Starting phenix.real_space_refine (version: dev) on Sun May 15 15:17:19 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t72_10389/05_2022/6t72_10389_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t72_10389/05_2022/6t72_10389.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t72_10389/05_2022/6t72_10389_ligands.cif 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 { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t72_10389/05_2022/6t72_10389_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t72_10389/05_2022/6t72_10389_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t72_10389/05_2022/6t72_10389.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t72_10389/05_2022/6t72_10389.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t72_10389/05_2022/6t72_10389_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t72_10389/05_2022/6t72_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 Convert atoms to be neutral 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 "B TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 79": "OD1" <-> "OD2" Residue "B PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 90": "OD1" <-> "OD2" Residue "B TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 165": "NH1" <-> "NH2" Residue "B 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 "D TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 79": "OD1" <-> "OD2" Residue "D PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 90": "OD1" <-> "OD2" Residue "D TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 165": "NH1" <-> "NH2" Residue "D 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 "F TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 79": "OD1" <-> "OD2" Residue "F PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 90": "OD1" <-> "OD2" Residue "F TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 165": "NH1" <-> "NH2" Residue "F 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 "H TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 79": "OD1" <-> "OD2" Residue "H PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 90": "OD1" <-> "OD2" Residue "H TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 165": "NH1" <-> "NH2" Residue "H 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 "J TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 79": "OD1" <-> "OD2" Residue "J PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 90": "OD1" <-> "OD2" Residue "J TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 165": "NH1" <-> "NH2" Residue "J 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 "L TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 79": "OD1" <-> "OD2" Residue "L PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 90": "OD1" <-> "OD2" Residue "L TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 165": "NH1" <-> "NH2" Residue "L 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 "N TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 79": "OD1" <-> "OD2" Residue "N PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 90": "OD1" <-> "OD2" Residue "N TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 165": "NH1" <-> "NH2" Residue "N ARG 177": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 26278 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1877 Unusual residues: {' CA': 3, 'MRH': 8, 'BMA': 4} Classifications: {'undetermined': 15, 'peptide': 242} Link IDs: {'PTRANS': 4, 'TRANS': 237, None: 15} Not linked: pdbres="PRO A 243 " pdbres=" CA A 301 " Not linked: pdbres=" CA A 301 " pdbres=" CA A 302 " Not linked: pdbres=" CA A 302 " pdbres=" CA A 303 " Not linked: pdbres=" CA A 303 " pdbres="BMA A 304 " Not linked: pdbres="BMA A 304 " pdbres="MRH A 305 " ... (remaining 10 not shown) Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 1877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1877 Unusual residues: {' CA': 3, 'MRH': 8, 'BMA': 4} Classifications: {'undetermined': 15, 'peptide': 242} Link IDs: {'PTRANS': 4, 'TRANS': 237, None: 15} Not linked: pdbres="PRO B 243 " pdbres=" CA B 301 " Not linked: pdbres=" CA B 301 " pdbres=" CA B 302 " Not linked: pdbres=" CA B 302 " pdbres=" CA B 303 " Not linked: pdbres=" CA B 303 " pdbres="BMA B 304 " Not linked: pdbres="BMA B 304 " pdbres="MRH B 305 " ... (remaining 10 not shown) Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 12 Chain: "C" Number of atoms: 1877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1877 Unusual residues: {' CA': 3, 'MRH': 8, 'BMA': 4} Classifications: {'undetermined': 15, 'peptide': 242} Link IDs: {'PTRANS': 4, 'TRANS': 237, None: 15} Not linked: pdbres="PRO C 243 " pdbres=" CA C 301 " Not linked: pdbres=" CA C 301 " pdbres=" CA C 302 " Not linked: pdbres=" CA C 302 " pdbres=" CA C 303 " Not linked: pdbres=" CA C 303 " pdbres="BMA C 304 " Not linked: pdbres="BMA C 304 " pdbres="MRH C 305 " ... (remaining 10 not shown) Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 12 Chain: "D" Number of atoms: 1877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1877 Unusual residues: {' CA': 3, 'MRH': 8, 'BMA': 4} Classifications: {'undetermined': 15, 'peptide': 242} Link IDs: {'PTRANS': 4, 'TRANS': 237, None: 15} Not linked: pdbres="PRO D 243 " pdbres=" CA D 301 " Not linked: pdbres=" CA D 301 " pdbres=" CA D 302 " Not linked: pdbres=" CA D 302 " pdbres=" CA D 303 " Not linked: pdbres=" CA D 303 " pdbres="BMA D 304 " Not linked: pdbres="BMA D 304 " pdbres="MRH D 305 " ... (remaining 10 not shown) Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 12 Chain: "E" Number of atoms: 1877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1877 Unusual residues: {' CA': 3, 'MRH': 8, 'BMA': 4} Classifications: {'undetermined': 15, 'peptide': 242} Link IDs: {'PTRANS': 4, 'TRANS': 237, None: 15} Not linked: pdbres="PRO E 243 " pdbres=" CA E 301 " Not linked: pdbres=" CA E 301 " pdbres=" CA E 302 " Not linked: pdbres=" CA E 302 " pdbres=" CA E 303 " Not linked: pdbres=" CA E 303 " pdbres="BMA E 304 " Not linked: pdbres="BMA E 304 " pdbres="MRH E 305 " ... (remaining 10 not shown) Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 12 Chain: "F" Number of atoms: 1877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1877 Unusual residues: {' CA': 3, 'MRH': 8, 'BMA': 4} Classifications: {'undetermined': 15, 'peptide': 242} Link IDs: {'PTRANS': 4, 'TRANS': 237, None: 15} Not linked: pdbres="PRO F 243 " pdbres=" CA F 301 " Not linked: pdbres=" CA F 301 " pdbres=" CA F 302 " Not linked: pdbres=" CA F 302 " pdbres=" CA F 303 " Not linked: pdbres=" CA F 303 " pdbres="BMA F 304 " Not linked: pdbres="BMA F 304 " pdbres="MRH F 305 " ... (remaining 10 not shown) Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 12 Chain: "G" Number of atoms: 1877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1877 Unusual residues: {' CA': 3, 'MRH': 8, 'BMA': 4} Classifications: {'undetermined': 15, 'peptide': 242} Link IDs: {'PTRANS': 4, 'TRANS': 237, None: 15} Not linked: pdbres="PRO G 243 " pdbres=" CA G 301 " Not linked: pdbres=" CA G 301 " pdbres=" CA G 302 " Not linked: pdbres=" CA G 302 " pdbres=" CA G 303 " Not linked: pdbres=" CA G 303 " pdbres="BMA G 304 " Not linked: pdbres="BMA G 304 " pdbres="MRH G 305 " ... (remaining 10 not shown) Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 12 Chain: "H" Number of atoms: 1877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1877 Unusual residues: {' CA': 3, 'MRH': 8, 'BMA': 4} Classifications: {'undetermined': 15, 'peptide': 242} Link IDs: {'PTRANS': 4, 'TRANS': 237, None: 15} Not linked: pdbres="PRO H 243 " pdbres=" CA H 301 " Not linked: pdbres=" CA H 301 " pdbres=" CA H 302 " Not linked: pdbres=" CA H 302 " pdbres=" CA H 303 " Not linked: pdbres=" CA H 303 " pdbres="BMA H 304 " Not linked: pdbres="BMA H 304 " pdbres="MRH H 305 " ... (remaining 10 not shown) Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 12 Chain: "I" Number of atoms: 1877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1877 Unusual residues: {' CA': 3, 'MRH': 8, 'BMA': 4} Classifications: {'undetermined': 15, 'peptide': 242} Link IDs: {'PTRANS': 4, 'TRANS': 237, None: 15} Not linked: pdbres="PRO I 243 " pdbres=" CA I 301 " Not linked: pdbres=" CA I 301 " pdbres=" CA I 302 " Not linked: pdbres=" CA I 302 " pdbres=" CA I 303 " Not linked: pdbres=" CA I 303 " pdbres="BMA I 304 " Not linked: pdbres="BMA I 304 " pdbres="MRH I 305 " ... (remaining 10 not shown) Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 12 Chain: "J" Number of atoms: 1877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1877 Unusual residues: {' CA': 3, 'MRH': 8, 'BMA': 4} Classifications: {'undetermined': 15, 'peptide': 242} Link IDs: {'PTRANS': 4, 'TRANS': 237, None: 15} Not linked: pdbres="PRO J 243 " pdbres=" CA J 301 " Not linked: pdbres=" CA J 301 " pdbres=" CA J 302 " Not linked: pdbres=" CA J 302 " pdbres=" CA J 303 " Not linked: pdbres=" CA J 303 " pdbres="BMA J 304 " Not linked: pdbres="BMA J 304 " pdbres="MRH J 305 " ... (remaining 10 not shown) Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 12 Chain: "K" Number of atoms: 1877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1877 Unusual residues: {' CA': 3, 'MRH': 8, 'BMA': 4} Classifications: {'undetermined': 15, 'peptide': 242} Link IDs: {'PTRANS': 4, 'TRANS': 237, None: 15} Not linked: pdbres="PRO K 243 " pdbres=" CA K 301 " Not linked: pdbres=" CA K 301 " pdbres=" CA K 302 " Not linked: pdbres=" CA K 302 " pdbres=" CA K 303 " Not linked: pdbres=" CA K 303 " pdbres="BMA K 304 " Not linked: pdbres="BMA K 304 " pdbres="MRH K 305 " ... (remaining 10 not shown) Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 12 Chain: "L" Number of atoms: 1877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1877 Unusual residues: {' CA': 3, 'MRH': 8, 'BMA': 4} Classifications: {'undetermined': 15, 'peptide': 242} Link IDs: {'PTRANS': 4, 'TRANS': 237, None: 15} Not linked: pdbres="PRO L 243 " pdbres=" CA L 301 " Not linked: pdbres=" CA L 301 " pdbres=" CA L 302 " Not linked: pdbres=" CA L 302 " pdbres=" CA L 303 " Not linked: pdbres=" CA L 303 " pdbres="BMA L 304 " Not linked: pdbres="BMA L 304 " pdbres="MRH L 305 " ... (remaining 10 not shown) Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 12 Chain: "M" Number of atoms: 1877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1877 Unusual residues: {' CA': 3, 'MRH': 8, 'BMA': 4} Classifications: {'undetermined': 15, 'peptide': 242} Link IDs: {'PTRANS': 4, 'TRANS': 237, None: 15} Not linked: pdbres="PRO M 243 " pdbres=" CA M 301 " Not linked: pdbres=" CA M 301 " pdbres=" CA M 302 " Not linked: pdbres=" CA M 302 " pdbres=" CA M 303 " Not linked: pdbres=" CA M 303 " pdbres="BMA M 304 " Not linked: pdbres="BMA M 304 " pdbres="MRH M 305 " ... (remaining 10 not shown) Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 12 Chain: "N" Number of atoms: 1877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1877 Unusual residues: {' CA': 3, 'MRH': 8, 'BMA': 4} Classifications: {'undetermined': 15, 'peptide': 242} Link IDs: {'PTRANS': 4, 'TRANS': 237, None: 15} Not linked: pdbres="PRO N 243 " pdbres=" CA N 301 " Not linked: pdbres=" CA N 301 " pdbres=" CA N 302 " Not linked: pdbres=" CA N 302 " pdbres=" CA N 303 " Not linked: pdbres=" CA N 303 " pdbres="BMA N 304 " Not linked: pdbres="BMA N 304 " pdbres="MRH N 305 " ... (remaining 10 not shown) Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 14.99, per 1000 atoms: 0.57 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 A 304 " - " MRH A 305 " " MRH A 305 " - " MRH A 306 " " BMA A 307 " - " MRH A 308 " " MRH A 308 " - " MRH A 309 " " BMA A 310 " - " MRH A 311 " " MRH A 311 " - " MRH A 312 " " BMA A 313 " - " MRH A 314 " " MRH A 314 " - " MRH A 315 " " BMA B 304 " - " MRH B 305 " " MRH B 305 " - " MRH B 306 " " BMA B 307 " - " MRH B 308 " " MRH B 308 " - " MRH B 309 " " BMA B 310 " - " MRH B 311 " " MRH B 311 " - " MRH B 312 " " BMA B 313 " - " MRH B 314 " " MRH B 314 " - " MRH B 315 " " BMA C 304 " - " MRH C 305 " " MRH C 305 " - " MRH C 306 " " BMA C 307 " - " MRH C 308 " " MRH C 308 " - " MRH C 309 " " BMA C 310 " - " MRH C 311 " " MRH C 311 " - " MRH C 312 " " BMA C 313 " - " MRH C 314 " " MRH C 314 " - " MRH C 315 " " BMA D 304 " - " MRH D 305 " " MRH D 305 " - " MRH D 306 " " BMA D 307 " - " MRH D 308 " " MRH D 308 " - " MRH D 309 " " BMA D 310 " - " MRH D 311 " " MRH D 311 " - " MRH D 312 " " BMA D 313 " - " MRH D 314 " " MRH D 314 " - " MRH D 315 " " BMA E 304 " - " MRH E 305 " " MRH E 305 " - " MRH E 306 " " BMA E 307 " - " MRH E 308 " " MRH E 308 " - " MRH E 309 " " BMA E 310 " - " MRH E 311 " " MRH E 311 " - " MRH E 312 " " BMA E 313 " - " MRH E 314 " " MRH E 314 " - " MRH E 315 " " BMA F 304 " - " MRH F 305 " " MRH F 305 " - " MRH F 306 " " BMA F 307 " - " MRH F 308 " " MRH F 308 " - " MRH F 309 " " BMA F 310 " - " MRH F 311 " " MRH F 311 " - " MRH F 312 " " BMA F 313 " - " MRH F 314 " " MRH F 314 " - " MRH F 315 " " BMA G 304 " - " MRH G 305 " " MRH G 305 " - " MRH G 306 " " BMA G 307 " - " MRH G 308 " " MRH G 308 " - " MRH G 309 " " BMA G 310 " - " MRH G 311 " " MRH G 311 " - " MRH G 312 " " BMA G 313 " - " MRH G 314 " " MRH G 314 " - " MRH G 315 " " BMA H 304 " - " MRH H 305 " " MRH H 305 " - " MRH H 306 " " BMA H 307 " - " MRH H 308 " " MRH H 308 " - " MRH H 309 " " BMA H 310 " - " MRH H 311 " " MRH H 311 " - " MRH H 312 " " BMA H 313 " - " MRH H 314 " " MRH H 314 " - " MRH H 315 " " BMA I 304 " - " MRH I 305 " " MRH I 305 " - " MRH I 306 " " BMA I 307 " - " MRH I 308 " " MRH I 308 " - " MRH I 309 " " BMA I 310 " - " MRH I 311 " " MRH I 311 " - " MRH I 312 " " BMA I 313 " - " MRH I 314 " " MRH I 314 " - " MRH I 315 " " BMA J 304 " - " MRH J 305 " " MRH J 305 " - " MRH J 306 " " BMA J 307 " - " MRH J 308 " " MRH J 308 " - " MRH J 309 " " BMA J 310 " - " MRH J 311 " " MRH J 311 " - " MRH J 312 " " BMA J 313 " - " MRH J 314 " " MRH J 314 " - " MRH J 315 " " BMA K 304 " - " MRH K 305 " " MRH K 305 " - " MRH K 306 " " BMA K 307 " - " MRH K 308 " " MRH K 308 " - " MRH K 309 " " BMA K 310 " - " MRH K 311 " " MRH K 311 " - " MRH K 312 " " BMA K 313 " - " MRH K 314 " " MRH K 314 " - " MRH K 315 " " BMA L 304 " - " MRH L 305 " " MRH L 305 " - " MRH L 306 " " BMA L 307 " - " MRH L 308 " " MRH L 308 " - " MRH L 309 " " BMA L 310 " - " MRH L 311 " " MRH L 311 " - " MRH L 312 " " BMA L 313 " - " MRH L 314 " " MRH L 314 " - " MRH L 315 " " BMA M 304 " - " MRH M 305 " " MRH M 305 " - " MRH M 306 " " BMA M 307 " - " MRH M 308 " " MRH M 308 " - " MRH M 309 " " BMA M 310 " - " MRH M 311 " " MRH M 311 " - " MRH M 312 " " BMA M 313 " - " MRH M 314 " " MRH M 314 " - " MRH M 315 " " BMA N 304 " - " MRH N 305 " " MRH N 305 " - " MRH N 306 " " BMA N 307 " - " MRH N 308 " " MRH N 308 " - " MRH N 309 " " BMA N 310 " - " MRH N 311 " " MRH N 311 " - " MRH N 312 " " BMA N 313 " - " MRH N 314 " " MRH N 314 " - " MRH N 315 " BETA1-3 " MRH A 306 " - " BMA A 307 " " MRH A 309 " - " BMA A 310 " " MRH A 312 " - " BMA A 313 " " MRH B 306 " - " BMA B 307 " " MRH B 309 " - " BMA B 310 " " MRH B 312 " - " BMA B 313 " " MRH C 306 " - " BMA C 307 " " MRH C 309 " - " BMA C 310 " " MRH C 312 " - " BMA C 313 " " MRH D 306 " - " BMA D 307 " " MRH D 309 " - " BMA D 310 " " MRH D 312 " - " BMA D 313 " " MRH E 306 " - " BMA E 307 " " MRH E 309 " - " BMA E 310 " " MRH E 312 " - " BMA E 313 " " MRH F 306 " - " BMA F 307 " " MRH F 309 " - " BMA F 310 " " MRH F 312 " - " BMA F 313 " " MRH G 306 " - " BMA G 307 " " MRH G 309 " - " BMA G 310 " " MRH G 312 " - " BMA G 313 " " MRH H 306 " - " BMA H 307 " " MRH H 309 " - " BMA H 310 " " MRH H 312 " - " BMA H 313 " " MRH I 306 " - " BMA I 307 " " MRH I 309 " - " BMA I 310 " " MRH I 312 " - " BMA I 313 " " MRH J 306 " - " BMA J 307 " " MRH J 309 " - " BMA J 310 " " MRH J 312 " - " BMA J 313 " " MRH K 306 " - " BMA K 307 " " MRH K 309 " - " BMA K 310 " " MRH K 312 " - " BMA K 313 " " MRH L 306 " - " BMA L 307 " " MRH L 309 " - " BMA L 310 " " MRH L 312 " - " BMA L 313 " " MRH M 306 " - " BMA M 307 " " MRH M 309 " - " BMA M 310 " " MRH M 312 " - " BMA M 313 " " MRH N 306 " - " BMA N 307 " " MRH N 309 " - " BMA N 310 " " MRH N 312 " - " BMA N 313 " Time building additional restraints: 15.58 Conformation dependent library (CDL) restraints added in 4.0 seconds 6720 Ramachandran restraints generated. 3360 Oldfield, 0 Emsley, 3360 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6300 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 210 helices and 0 sheets defined 67.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.11 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 'B' and resid 5 through 15 removed outlier: 3.558A pdb=" N VAL B 9 " --> pdb=" O THR B 5 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR B 10 " --> pdb=" O ALA B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 37 removed outlier: 3.569A pdb=" N THR B 36 " --> pdb=" O TYR B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 54 removed outlier: 3.506A pdb=" N LEU B 53 " --> pdb=" O ASN B 49 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N VAL B 54 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 69 removed outlier: 3.591A pdb=" N THR B 64 " --> pdb=" O VAL B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 82 Processing helix chain 'B' and resid 94 through 96 No H-bonds generated for 'chain 'B' and resid 94 through 96' Processing helix chain 'B' and resid 101 through 114 Processing helix chain 'B' and resid 120 through 126 removed outlier: 3.523A pdb=" N ALA B 125 " --> pdb=" O THR B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 144 Processing helix chain 'B' and resid 147 through 152 Processing helix chain 'B' and resid 156 through 164 Processing helix chain 'B' and resid 166 through 179 Processing helix chain 'B' and resid 185 through 205 removed outlier: 3.599A pdb=" N ASP B 189 " --> pdb=" O ALA B 185 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS B 193 " --> pdb=" O ASP B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 225 removed outlier: 4.377A pdb=" N ASP B 225 " --> pdb=" O ASN B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 241 No H-bonds generated for 'chain 'B' and resid 238 through 241' Processing helix chain 'C' and resid 5 through 15 removed outlier: 3.559A pdb=" N VAL C 9 " --> pdb=" O THR C 5 " (cutoff:3.500A) removed outlier: 3.859A 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: 3.507A 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: 3.545A pdb=" N LYS C 193 " --> pdb=" O ASP C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 225 removed outlier: 4.378A 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 'D' and resid 5 through 15 removed outlier: 3.559A pdb=" N VAL D 9 " --> pdb=" O THR D 5 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THR D 10 " --> pdb=" O ALA D 6 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 37 removed outlier: 3.570A pdb=" N THR D 36 " --> pdb=" O TYR D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 54 removed outlier: 3.506A pdb=" N LEU D 53 " --> pdb=" O ASN D 49 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N VAL D 54 " --> pdb=" O THR D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 69 removed outlier: 3.590A pdb=" N THR D 64 " --> pdb=" O VAL D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 82 Processing helix chain 'D' and resid 94 through 96 No H-bonds generated for 'chain 'D' and resid 94 through 96' Processing helix chain 'D' and resid 101 through 114 Processing helix chain 'D' and resid 120 through 126 removed outlier: 3.523A pdb=" N ALA D 125 " --> pdb=" O THR D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 144 Processing helix chain 'D' and resid 147 through 152 Processing helix chain 'D' and resid 156 through 164 Processing helix chain 'D' and resid 166 through 179 Processing helix chain 'D' and resid 185 through 205 removed outlier: 3.599A pdb=" N ASP D 189 " --> pdb=" O ALA D 185 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS D 193 " --> pdb=" O ASP D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 225 removed outlier: 4.377A pdb=" N ASP D 225 " --> pdb=" O ASN D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 241 No H-bonds generated for 'chain 'D' and resid 238 through 241' Processing helix chain 'E' and resid 5 through 15 removed outlier: 3.558A 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: 3.506A 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: 3.546A 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 'F' and resid 5 through 15 removed outlier: 3.559A pdb=" N VAL F 9 " --> pdb=" O THR F 5 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR F 10 " --> pdb=" O ALA F 6 " (cutoff:3.500A) Processing helix chain 'F' and resid 23 through 37 removed outlier: 3.570A pdb=" N THR F 36 " --> pdb=" O TYR F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 43 through 54 removed outlier: 3.507A pdb=" N LEU F 53 " --> pdb=" O ASN F 49 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N VAL F 54 " --> pdb=" O THR F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 59 through 69 removed outlier: 3.590A pdb=" N THR F 64 " --> pdb=" O VAL F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 82 Processing helix chain 'F' and resid 94 through 96 No H-bonds generated for 'chain 'F' and resid 94 through 96' Processing helix chain 'F' and resid 101 through 114 Processing helix chain 'F' and resid 120 through 126 removed outlier: 3.523A pdb=" N ALA F 125 " --> pdb=" O THR F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 144 Processing helix chain 'F' and resid 147 through 152 Processing helix chain 'F' and resid 156 through 164 Processing helix chain 'F' and resid 166 through 179 Processing helix chain 'F' and resid 185 through 205 removed outlier: 3.599A pdb=" N ASP F 189 " --> pdb=" O ALA F 185 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS F 193 " --> pdb=" O ASP F 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 211 through 225 removed outlier: 4.378A pdb=" N ASP F 225 " --> pdb=" O ASN F 221 " (cutoff:3.500A) Processing helix chain 'F' and resid 238 through 241 No H-bonds generated for 'chain 'F' 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: 3.858A pdb=" N THR G 10 " --> pdb=" O ALA G 6 " (cutoff:3.500A) Processing helix chain 'G' and resid 23 through 37 removed outlier: 3.569A 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: 3.591A 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: 3.522A 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: 3.546A 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 'H' and resid 5 through 15 removed outlier: 3.558A pdb=" N VAL H 9 " --> pdb=" O THR H 5 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR H 10 " --> pdb=" O ALA H 6 " (cutoff:3.500A) Processing helix chain 'H' and resid 23 through 37 removed outlier: 3.569A pdb=" N THR H 36 " --> pdb=" O TYR H 32 " (cutoff:3.500A) Processing helix chain 'H' and resid 43 through 54 removed outlier: 3.507A pdb=" N LEU H 53 " --> pdb=" O ASN H 49 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N VAL H 54 " --> pdb=" O THR H 50 " (cutoff:3.500A) Processing helix chain 'H' and resid 59 through 69 removed outlier: 3.591A pdb=" N THR H 64 " --> pdb=" O VAL H 60 " (cutoff:3.500A) Processing helix chain 'H' and resid 75 through 82 Processing helix chain 'H' and resid 94 through 96 No H-bonds generated for 'chain 'H' and resid 94 through 96' Processing helix chain 'H' and resid 101 through 114 Processing helix chain 'H' and resid 120 through 126 removed outlier: 3.523A pdb=" N ALA H 125 " --> pdb=" O THR H 121 " (cutoff:3.500A) Processing helix chain 'H' and resid 132 through 144 Processing helix chain 'H' and resid 147 through 152 Processing helix chain 'H' and resid 156 through 164 Processing helix chain 'H' and resid 166 through 179 Processing helix chain 'H' and resid 185 through 205 removed outlier: 3.599A pdb=" N ASP H 189 " --> pdb=" O ALA H 185 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS H 193 " --> pdb=" O ASP H 189 " (cutoff:3.500A) Processing helix chain 'H' and resid 211 through 225 removed outlier: 4.378A pdb=" N ASP H 225 " --> pdb=" O ASN H 221 " (cutoff:3.500A) Processing helix chain 'H' and resid 238 through 241 No H-bonds generated for 'chain 'H' 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: 3.507A 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 'J' and resid 5 through 15 removed outlier: 3.559A pdb=" N VAL J 9 " --> pdb=" O THR J 5 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR J 10 " --> pdb=" O ALA J 6 " (cutoff:3.500A) Processing helix chain 'J' and resid 23 through 37 removed outlier: 3.570A pdb=" N THR J 36 " --> pdb=" O TYR J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 43 through 54 removed outlier: 3.506A pdb=" N LEU J 53 " --> pdb=" O ASN J 49 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N VAL J 54 " --> pdb=" O THR J 50 " (cutoff:3.500A) Processing helix chain 'J' and resid 59 through 69 removed outlier: 3.591A pdb=" N THR J 64 " --> pdb=" O VAL J 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 75 through 82 Processing helix chain 'J' and resid 94 through 96 No H-bonds generated for 'chain 'J' and resid 94 through 96' Processing helix chain 'J' and resid 101 through 114 Processing helix chain 'J' and resid 120 through 126 removed outlier: 3.523A pdb=" N ALA J 125 " --> pdb=" O THR J 121 " (cutoff:3.500A) Processing helix chain 'J' and resid 132 through 144 Processing helix chain 'J' and resid 147 through 152 Processing helix chain 'J' and resid 156 through 164 Processing helix chain 'J' and resid 166 through 179 Processing helix chain 'J' and resid 185 through 205 removed outlier: 3.599A pdb=" N ASP J 189 " --> pdb=" O ALA J 185 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS J 193 " --> pdb=" O ASP J 189 " (cutoff:3.500A) Processing helix chain 'J' and resid 211 through 225 removed outlier: 4.377A pdb=" N ASP J 225 " --> pdb=" O ASN J 221 " (cutoff:3.500A) Processing helix chain 'J' and resid 238 through 241 No H-bonds generated for 'chain 'J' and resid 238 through 241' Processing helix chain 'K' and resid 5 through 15 removed outlier: 3.558A 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: 3.569A pdb=" N THR K 36 " --> pdb=" O TYR K 32 " (cutoff:3.500A) Processing helix chain 'K' and resid 43 through 54 removed outlier: 3.506A 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: 3.591A 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: 4.377A 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 'L' and resid 5 through 15 removed outlier: 3.558A pdb=" N VAL L 9 " --> pdb=" O THR L 5 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THR L 10 " --> pdb=" O ALA L 6 " (cutoff:3.500A) Processing helix chain 'L' and resid 23 through 37 removed outlier: 3.569A pdb=" N THR L 36 " --> pdb=" O TYR L 32 " (cutoff:3.500A) Processing helix chain 'L' and resid 43 through 54 removed outlier: 3.506A pdb=" N LEU L 53 " --> pdb=" O ASN L 49 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N VAL L 54 " --> pdb=" O THR L 50 " (cutoff:3.500A) Processing helix chain 'L' and resid 59 through 69 removed outlier: 3.590A pdb=" N THR L 64 " --> pdb=" O VAL L 60 " (cutoff:3.500A) Processing helix chain 'L' and resid 75 through 82 Processing helix chain 'L' and resid 94 through 96 No H-bonds generated for 'chain 'L' and resid 94 through 96' Processing helix chain 'L' and resid 101 through 114 Processing helix chain 'L' and resid 120 through 126 removed outlier: 3.522A pdb=" N ALA L 125 " --> pdb=" O THR L 121 " (cutoff:3.500A) Processing helix chain 'L' and resid 132 through 144 Processing helix chain 'L' and resid 147 through 152 Processing helix chain 'L' and resid 156 through 164 Processing helix chain 'L' and resid 166 through 179 Processing helix chain 'L' and resid 185 through 205 removed outlier: 3.600A pdb=" N ASP L 189 " --> pdb=" O ALA L 185 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS L 193 " --> pdb=" O ASP L 189 " (cutoff:3.500A) Processing helix chain 'L' and resid 211 through 225 removed outlier: 4.378A pdb=" N ASP L 225 " --> pdb=" O ASN L 221 " (cutoff:3.500A) Processing helix chain 'L' and resid 238 through 241 No H-bonds generated for 'chain 'L' 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: 3.859A pdb=" N THR M 10 " --> pdb=" O ALA M 6 " (cutoff:3.500A) Processing helix chain 'M' and resid 23 through 37 removed outlier: 3.570A pdb=" N THR M 36 " --> pdb=" O TYR M 32 " (cutoff:3.500A) Processing helix chain 'M' and resid 43 through 54 removed outlier: 3.507A 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: 3.523A 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: 3.598A 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 'N' and resid 5 through 15 removed outlier: 3.559A pdb=" N VAL N 9 " --> pdb=" O THR N 5 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THR N 10 " --> pdb=" O ALA N 6 " (cutoff:3.500A) Processing helix chain 'N' and resid 23 through 37 removed outlier: 3.570A pdb=" N THR N 36 " --> pdb=" O TYR N 32 " (cutoff:3.500A) Processing helix chain 'N' and resid 43 through 54 removed outlier: 3.506A pdb=" N LEU N 53 " --> pdb=" O ASN N 49 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N VAL N 54 " --> pdb=" O THR N 50 " (cutoff:3.500A) Processing helix chain 'N' and resid 59 through 69 removed outlier: 3.590A pdb=" N THR N 64 " --> pdb=" O VAL N 60 " (cutoff:3.500A) Processing helix chain 'N' and resid 75 through 82 Processing helix chain 'N' and resid 94 through 96 No H-bonds generated for 'chain 'N' and resid 94 through 96' Processing helix chain 'N' and resid 101 through 114 Processing helix chain 'N' and resid 120 through 126 removed outlier: 3.523A pdb=" N ALA N 125 " --> pdb=" O THR N 121 " (cutoff:3.500A) Processing helix chain 'N' and resid 132 through 144 Processing helix chain 'N' and resid 147 through 152 Processing helix chain 'N' and resid 156 through 164 Processing helix chain 'N' and resid 166 through 179 Processing helix chain 'N' and resid 185 through 205 removed outlier: 3.600A pdb=" N ASP N 189 " --> pdb=" O ALA N 185 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS N 193 " --> pdb=" O ASP N 189 " (cutoff:3.500A) Processing helix chain 'N' and resid 211 through 225 removed outlier: 4.377A pdb=" N ASP N 225 " --> pdb=" O ASN N 221 " (cutoff:3.500A) Processing helix chain 'N' and resid 238 through 241 No H-bonds generated for 'chain 'N' 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: 8.52 Time building geometry restraints manager: 16.14 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=" C7 MRH M 311 " pdb=" N4 MRH M 311 " ideal model delta sigma weight residual 1.463 1.329 0.134 2.00e-02 2.50e+03 4.47e+01 bond pdb=" C7 MRH F 311 " pdb=" N4 MRH F 311 " ideal model delta sigma weight residual 1.463 1.329 0.134 2.00e-02 2.50e+03 4.46e+01 bond pdb=" C7 MRH J 311 " pdb=" N4 MRH J 311 " ideal model delta sigma weight residual 1.463 1.329 0.134 2.00e-02 2.50e+03 4.46e+01 bond pdb=" C7 MRH K 311 " pdb=" N4 MRH K 311 " ideal model delta sigma weight residual 1.463 1.330 0.133 2.00e-02 2.50e+03 4.45e+01 bond pdb=" C7 MRH C 311 " pdb=" N4 MRH C 311 " ideal model delta sigma weight residual 1.463 1.330 0.133 2.00e-02 2.50e+03 4.45e+01 ... (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 K 93 " pdb=" N ALA K 94 " pdb=" CA ALA K 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 D 93 " pdb=" N ALA D 94 " pdb=" CA ALA D 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 M 93 " pdb=" N ALA M 94 " pdb=" CA ALA M 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 E 93 " pdb=" N ALA E 94 " pdb=" CA ALA E 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 J 93 " pdb=" N ALA J 94 " pdb=" CA ALA J 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: 13314 17.37 - 34.74: 1078 34.74 - 52.11: 280 52.11 - 69.49: 14 69.49 - 86.86: 42 Dihedral angle restraints: 14728 sinusoidal: 4886 harmonic: 9842 Sorted by residual: dihedral pdb=" CA ALA G 113 " pdb=" C ALA G 113 " pdb=" N THR G 114 " pdb=" CA THR G 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 F 113 " pdb=" C ALA F 113 " pdb=" N THR F 114 " pdb=" CA THR F 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 J 113 " pdb=" C ALA J 113 " pdb=" N THR J 114 " pdb=" CA THR J 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 14725 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 2211 0.063 - 0.127: 1741 0.127 - 0.190: 609 0.190 - 0.253: 272 0.253 - 0.316: 151 Chirality restraints: 4984 Sorted by residual: chirality pdb=" C1 BMA J 313 " pdb=" O3 MRH J 312 " pdb=" C2 BMA J 313 " pdb=" O5 BMA J 313 " 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 C 313 " pdb=" O3 MRH C 312 " pdb=" C2 BMA C 313 " pdb=" O5 BMA C 313 " 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 N 313 " pdb=" O3 MRH N 312 " pdb=" C2 BMA N 313 " pdb=" O5 BMA N 313 " 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 L 315 " -0.284 2.00e-02 2.50e+03 2.50e-01 7.79e+02 pdb=" C7 MRH L 315 " 0.041 2.00e-02 2.50e+03 pdb=" C8 MRH L 315 " -0.022 2.00e-02 2.50e+03 pdb=" N4 MRH L 315 " 0.443 2.00e-02 2.50e+03 pdb=" O7 MRH L 315 " -0.178 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C4 MRH D 315 " -0.284 2.00e-02 2.50e+03 2.50e-01 7.78e+02 pdb=" C7 MRH D 315 " 0.041 2.00e-02 2.50e+03 pdb=" C8 MRH D 315 " -0.022 2.00e-02 2.50e+03 pdb=" N4 MRH D 315 " 0.443 2.00e-02 2.50e+03 pdb=" O7 MRH D 315 " -0.178 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C4 MRH M 315 " -0.284 2.00e-02 2.50e+03 2.50e-01 7.78e+02 pdb=" C7 MRH M 315 " 0.042 2.00e-02 2.50e+03 pdb=" C8 MRH M 315 " -0.022 2.00e-02 2.50e+03 pdb=" N4 MRH M 315 " 0.443 2.00e-02 2.50e+03 pdb=" O7 MRH M 315 " -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 D 124 " pdb=" OG1 THR D 128 " model vdw 2.167 2.440 nonbonded pdb=" O ALA M 124 " pdb=" OG1 THR M 128 " model vdw 2.167 2.440 nonbonded pdb=" O ALA L 124 " pdb=" OG1 THR L 128 " model vdw 2.167 2.440 nonbonded pdb=" O ALA I 124 " pdb=" OG1 THR I 128 " model vdw 2.167 2.440 nonbonded pdb=" O ALA G 124 " pdb=" OG1 THR G 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 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators 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. 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: 1.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 8.300 Check model and map are aligned: 0.400 Convert atoms to be neutral: 0.230 Process input model: 72.520 Find NCS groups from input model: 2.000 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 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 : 0.013 0.134 26600 Z= 0.879 Angle : 1.638 7.918 36554 Z= 1.051 Chirality : 0.108 0.316 4984 Planarity : 0.024 0.250 4480 Dihedral : 14.695 86.857 8428 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 : 2.716 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 370 average time/residue: 0.3839 time to fit residues: 219.9555 Evaluate side-chains 156 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 2.839 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.4688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 295 optimal weight: 8.9990 chunk 265 optimal weight: 0.0970 chunk 147 optimal weight: 1.9990 chunk 90 optimal weight: 0.0670 chunk 178 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 chunk 274 optimal weight: 0.9990 chunk 106 optimal weight: 0.6980 chunk 166 optimal weight: 1.9990 chunk 204 optimal weight: 0.9990 chunk 317 optimal weight: 9.9990 overall best weight: 0.5720 ------------------------------------------------------------------------------- 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 B 49 ASN B 63 GLN ** B 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 107 ASN B 111 ASN ** B 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN C 49 ASN C 63 GLN C 92 ASN C 107 ASN C 111 ASN C 134 GLN ** C 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 237 ASN D 49 ASN D 63 GLN D 89 ASN D 92 ASN D 107 ASN D 111 ASN D 134 GLN ** D 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 237 ASN E 49 ASN ** E 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 ASN E 111 ASN E 134 GLN F 49 ASN F 63 GLN F 107 ASN F 111 ASN F 237 ASN G 49 ASN G 107 ASN G 134 GLN ** G 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 237 ASN H 49 ASN H 101 GLN H 107 ASN H 111 ASN H 237 ASN I 49 ASN I 63 GLN ** I 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 101 GLN I 107 ASN I 111 ASN I 134 GLN I 168 ASN ** I 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 237 ASN J 49 ASN J 63 GLN J 89 ASN ** J 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 107 ASN J 111 ASN J 134 GLN ** J 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 237 ASN K 49 ASN K 63 GLN K 107 ASN K 111 ASN ** K 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 237 ASN L 49 ASN L 63 GLN ** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 107 ASN L 111 ASN L 134 GLN ** L 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 237 ASN M 49 ASN M 63 GLN M 107 ASN M 111 ASN M 134 GLN ** M 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 237 ASN N 49 ASN ** N 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 101 GLN N 107 ASN N 134 GLN ** N 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 237 ASN Total number of N/Q/H flips: 81 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 26600 Z= 0.166 Angle : 0.572 7.647 36554 Z= 0.295 Chirality : 0.036 0.235 4984 Planarity : 0.003 0.035 4480 Dihedral : 5.996 30.908 4144 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer Outliers : 2.64 % 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: 0.32 (0.14), residues: 3360 helix: 0.83 (0.11), residues: 2268 sheet: None (None), residues: 0 loop : -1.00 (0.18), residues: 1092 *********************** 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 267 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 205 time to evaluate : 2.683 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 62 outliers final: 28 residues processed: 262 average time/residue: 0.4082 time to fit residues: 164.7238 Evaluate side-chains 160 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 132 time to evaluate : 3.030 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.2744 time to fit residues: 17.6100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 176 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 264 optimal weight: 0.5980 chunk 216 optimal weight: 10.0000 chunk 87 optimal weight: 4.9990 chunk 318 optimal weight: 4.9990 chunk 343 optimal weight: 2.9990 chunk 283 optimal weight: 9.9990 chunk 315 optimal weight: 6.9990 chunk 108 optimal weight: 9.9990 chunk 255 optimal weight: 4.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- 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** B 89 ASN ** B 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 ASN ** C 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 ASN D 101 GLN ** D 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 237 ASN E 92 ASN G 89 ASN ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 GLN H 179 ASN I 89 ASN ** J 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 111 ASN K 89 ASN K 111 ASN ** K 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 ASN ** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 166 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.060 26600 Z= 0.331 Angle : 0.606 8.242 36554 Z= 0.308 Chirality : 0.040 0.241 4984 Planarity : 0.003 0.074 4480 Dihedral : 5.177 45.876 4144 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % 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: 0.59 (0.14), residues: 3360 helix: 1.07 (0.11), residues: 2338 sheet: None (None), residues: 0 loop : -1.11 (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 213 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 153 time to evaluate : 2.821 Fit side-chains outliers start: 60 outliers final: 41 residues processed: 207 average time/residue: 0.3708 time to fit residues: 122.3033 Evaluate side-chains 163 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 122 time to evaluate : 2.764 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 0 residues processed: 41 average time/residue: 0.2302 time to fit residues: 21.0609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 314 optimal weight: 5.9990 chunk 239 optimal weight: 4.9990 chunk 165 optimal weight: 0.0050 chunk 35 optimal weight: 0.5980 chunk 151 optimal weight: 0.9980 chunk 213 optimal weight: 2.9990 chunk 319 optimal weight: 0.7980 chunk 338 optimal weight: 10.0000 chunk 166 optimal weight: 2.9990 chunk 302 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 overall best weight: 1.0796 ------------------------------------------------------------------------------- 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 179 ASN ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 ASN ** C 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 ASN ** D 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 63 GLN ** G 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 GLN ** J 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 37 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 26600 Z= 0.142 Angle : 0.459 8.444 36554 Z= 0.235 Chirality : 0.034 0.204 4984 Planarity : 0.002 0.025 4480 Dihedral : 4.828 51.389 4144 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer Outliers : 1.06 % 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: 1.24 (0.15), residues: 3360 helix: 1.63 (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 180 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 155 time to evaluate : 2.730 Fit side-chains revert: symmetry clash outliers start: 25 outliers final: 16 residues processed: 178 average time/residue: 0.3718 time to fit residues: 104.9609 Evaluate side-chains 134 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 118 time to evaluate : 2.834 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.2243 time to fit residues: 10.0462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 281 optimal weight: 0.7980 chunk 192 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 251 optimal weight: 1.9990 chunk 139 optimal weight: 4.9990 chunk 288 optimal weight: 3.9990 chunk 233 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 172 optimal weight: 5.9990 chunk 303 optimal weight: 10.0000 chunk 85 optimal weight: 3.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 92 ASN B 111 ASN C 101 GLN ** C 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 ASN ** D 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 237 ASN J 89 ASN J 92 ASN ** L 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.3328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.060 26600 Z= 0.276 Angle : 0.537 8.562 36554 Z= 0.269 Chirality : 0.037 0.219 4984 Planarity : 0.002 0.028 4480 Dihedral : 4.814 59.877 4144 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % 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: 1.14 (0.15), residues: 3360 helix: 1.51 (0.11), residues: 2324 sheet: None (None), residues: 0 loop : -0.93 (0.19), residues: 1036 *********************** 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 157 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 130 time to evaluate : 2.822 Fit side-chains outliers start: 27 outliers final: 13 residues processed: 152 average time/residue: 0.3990 time to fit residues: 94.9787 Evaluate side-chains 128 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 115 time to evaluate : 2.599 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2418 time to fit residues: 8.9717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 113 optimal weight: 5.9990 chunk 304 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 chunk 198 optimal weight: 7.9990 chunk 83 optimal weight: 7.9990 chunk 338 optimal weight: 1.9990 chunk 281 optimal weight: 1.9990 chunk 156 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 112 optimal weight: 0.9990 chunk 177 optimal weight: 5.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- 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** B 92 ASN B 107 ASN B 111 ASN ** D 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 89 ASN ** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 37 GLN ** N 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.3497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 26600 Z= 0.161 Angle : 0.457 8.492 36554 Z= 0.231 Chirality : 0.034 0.206 4984 Planarity : 0.002 0.032 4480 Dihedral : 4.563 59.761 4144 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % 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: 1.48 (0.15), residues: 3360 helix: 1.82 (0.11), residues: 2268 sheet: None (None), residues: 0 loop : -0.80 (0.19), residues: 1092 *********************** 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 160 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 138 time to evaluate : 3.004 Fit side-chains outliers start: 22 outliers final: 11 residues processed: 156 average time/residue: 0.4010 time to fit residues: 97.6262 Evaluate side-chains 135 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 124 time to evaluate : 2.664 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2256 time to fit residues: 7.9679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 326 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 192 optimal weight: 6.9990 chunk 247 optimal weight: 1.9990 chunk 191 optimal weight: 6.9990 chunk 285 optimal weight: 4.9990 chunk 189 optimal weight: 3.9990 chunk 337 optimal weight: 2.9990 chunk 211 optimal weight: 10.0000 chunk 205 optimal weight: 0.9990 chunk 155 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 ASN A 237 ASN B 92 ASN C 237 ASN D 92 ASN E 202 ASN G 89 ASN ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 89 ASN M 37 GLN N 237 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.3599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 26600 Z= 0.232 Angle : 0.504 8.562 36554 Z= 0.252 Chirality : 0.035 0.215 4984 Planarity : 0.002 0.033 4480 Dihedral : 4.514 54.239 4144 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer Outliers : 0.98 % 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: 1.31 (0.15), residues: 3360 helix: 1.60 (0.11), residues: 2338 sheet: None (None), residues: 0 loop : -0.81 (0.19), residues: 1022 *********************** 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 149 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 126 time to evaluate : 2.750 Fit side-chains outliers start: 23 outliers final: 4 residues processed: 148 average time/residue: 0.4031 time to fit residues: 93.0915 Evaluate side-chains 125 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 121 time to evaluate : 2.928 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2244 time to fit residues: 5.2796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 208 optimal weight: 0.9980 chunk 134 optimal weight: 4.9990 chunk 201 optimal weight: 0.6980 chunk 101 optimal weight: 0.9990 chunk 66 optimal weight: 7.9990 chunk 65 optimal weight: 0.5980 chunk 214 optimal weight: 0.5980 chunk 229 optimal weight: 0.1980 chunk 166 optimal weight: 9.9990 chunk 31 optimal weight: 1.9990 chunk 265 optimal weight: 7.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 ASN ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 237 ASN ** C 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 ASN D 166 GLN ** D 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 63 GLN G 89 ASN ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 89 ASN L 89 ASN ** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 37 GLN N 63 GLN ** N 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.3788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.022 26600 Z= 0.112 Angle : 0.427 8.447 36554 Z= 0.216 Chirality : 0.032 0.202 4984 Planarity : 0.002 0.029 4480 Dihedral : 4.303 59.381 4144 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % 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: 1.75 (0.15), residues: 3360 helix: 1.98 (0.11), residues: 2282 sheet: None (None), residues: 0 loop : -0.63 (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 168 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 153 time to evaluate : 2.582 Fit side-chains outliers start: 15 outliers final: 5 residues processed: 166 average time/residue: 0.4046 time to fit residues: 104.0614 Evaluate side-chains 126 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 121 time to evaluate : 2.480 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2164 time to fit residues: 5.2366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 306 optimal weight: 4.9990 chunk 323 optimal weight: 3.9990 chunk 294 optimal weight: 0.9980 chunk 314 optimal weight: 4.9990 chunk 189 optimal weight: 5.9990 chunk 136 optimal weight: 10.0000 chunk 246 optimal weight: 4.9990 chunk 96 optimal weight: 0.6980 chunk 284 optimal weight: 8.9990 chunk 297 optimal weight: 8.9990 chunk 313 optimal weight: 1.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 ASN A 237 ASN ** C 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 89 ASN ** L 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.3767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 26600 Z= 0.260 Angle : 0.520 8.594 36554 Z= 0.261 Chirality : 0.036 0.255 4984 Planarity : 0.002 0.045 4480 Dihedral : 4.430 58.767 4144 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % 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: 1.48 (0.15), residues: 3360 helix: 1.72 (0.11), residues: 2338 sheet: None (None), residues: 0 loop : -0.73 (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 138 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 123 time to evaluate : 2.739 Fit side-chains outliers start: 15 outliers final: 5 residues processed: 137 average time/residue: 0.4110 time to fit residues: 88.3101 Evaluate side-chains 120 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 115 time to evaluate : 2.725 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2170 time to fit residues: 5.4005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 206 optimal weight: 0.9990 chunk 332 optimal weight: 2.9990 chunk 202 optimal weight: 2.9990 chunk 157 optimal weight: 0.5980 chunk 231 optimal weight: 0.9980 chunk 348 optimal weight: 5.9990 chunk 320 optimal weight: 0.2980 chunk 277 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 214 optimal weight: 1.9990 chunk 170 optimal weight: 5.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 ASN A 92 ASN A 237 ASN ** D 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 179 ASN ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 89 ASN L 89 ASN ** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.3918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 26600 Z= 0.122 Angle : 0.442 8.466 36554 Z= 0.224 Chirality : 0.033 0.296 4984 Planarity : 0.002 0.036 4480 Dihedral : 4.147 58.887 4144 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % 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: 1.81 (0.15), residues: 3360 helix: 2.00 (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 144 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 136 time to evaluate : 4.513 Fit side-chains outliers start: 8 outliers final: 2 residues processed: 144 average time/residue: 0.4270 time to fit residues: 95.6069 Evaluate side-chains 127 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 125 time to evaluate : 2.517 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2230 time to fit residues: 4.2590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 220 optimal weight: 5.9990 chunk 295 optimal weight: 8.9990 chunk 85 optimal weight: 0.5980 chunk 256 optimal weight: 0.7980 chunk 40 optimal weight: 9.9990 chunk 77 optimal weight: 1.9990 chunk 278 optimal weight: 0.8980 chunk 116 optimal weight: 0.2980 chunk 285 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 51 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 ASN ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 237 ASN ** D 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 89 ASN L 89 ASN ** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.100261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.083844 restraints weight = 49680.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.084019 restraints weight = 39967.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.084372 restraints weight = 37762.338| |-----------------------------------------------------------------------------| r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.4000 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= 0.116 Angle : 0.435 8.630 36554 Z= 0.221 Chirality : 0.033 0.286 4984 Planarity : 0.002 0.036 4480 Dihedral : 3.944 55.874 4144 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer Outliers : 0.13 % 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: 1.93 (0.15), residues: 3360 helix: 2.10 (0.11), residues: 2282 sheet: None (None), residues: 0 loop : -0.50 (0.19), residues: 1078 =============================================================================== Job complete usr+sys time: 3499.28 seconds wall clock time: 66 minutes 22.90 seconds (3982.90 seconds total)