Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 27 19:56:21 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t72_10389/04_2023/6t72_10389_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t72_10389/04_2023/6t72_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_10389/04_2023/6t72_10389.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t72_10389/04_2023/6t72_10389.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t72_10389/04_2023/6t72_10389_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t72_10389/04_2023/6t72_10389_updated.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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 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 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 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 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 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 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 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 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 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 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 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 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 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 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: 12.90, per 1000 atoms: 0.49 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: 13.78 Conformation dependent library (CDL) restraints added in 3.7 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: 1.96 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: 7.45 Time building geometry restraints manager: 14.53 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 - 17.37: 12880 17.37 - 34.74: 952 34.74 - 52.11: 280 52.11 - 69.49: 14 69.49 - 86.86: 42 Dihedral angle restraints: 14168 sinusoidal: 4326 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 14165 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: 1.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 8.240 Check model and map are aligned: 0.380 Set scattering table: 0.200 Process input model: 64.340 Find NCS groups from input model: 1.830 Set up NCS constraints: 0.220 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.550 ------------------------------------------------------------------------------- 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 : 14.783 86.857 7868 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 % 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 *********************** 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 : 2.704 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 370 average time/residue: 0.3930 time to fit residues: 224.6151 Evaluate side-chains 156 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 2.638 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1832 ------------------------------------------------------------------------------- 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: 2.9990 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 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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 89 ASN 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: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 26600 Z= 0.189 Angle : 0.571 8.875 36554 Z= 0.296 Chirality : 0.038 0.280 4984 Planarity : 0.003 0.044 4480 Dihedral : 4.861 19.049 3584 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer Outliers : 2.55 % 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: 0.26 (0.14), residues: 3360 helix: 0.81 (0.11), residues: 2282 sheet: None (None), residues: 0 loop : -1.12 (0.17), residues: 1078 *********************** 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 244 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 184 time to evaluate : 2.746 Fit side-chains revert: symmetry clash outliers start: 60 outliers final: 30 residues processed: 239 average time/residue: 0.4314 time to fit residues: 157.3880 Evaluate side-chains 144 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 114 time to evaluate : 2.568 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.2424 time to fit residues: 16.6797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 169 optimal weight: 2.9990 chunk 94 optimal weight: 10.0000 chunk 253 optimal weight: 4.9990 chunk 207 optimal weight: 0.0060 chunk 84 optimal weight: 0.7980 chunk 305 optimal weight: 3.9990 chunk 330 optimal weight: 6.9990 chunk 272 optimal weight: 6.9990 chunk 303 optimal weight: 20.0000 chunk 104 optimal weight: 7.9990 chunk 245 optimal weight: 4.9990 overall best weight: 2.5602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 111 ASN A 179 ASN ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 ASN C 111 ASN ** C 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 92 ASN G 101 GLN ** G 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 237 ASN I 92 ASN K 111 ASN ** M 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 89 ASN O 179 ASN ** S 89 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 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 166 GLN ** 0 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 26600 Z= 0.263 Angle : 0.578 9.645 36554 Z= 0.288 Chirality : 0.038 0.273 4984 Planarity : 0.003 0.071 4480 Dihedral : 4.349 17.992 3584 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer Outliers : 2.08 % 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: 0.69 (0.14), residues: 3360 helix: 1.14 (0.11), residues: 2338 sheet: None (None), residues: 0 loop : -1.08 (0.18), residues: 1022 *********************** 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 202 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 153 time to evaluate : 2.745 Fit side-chains outliers start: 49 outliers final: 30 residues processed: 197 average time/residue: 0.4057 time to fit residues: 125.5435 Evaluate side-chains 148 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 118 time to evaluate : 2.571 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.2656 time to fit residues: 17.8244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 302 optimal weight: 0.7980 chunk 229 optimal weight: 3.9990 chunk 158 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 chunk 145 optimal weight: 0.9990 chunk 205 optimal weight: 4.9990 chunk 306 optimal weight: 10.0000 chunk 324 optimal weight: 2.9990 chunk 160 optimal weight: 10.0000 chunk 290 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 ASN ** C 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 92 ASN ** G 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 63 GLN ** M 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 89 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 37 GLN 0 89 ASN ** 0 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 26600 Z= 0.177 Angle : 0.509 9.678 36554 Z= 0.251 Chirality : 0.036 0.255 4984 Planarity : 0.002 0.045 4480 Dihedral : 4.089 18.485 3584 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer Outliers : 1.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.15), residues: 3360 helix: 1.56 (0.11), residues: 2282 sheet: None (None), residues: 0 loop : -0.94 (0.19), residues: 1078 *********************** 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 168 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 141 time to evaluate : 2.734 Fit side-chains outliers start: 27 outliers final: 14 residues processed: 166 average time/residue: 0.4046 time to fit residues: 105.5481 Evaluate side-chains 131 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 117 time to evaluate : 2.621 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.2180 time to fit residues: 9.0662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 270 optimal weight: 0.7980 chunk 184 optimal weight: 7.9990 chunk 4 optimal weight: 3.9990 chunk 241 optimal weight: 0.7980 chunk 134 optimal weight: 3.9990 chunk 277 optimal weight: 2.9990 chunk 224 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 165 optimal weight: 0.0970 chunk 291 optimal weight: 7.9990 chunk 81 optimal weight: 6.9990 overall best weight: 1.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 ASN C 107 ASN C 111 ASN ** E 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 92 ASN G 166 GLN ** G 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 111 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 37 GLN 0 89 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 26600 Z= 0.190 Angle : 0.503 9.708 36554 Z= 0.246 Chirality : 0.035 0.258 4984 Planarity : 0.002 0.040 4480 Dihedral : 3.901 17.844 3584 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer Outliers : 0.81 % 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: 1.37 (0.15), residues: 3360 helix: 1.73 (0.11), residues: 2268 sheet: None (None), residues: 0 loop : -0.83 (0.19), residues: 1092 *********************** 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 161 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 142 time to evaluate : 2.785 Fit side-chains outliers start: 19 outliers final: 8 residues processed: 160 average time/residue: 0.4193 time to fit residues: 105.1179 Evaluate side-chains 133 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 125 time to evaluate : 2.664 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2288 time to fit residues: 6.9186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 109 optimal weight: 7.9990 chunk 292 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 190 optimal weight: 10.0000 chunk 80 optimal weight: 0.2980 chunk 325 optimal weight: 10.0000 chunk 269 optimal weight: 4.9990 chunk 150 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 170 optimal weight: 6.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 ASN E 101 GLN ** 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 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 89 ASN S 92 ASN ** S 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 37 GLN 0 63 GLN 0 89 ASN ** 0 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 26600 Z= 0.162 Angle : 0.479 9.709 36554 Z= 0.234 Chirality : 0.035 0.254 4984 Planarity : 0.002 0.034 4480 Dihedral : 3.704 16.712 3584 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer Outliers : 1.02 % 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: 1.55 (0.15), residues: 3360 helix: 1.84 (0.11), residues: 2282 sheet: None (None), residues: 0 loop : -0.72 (0.19), residues: 1078 *********************** 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 170 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 146 time to evaluate : 2.734 Fit side-chains outliers start: 24 outliers final: 10 residues processed: 167 average time/residue: 0.4362 time to fit residues: 112.9058 Evaluate side-chains 136 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 126 time to evaluate : 2.728 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2476 time to fit residues: 7.8766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 313 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 185 optimal weight: 7.9990 chunk 237 optimal weight: 4.9990 chunk 183 optimal weight: 4.9990 chunk 273 optimal weight: 1.9990 chunk 181 optimal weight: 5.9990 chunk 323 optimal weight: 4.9990 chunk 202 optimal weight: 0.9980 chunk 197 optimal weight: 0.2980 chunk 149 optimal weight: 6.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 ASN ** E 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 92 ASN G 166 GLN ** G 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 107 ASN M 111 ASN S 89 ASN W 89 ASN ** W 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 37 GLN 0 89 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.060 26600 Z= 0.151 Angle : 0.473 9.693 36554 Z= 0.230 Chirality : 0.034 0.254 4984 Planarity : 0.002 0.029 4480 Dihedral : 3.602 16.291 3584 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer Outliers : 0.94 % 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: 1.66 (0.15), residues: 3360 helix: 1.92 (0.11), residues: 2282 sheet: None (None), residues: 0 loop : -0.68 (0.19), residues: 1078 *********************** 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 165 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 143 time to evaluate : 2.798 Fit side-chains outliers start: 22 outliers final: 11 residues processed: 162 average time/residue: 0.4188 time to fit residues: 107.1189 Evaluate side-chains 133 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 122 time to evaluate : 2.565 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2292 time to fit residues: 8.0960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 200 optimal weight: 8.9990 chunk 129 optimal weight: 0.9980 chunk 193 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 chunk 63 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 205 optimal weight: 5.9990 chunk 220 optimal weight: 0.9980 chunk 160 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 254 optimal weight: 3.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** I 202 ASN K 179 ASN M 63 GLN ** M 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 107 ASN M 111 ASN O 111 ASN S 89 ASN W 89 ASN ** W 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 37 GLN 0 89 ASN 0 237 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 26600 Z= 0.146 Angle : 0.469 9.686 36554 Z= 0.228 Chirality : 0.034 0.254 4984 Planarity : 0.002 0.030 4480 Dihedral : 3.535 16.854 3584 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer Outliers : 0.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.15), residues: 3360 helix: 1.97 (0.11), residues: 2282 sheet: None (None), residues: 0 loop : -0.62 (0.19), residues: 1078 *********************** 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 153 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 143 time to evaluate : 2.579 Fit side-chains outliers start: 10 outliers final: 2 residues processed: 151 average time/residue: 0.4592 time to fit residues: 107.0178 Evaluate side-chains 124 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 122 time to evaluate : 2.584 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2722 time to fit residues: 4.2821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 294 optimal weight: 3.9990 chunk 310 optimal weight: 8.9990 chunk 283 optimal weight: 3.9990 chunk 301 optimal weight: 5.9990 chunk 181 optimal weight: 5.9990 chunk 131 optimal weight: 4.9990 chunk 236 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 chunk 272 optimal weight: 3.9990 chunk 285 optimal weight: 3.9990 chunk 300 optimal weight: 0.8980 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 ASN ** E 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 166 GLN ** G 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 107 ASN M 111 ASN Q 237 ASN S 89 ASN W 89 ASN W 146 ASN W 179 ASN Y 37 GLN Y 237 ASN 0 89 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.3697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.043 26600 Z= 0.327 Angle : 0.594 9.842 36554 Z= 0.291 Chirality : 0.039 0.271 4984 Planarity : 0.003 0.039 4480 Dihedral : 3.927 18.985 3584 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer Outliers : 0.64 % 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: 1.21 (0.15), residues: 3360 helix: 1.49 (0.11), residues: 2338 sheet: None (None), residues: 0 loop : -0.76 (0.19), residues: 1022 *********************** 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 135 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 120 time to evaluate : 2.413 Fit side-chains outliers start: 15 outliers final: 10 residues processed: 133 average time/residue: 0.4373 time to fit residues: 89.9555 Evaluate side-chains 124 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 114 time to evaluate : 2.487 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2271 time to fit residues: 7.7840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 198 optimal weight: 0.9990 chunk 319 optimal weight: 4.9990 chunk 194 optimal weight: 0.9990 chunk 151 optimal weight: 0.5980 chunk 221 optimal weight: 5.9990 chunk 334 optimal weight: 0.8980 chunk 308 optimal weight: 0.0040 chunk 266 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 205 optimal weight: 3.9990 chunk 163 optimal weight: 6.9990 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 92 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** M 107 ASN ** O 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 89 ASN U 166 GLN ** W 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 37 GLN 0 89 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.3845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 26600 Z= 0.122 Angle : 0.474 9.708 36554 Z= 0.232 Chirality : 0.034 0.249 4984 Planarity : 0.002 0.034 4480 Dihedral : 3.600 16.942 3584 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer Outliers : 0.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.15), residues: 3360 helix: 1.93 (0.11), residues: 2282 sheet: None (None), residues: 0 loop : -0.55 (0.20), residues: 1078 ********************** 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 149 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 144 time to evaluate : 2.973 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 149 average time/residue: 0.4458 time to fit residues: 103.1348 Evaluate side-chains 126 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 125 time to evaluate : 2.593 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2389 time to fit residues: 3.7932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 211 optimal weight: 0.9990 chunk 283 optimal weight: 8.9990 chunk 81 optimal weight: 6.9990 chunk 245 optimal weight: 0.3980 chunk 39 optimal weight: 8.9990 chunk 74 optimal weight: 7.9990 chunk 266 optimal weight: 0.9990 chunk 111 optimal weight: 10.0000 chunk 274 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- 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** E 237 ASN ** 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 168 ASN S 89 ASN W 89 ASN ** W 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 37 GLN 0 89 ASN ** 0 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.099819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.083308 restraints weight = 49821.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.083535 restraints weight = 39746.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.083970 restraints weight = 37136.235| |-----------------------------------------------------------------------------| r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.3929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.039 26600 Z= 0.128 Angle : 0.467 9.710 36554 Z= 0.229 Chirality : 0.034 0.252 4984 Planarity : 0.002 0.032 4480 Dihedral : 3.440 16.267 3584 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer Outliers : 0.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.15), residues: 3360 helix: 2.03 (0.11), residues: 2282 sheet: None (None), residues: 0 loop : -0.53 (0.20), residues: 1078 =============================================================================== Job complete usr+sys time: 3557.55 seconds wall clock time: 67 minutes 41.54 seconds (4061.54 seconds total)