (mm-40) cc_final: 0.7626 (tm-30) REVERT: 0 89 ASN cc_start: 0.7896 (OUTLIER) cc_final: 0.7614 (p0) REVERT: 0 165 ARG cc_start: 0.7382 (OUTLIER) cc_final: 0.6889 (pmt-80) outliers start: 79 outliers final: 64 residues processed: 219 average time/residue: 0.3579 time to fit residues: 125.3590 Evaluate side-chains 206 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 133 time to evaluate : 2.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 189 ASP Chi-restraints excluded: chain E residue 89 ASN Chi-restraints excluded: chain E residue 90 ASP Chi-restraints excluded: chain E residue 97 SER Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain G residue 65 TYR Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain G residue 89 ASN Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain G residue 155 ASP Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 209 ILE Chi-restraints excluded: chain I residue 89 ASN Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain I residue 91 LEU Chi-restraints excluded: chain I residue 121 THR Chi-restraints excluded: chain I residue 130 VAL Chi-restraints excluded: chain I residue 206 VAL Chi-restraints excluded: chain I residue 230 THR Chi-restraints excluded: chain I residue 240 THR Chi-restraints excluded: chain K residue 27 LEU Chi-restraints excluded: chain K residue 79 ASP Chi-restraints excluded: chain K residue 93 ASP Chi-restraints excluded: chain K residue 110 ILE Chi-restraints excluded: chain K residue 130 VAL Chi-restraints excluded: chain K residue 206 VAL Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 89 ASN Chi-restraints excluded: chain M residue 130 VAL Chi-restraints excluded: chain M residue 135 THR Chi-restraints excluded: chain M residue 156 VAL Chi-restraints excluded: chain M residue 187 ASP Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain O residue 51 LEU Chi-restraints excluded: chain O residue 89 ASN Chi-restraints excluded: chain O residue 156 VAL Chi-restraints excluded: chain O residue 180 THR Chi-restraints excluded: chain Q residue 90 ASP Chi-restraints excluded: chain Q residue 236 VAL Chi-restraints excluded: chain S residue 60 VAL Chi-restraints excluded: chain S residue 65 TYR Chi-restraints excluded: chain S residue 89 ASN Chi-restraints excluded: chain S residue 121 THR Chi-restraints excluded: chain S residue 156 VAL Chi-restraints excluded: chain S residue 206 VAL Chi-restraints excluded: chain U residue 22 ASP Chi-restraints excluded: chain U residue 89 ASN Chi-restraints excluded: chain U residue 93 ASP Chi-restraints excluded: chain U residue 130 VAL Chi-restraints excluded: chain U residue 172 LEU Chi-restraints excluded: chain U residue 206 VAL Chi-restraints excluded: chain W residue 60 VAL Chi-restraints excluded: chain W residue 89 ASN Chi-restraints excluded: chain W residue 130 VAL Chi-restraints excluded: chain W residue 206 VAL Chi-restraints excluded: chain W residue 228 LEU Chi-restraints excluded: chain Y residue 89 ASN Chi-restraints excluded: chain Y residue 220 ILE Chi-restraints excluded: chain 0 residue 89 ASN Chi-restraints excluded: chain 0 residue 165 ARG Chi-restraints excluded: chain 0 residue 206 VAL Chi-restraints excluded: chain 0 residue 236 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 294 optimal weight: 3.9990 chunk 310 optimal weight: 2.9990 chunk 283 optimal weight: 8.9990 chunk 301 optimal weight: 0.9990 chunk 181 optimal weight: 10.0000 chunk 131 optimal weight: 10.0000 chunk 236 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 chunk 272 optimal weight: 7.9990 chunk 285 optimal weight: 3.9990 chunk 300 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 ASN A 92 ASN A 237 ASN E 107 ASN ** E 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 92 ASN ** G 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 89 ASN I 202 ASN M 63 GLN ** M 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 89 ASN S 89 ASN ** S 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 89 ASN Y 37 GLN Y 111 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 26600 Z= 0.301 Angle : 0.569 9.891 36554 Z= 0.275 Chirality : 0.040 0.294 4984 Planarity : 0.002 0.034 4480 Dihedral : 7.067 53.910 6776 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.44 % Allowed : 15.52 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.15), residues: 3360 helix: 1.53 (0.11), residues: 2296 sheet: None (None), residues: 0 loop : -0.94 (0.19), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.022 0.002 PHE K 175 TYR 0.026 0.001 TYR Y 171 ARG 0.008 0.001 ARG I 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 213 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 132 time to evaluate : 2.774 Fit side-chains REVERT: A 83 ASP cc_start: 0.7953 (t0) cc_final: 0.7704 (t70) REVERT: C 170 ASP cc_start: 0.8794 (m-30) cc_final: 0.8520 (m-30) REVERT: E 98 LYS cc_start: 0.8738 (mttt) cc_final: 0.8461 (ttmm) REVERT: E 166 GLN cc_start: 0.8029 (tp40) cc_final: 0.7349 (tm-30) REVERT: G 30 ASP cc_start: 0.8595 (t70) cc_final: 0.8112 (t0) REVERT: G 52 LYS cc_start: 0.9030 (tttt) cc_final: 0.8671 (ttmm) REVERT: G 65 TYR cc_start: 0.9191 (OUTLIER) cc_final: 0.8746 (m-80) REVERT: G 89 ASN cc_start: 0.8464 (OUTLIER) cc_final: 0.8156 (p0) REVERT: G 166 GLN cc_start: 0.7940 (tp-100) cc_final: 0.7565 (tp-100) REVERT: I 89 ASN cc_start: 0.8099 (OUTLIER) cc_final: 0.7342 (p0) REVERT: K 62 ILE cc_start: 0.9257 (mm) cc_final: 0.9030 (mt) REVERT: K 93 ASP cc_start: 0.8977 (OUTLIER) cc_final: 0.8585 (m-30) REVERT: K 162 PHE cc_start: 0.8022 (t80) cc_final: 0.7494 (t80) REVERT: K 171 TYR cc_start: 0.8193 (t80) cc_final: 0.7924 (t80) REVERT: M 35 GLN cc_start: 0.9063 (mm110) cc_final: 0.8501 (mm110) REVERT: M 98 LYS cc_start: 0.9224 (mmtm) cc_final: 0.8966 (mmmt) REVERT: O 101 GLN cc_start: 0.8377 (tt0) cc_final: 0.7997 (tt0) REVERT: Q 19 LYS cc_start: 0.8766 (tptp) cc_final: 0.8516 (tptp) REVERT: Q 90 ASP cc_start: 0.8722 (OUTLIER) cc_final: 0.8093 (p0) REVERT: S 98 LYS cc_start: 0.8776 (mmtt) cc_final: 0.8258 (mtpp) REVERT: U 111 ASN cc_start: 0.8154 (m110) cc_final: 0.7862 (m110) REVERT: U 162 PHE cc_start: 0.8518 (t80) cc_final: 0.8269 (t80) REVERT: W 30 ASP cc_start: 0.8229 (t70) cc_final: 0.7803 (t0) REVERT: W 52 LYS cc_start: 0.8918 (tttt) cc_final: 0.8598 (ttmm) REVERT: Y 231 ASP cc_start: 0.8437 (t0) cc_final: 0.8105 (t0) REVERT: 0 35 GLN cc_start: 0.8297 (mm-40) cc_final: 0.7738 (tm-30) REVERT: 0 89 ASN cc_start: 0.7843 (OUTLIER) cc_final: 0.7526 (p0) REVERT: 0 165 ARG cc_start: 0.7347 (OUTLIER) cc_final: 0.6902 (pmt-80) outliers start: 81 outliers final: 68 residues processed: 207 average time/residue: 0.3631 time to fit residues: 120.1740 Evaluate side-chains 205 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 130 time to evaluate : 2.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 65 TYR Chi-restraints excluded: chain E residue 89 ASN Chi-restraints excluded: chain E residue 90 ASP Chi-restraints excluded: chain E residue 97 SER Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain G residue 65 TYR Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain G residue 89 ASN Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain G residue 92 ASN Chi-restraints excluded: chain G residue 155 ASP Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 209 ILE Chi-restraints excluded: chain I residue 89 ASN Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain I residue 91 LEU Chi-restraints excluded: chain I residue 121 THR Chi-restraints excluded: chain I residue 130 VAL Chi-restraints excluded: chain I residue 206 VAL Chi-restraints excluded: chain I residue 230 THR Chi-restraints excluded: chain I residue 240 THR Chi-restraints excluded: chain K residue 27 LEU Chi-restraints excluded: chain K residue 93 ASP Chi-restraints excluded: chain K residue 110 ILE Chi-restraints excluded: chain K residue 130 VAL Chi-restraints excluded: chain K residue 206 VAL Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 89 ASN Chi-restraints excluded: chain M residue 130 VAL Chi-restraints excluded: chain M residue 135 THR Chi-restraints excluded: chain M residue 156 VAL Chi-restraints excluded: chain M residue 187 ASP Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain O residue 51 LEU Chi-restraints excluded: chain O residue 89 ASN Chi-restraints excluded: chain O residue 156 VAL Chi-restraints excluded: chain O residue 180 THR Chi-restraints excluded: chain Q residue 90 ASP Chi-restraints excluded: chain Q residue 205 THR Chi-restraints excluded: chain Q residue 236 VAL Chi-restraints excluded: chain S residue 60 VAL Chi-restraints excluded: chain S residue 65 TYR Chi-restraints excluded: chain S residue 83 ASP Chi-restraints excluded: chain S residue 89 ASN Chi-restraints excluded: chain S residue 121 THR Chi-restraints excluded: chain S residue 156 VAL Chi-restraints excluded: chain S residue 206 VAL Chi-restraints excluded: chain U residue 89 ASN Chi-restraints excluded: chain U residue 93 ASP Chi-restraints excluded: chain U residue 130 VAL Chi-restraints excluded: chain U residue 172 LEU Chi-restraints excluded: chain U residue 206 VAL Chi-restraints excluded: chain W residue 60 VAL Chi-restraints excluded: chain W residue 89 ASN Chi-restraints excluded: chain W residue 130 VAL Chi-restraints excluded: chain W residue 206 VAL Chi-restraints excluded: chain W residue 228 LEU Chi-restraints excluded: chain Y residue 89 ASN Chi-restraints excluded: chain Y residue 91 LEU Chi-restraints excluded: chain Y residue 220 ILE Chi-restraints excluded: chain 0 residue 89 ASN Chi-restraints excluded: chain 0 residue 91 LEU Chi-restraints excluded: chain 0 residue 165 ARG Chi-restraints excluded: chain 0 residue 206 VAL Chi-restraints excluded: chain 0 residue 236 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 198 optimal weight: 0.9980 chunk 319 optimal weight: 4.9990 chunk 194 optimal weight: 1.9990 chunk 151 optimal weight: 0.9980 chunk 221 optimal weight: 0.5980 chunk 334 optimal weight: 0.0040 chunk 308 optimal weight: 0.9980 chunk 266 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 205 optimal weight: 2.9990 chunk 163 optimal weight: 0.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 ASN A 92 ASN ** E 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 92 ASN ** G 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 179 ASN ** S 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 37 GLN Y 111 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.3682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.107 26600 Z= 0.214 Angle : 0.708 59.183 36554 Z= 0.384 Chirality : 0.039 0.472 4984 Planarity : 0.004 0.129 4480 Dihedral : 7.054 53.809 6776 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.44 % Allowed : 15.65 % Favored : 80.91 % Cbeta Deviations : 0.03 % 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: 1.18 (0.15), residues: 3360 helix: 1.57 (0.11), residues: 2296 sheet: None (None), residues: 0 loop : -0.94 (0.19), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.019 0.001 PHE K 175 TYR 0.022 0.001 TYR Y 171 ARG 0.006 0.001 ARG I 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 209 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 128 time to evaluate : 2.709 Fit side-chains REVERT: A 83 ASP cc_start: 0.7925 (t0) cc_final: 0.7680 (t70) REVERT: C 170 ASP cc_start: 0.8794 (m-30) cc_final: 0.8520 (m-30) REVERT: E 98 LYS cc_start: 0.8729 (mttt) cc_final: 0.8451 (ttmm) REVERT: E 166 GLN cc_start: 0.8025 (tp40) cc_final: 0.7350 (tm-30) REVERT: G 30 ASP cc_start: 0.8585 (t70) cc_final: 0.8101 (t0) REVERT: G 52 LYS cc_start: 0.9023 (tttt) cc_final: 0.8668 (ttmm) REVERT: G 65 TYR cc_start: 0.9185 (OUTLIER) cc_final: 0.8733 (m-80) REVERT: G 89 ASN cc_start: 0.8448 (OUTLIER) cc_final: 0.8134 (p0) REVERT: G 166 GLN cc_start: 0.7934 (tp-100) cc_final: 0.7562 (tp-100) REVERT: I 89 ASN cc_start: 0.7985 (OUTLIER) cc_final: 0.7549 (p0) REVERT: K 62 ILE cc_start: 0.9246 (mm) cc_final: 0.9016 (mt) REVERT: K 93 ASP cc_start: 0.8973 (OUTLIER) cc_final: 0.8580 (m-30) REVERT: K 162 PHE cc_start: 0.8017 (t80) cc_final: 0.7479 (t80) REVERT: K 171 TYR cc_start: 0.8187 (t80) cc_final: 0.7919 (t80) REVERT: M 35 GLN cc_start: 0.9071 (mm110) cc_final: 0.8518 (mm110) REVERT: M 98 LYS cc_start: 0.9222 (mmtm) cc_final: 0.8964 (mmmt) REVERT: O 101 GLN cc_start: 0.8369 (tt0) cc_final: 0.7988 (tt0) REVERT: Q 90 ASP cc_start: 0.8714 (OUTLIER) cc_final: 0.8080 (p0) REVERT: S 98 LYS cc_start: 0.8771 (mmtt) cc_final: 0.8258 (mtpp) REVERT: U 111 ASN cc_start: 0.8143 (m110) cc_final: 0.7847 (m110) REVERT: U 162 PHE cc_start: 0.8514 (t80) cc_final: 0.8268 (t80) REVERT: U 166 GLN cc_start: 0.8128 (tp40) cc_final: 0.7650 (tp-100) REVERT: W 30 ASP cc_start: 0.8211 (t70) cc_final: 0.7779 (t0) REVERT: W 52 LYS cc_start: 0.8910 (tttt) cc_final: 0.8588 (ttmm) REVERT: Y 231 ASP cc_start: 0.8432 (t0) cc_final: 0.8099 (t0) REVERT: 0 35 GLN cc_start: 0.8290 (mm-40) cc_final: 0.7730 (tm-30) REVERT: 0 89 ASN cc_start: 0.7837 (OUTLIER) cc_final: 0.7518 (p0) REVERT: 0 165 ARG cc_start: 0.7340 (OUTLIER) cc_final: 0.6902 (pmt-80) outliers start: 81 outliers final: 68 residues processed: 204 average time/residue: 0.3572 time to fit residues: 117.2882 Evaluate side-chains 203 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 128 time to evaluate : 2.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 89 ASN Chi-restraints excluded: chain E residue 90 ASP Chi-restraints excluded: chain E residue 97 SER Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain G residue 65 TYR Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain G residue 89 ASN Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain G residue 155 ASP Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 209 ILE Chi-restraints excluded: chain I residue 89 ASN Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain I residue 91 LEU Chi-restraints excluded: chain I residue 121 THR Chi-restraints excluded: chain I residue 130 VAL Chi-restraints excluded: chain I residue 206 VAL Chi-restraints excluded: chain I residue 230 THR Chi-restraints excluded: chain I residue 240 THR Chi-restraints excluded: chain K residue 27 LEU Chi-restraints excluded: chain K residue 93 ASP Chi-restraints excluded: chain K residue 110 ILE Chi-restraints excluded: chain K residue 130 VAL Chi-restraints excluded: chain K residue 206 VAL Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 89 ASN Chi-restraints excluded: chain M residue 130 VAL Chi-restraints excluded: chain M residue 135 THR Chi-restraints excluded: chain M residue 156 VAL Chi-restraints excluded: chain M residue 187 ASP Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain O residue 51 LEU Chi-restraints excluded: chain O residue 89 ASN Chi-restraints excluded: chain O residue 156 VAL Chi-restraints excluded: chain O residue 180 THR Chi-restraints excluded: chain Q residue 90 ASP Chi-restraints excluded: chain Q residue 205 THR Chi-restraints excluded: chain Q residue 236 VAL Chi-restraints excluded: chain S residue 60 VAL Chi-restraints excluded: chain S residue 65 TYR Chi-restraints excluded: chain S residue 83 ASP Chi-restraints excluded: chain S residue 121 THR Chi-restraints excluded: chain S residue 130 VAL Chi-restraints excluded: chain S residue 156 VAL Chi-restraints excluded: chain S residue 205 THR Chi-restraints excluded: chain S residue 206 VAL Chi-restraints excluded: chain U residue 22 ASP Chi-restraints excluded: chain U residue 93 ASP Chi-restraints excluded: chain U residue 130 VAL Chi-restraints excluded: chain U residue 172 LEU Chi-restraints excluded: chain U residue 206 VAL Chi-restraints excluded: chain W residue 60 VAL Chi-restraints excluded: chain W residue 89 ASN Chi-restraints excluded: chain W residue 130 VAL Chi-restraints excluded: chain W residue 206 VAL Chi-restraints excluded: chain W residue 228 LEU Chi-restraints excluded: chain Y residue 89 ASN Chi-restraints excluded: chain Y residue 91 LEU Chi-restraints excluded: chain Y residue 220 ILE Chi-restraints excluded: chain 0 residue 89 ASN Chi-restraints excluded: chain 0 residue 91 LEU Chi-restraints excluded: chain 0 residue 165 ARG Chi-restraints excluded: chain 0 residue 206 VAL Chi-restraints excluded: chain 0 residue 236 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 211 optimal weight: 0.7980 chunk 283 optimal weight: 3.9990 chunk 81 optimal weight: 9.9990 chunk 245 optimal weight: 0.9990 chunk 39 optimal weight: 10.0000 chunk 74 optimal weight: 4.9990 chunk 266 optimal weight: 0.9990 chunk 111 optimal weight: 0.0270 chunk 274 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 overall best weight: 0.6440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 37 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.096094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.079144 restraints weight = 50508.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.079298 restraints weight = 44157.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.079529 restraints weight = 40118.303| |-----------------------------------------------------------------------------| r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.3683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.270 26600 Z= 0.284 Angle : 0.869 59.200 36554 Z= 0.510 Chirality : 0.044 1.247 4984 Planarity : 0.004 0.098 4480 Dihedral : 7.054 53.781 6776 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.27 % Allowed : 15.73 % Favored : 80.99 % Cbeta Deviations : 0.10 % 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: 1.19 (0.15), residues: 3360 helix: 1.57 (0.11), residues: 2296 sheet: None (None), residues: 0 loop : -0.92 (0.19), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.016 0.001 PHE M 175 TYR 0.019 0.001 TYR Y 171 ARG 0.004 0.000 ARG I 177 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4007.91 seconds wall clock time: 74 minutes 53.74 seconds (4493.74 seconds total)