Starting phenix.real_space_refine on Thu Jun 26 08:32:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y6f_33639/06_2025/7y6f_33639_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y6f_33639/06_2025/7y6f_33639.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7y6f_33639/06_2025/7y6f_33639.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y6f_33639/06_2025/7y6f_33639.map" model { file = "/net/cci-nas-00/data/ceres_data/7y6f_33639/06_2025/7y6f_33639_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y6f_33639/06_2025/7y6f_33639_trim.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 59 7.16 5 S 96 5.16 5 C 19886 2.51 5 N 5356 2.21 5 O 6030 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 233 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 31427 Number of models: 1 Model: "" Number of chains: 48 Chain: "A" Number of atoms: 1290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1290 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 155} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 1280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1280 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 2, 'TRANS': 153} Chain: "D" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 1290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1290 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 155} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 1290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1290 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 155} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "J" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "M" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "N" Number of atoms: 1290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1290 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 155} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "O" Number of atoms: 1287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1287 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 2, 'TRANS': 154} Chain: "P" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "Q" Number of atoms: 1287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1287 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 2, 'TRANS': 154} Chain: "R" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "U" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "V" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "W" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "X" Number of atoms: 1290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1290 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 155} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 45 Unusual residues: {' FE': 1, 'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, 'FE2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 45 Unusual residues: {' FE': 1, 'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, 'FE2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, 'FE2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 45 Unusual residues: {' FE': 1, 'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 45 Unusual residues: {' FE': 1, 'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 45 Unusual residues: {' FE': 1, 'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, 'FE2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, 'FE2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 45 Unusual residues: {' FE': 1, 'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "L" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 45 Unusual residues: {' FE': 1, 'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "M" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, 'FE2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, 'FE2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 45 Unusual residues: {' FE': 1, 'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Q" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 45 Unusual residues: {' FE': 1, 'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "R" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, 'FE2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "S" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 45 Unusual residues: {' FE': 1, 'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "T" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 45 Unusual residues: {' FE': 1, 'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "U" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, 'FE2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, 'FE2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 45 Unusual residues: {' FE': 1, 'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "X" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, 'FE2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 16.41, per 1000 atoms: 0.52 Number of scatterers: 31427 At special positions: 0 Unit cell: (131.274, 131.274, 131.274, 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) Fe 59 26.01 S 96 16.00 O 6030 8.00 N 5356 7.00 C 19886 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 - 3.00 Amino acid : True - 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=31, symmetry=0 Number of additional bonds: simple=31, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.61 Conformation dependent library (CDL) restraints added in 3.3 seconds 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7256 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 0 sheets defined 83.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.14 Creating SS restraints... Processing helix chain 'A' and resid 4 through 35 Processing helix chain 'A' and resid 37 through 65 removed outlier: 3.520A pdb=" N LEU A 65 " --> pdb=" O ARG A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 110 removed outlier: 3.534A pdb=" N MET A 86 " --> pdb=" O SER A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 145 removed outlier: 3.876A pdb=" N ALA A 117 " --> pdb=" O ASP A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 151 Processing helix chain 'B' and resid 4 through 36 Processing helix chain 'B' and resid 37 through 65 removed outlier: 3.614A pdb=" N TYR B 43 " --> pdb=" O LYS B 39 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU B 65 " --> pdb=" O ARG B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 110 Processing helix chain 'B' and resid 113 through 145 removed outlier: 3.888A pdb=" N ALA B 117 " --> pdb=" O ASP B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 151 Processing helix chain 'C' and resid 4 through 35 Processing helix chain 'C' and resid 37 through 65 removed outlier: 3.500A pdb=" N LEU C 65 " --> pdb=" O ARG C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 110 Processing helix chain 'C' and resid 113 through 145 removed outlier: 3.900A pdb=" N ALA C 117 " --> pdb=" O ASP C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 151 Processing helix chain 'D' and resid 4 through 36 Processing helix chain 'D' and resid 37 through 65 removed outlier: 3.568A pdb=" N TYR D 43 " --> pdb=" O LYS D 39 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU D 65 " --> pdb=" O ARG D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 110 Processing helix chain 'D' and resid 113 through 145 removed outlier: 3.910A pdb=" N ALA D 117 " --> pdb=" O ASP D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 151 Processing helix chain 'E' and resid 4 through 35 Processing helix chain 'E' and resid 37 through 65 removed outlier: 3.515A pdb=" N LEU E 65 " --> pdb=" O ARG E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 110 Processing helix chain 'E' and resid 113 through 145 removed outlier: 3.872A pdb=" N ALA E 117 " --> pdb=" O ASP E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 151 Processing helix chain 'F' and resid 4 through 36 removed outlier: 3.511A pdb=" N GLY F 36 " --> pdb=" O GLN F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 37 through 65 removed outlier: 3.520A pdb=" N TYR F 43 " --> pdb=" O LYS F 39 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU F 65 " --> pdb=" O ARG F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 110 removed outlier: 3.572A pdb=" N MET F 86 " --> pdb=" O SER F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 145 removed outlier: 3.869A pdb=" N ALA F 117 " --> pdb=" O ASP F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 151 Processing helix chain 'G' and resid 4 through 35 Processing helix chain 'G' and resid 37 through 65 removed outlier: 3.526A pdb=" N LEU G 65 " --> pdb=" O ARG G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 110 Processing helix chain 'G' and resid 113 through 145 removed outlier: 3.876A pdb=" N ALA G 117 " --> pdb=" O ASP G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 151 Processing helix chain 'H' and resid 4 through 35 Processing helix chain 'H' and resid 37 through 65 removed outlier: 3.508A pdb=" N LEU H 65 " --> pdb=" O ARG H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 110 Processing helix chain 'H' and resid 113 through 145 removed outlier: 3.906A pdb=" N ALA H 117 " --> pdb=" O ASP H 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 151 Processing helix chain 'I' and resid 4 through 35 Processing helix chain 'I' and resid 37 through 65 removed outlier: 3.520A pdb=" N LEU I 65 " --> pdb=" O ARG I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 82 through 110 Processing helix chain 'I' and resid 113 through 145 removed outlier: 3.885A pdb=" N ALA I 117 " --> pdb=" O ASP I 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 145 through 151 Processing helix chain 'J' and resid 4 through 36 removed outlier: 3.539A pdb=" N GLY J 36 " --> pdb=" O GLN J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 37 through 65 removed outlier: 3.507A pdb=" N ALA J 41 " --> pdb=" O TRP J 37 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU J 65 " --> pdb=" O ARG J 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 82 through 110 Processing helix chain 'J' and resid 113 through 145 removed outlier: 3.872A pdb=" N ALA J 117 " --> pdb=" O ASP J 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 145 through 151 Processing helix chain 'K' and resid 4 through 35 Processing helix chain 'K' and resid 37 through 65 removed outlier: 3.616A pdb=" N TYR K 43 " --> pdb=" O LYS K 39 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU K 65 " --> pdb=" O ARG K 61 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 110 Processing helix chain 'K' and resid 113 through 145 removed outlier: 3.887A pdb=" N ALA K 117 " --> pdb=" O ASP K 113 " (cutoff:3.500A) Processing helix chain 'K' and resid 145 through 151 Processing helix chain 'L' and resid 4 through 35 removed outlier: 3.510A pdb=" N LYS L 35 " --> pdb=" O LEU L 31 " (cutoff:3.500A) Processing helix chain 'L' and resid 37 through 65 removed outlier: 3.626A pdb=" N ALA L 55 " --> pdb=" O GLU L 51 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU L 56 " --> pdb=" O MET L 52 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 111 Processing helix chain 'L' and resid 113 through 145 removed outlier: 3.791A pdb=" N ALA L 117 " --> pdb=" O ASP L 113 " (cutoff:3.500A) Processing helix chain 'L' and resid 145 through 151 Processing helix chain 'M' and resid 4 through 35 removed outlier: 3.503A pdb=" N ILE M 8 " --> pdb=" O ASP M 4 " (cutoff:3.500A) Processing helix chain 'M' and resid 37 through 65 Processing helix chain 'M' and resid 82 through 111 removed outlier: 3.506A pdb=" N LYS M 111 " --> pdb=" O VAL M 107 " (cutoff:3.500A) Processing helix chain 'M' and resid 113 through 145 removed outlier: 3.708A pdb=" N ALA M 117 " --> pdb=" O ASP M 113 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASP M 126 " --> pdb=" O ALA M 122 " (cutoff:3.500A) Processing helix chain 'M' and resid 145 through 151 Processing helix chain 'N' and resid 4 through 36 Processing helix chain 'N' and resid 37 through 65 Processing helix chain 'N' and resid 82 through 110 Processing helix chain 'N' and resid 113 through 145 removed outlier: 3.874A pdb=" N ALA N 117 " --> pdb=" O ASP N 113 " (cutoff:3.500A) Processing helix chain 'N' and resid 145 through 151 Processing helix chain 'O' and resid 4 through 35 Processing helix chain 'O' and resid 37 through 65 Processing helix chain 'O' and resid 82 through 111 removed outlier: 3.539A pdb=" N LYS O 111 " --> pdb=" O VAL O 107 " (cutoff:3.500A) Processing helix chain 'O' and resid 113 through 145 removed outlier: 3.823A pdb=" N ALA O 117 " --> pdb=" O ASP O 113 " (cutoff:3.500A) Processing helix chain 'O' and resid 145 through 151 Processing helix chain 'P' and resid 4 through 36 Processing helix chain 'P' and resid 37 through 65 removed outlier: 3.611A pdb=" N TYR P 43 " --> pdb=" O LYS P 39 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU P 65 " --> pdb=" O ARG P 61 " (cutoff:3.500A) Processing helix chain 'P' and resid 82 through 110 Processing helix chain 'P' and resid 113 through 145 removed outlier: 3.899A pdb=" N ALA P 117 " --> pdb=" O ASP P 113 " (cutoff:3.500A) Processing helix chain 'P' and resid 145 through 151 Processing helix chain 'Q' and resid 4 through 35 Processing helix chain 'Q' and resid 37 through 65 removed outlier: 3.522A pdb=" N ALA Q 41 " --> pdb=" O TRP Q 37 " (cutoff:3.500A) Processing helix chain 'Q' and resid 82 through 110 Processing helix chain 'Q' and resid 113 through 145 removed outlier: 3.902A pdb=" N ALA Q 117 " --> pdb=" O ASP Q 113 " (cutoff:3.500A) Processing helix chain 'Q' and resid 145 through 151 Processing helix chain 'R' and resid 4 through 36 Processing helix chain 'R' and resid 37 through 65 removed outlier: 3.572A pdb=" N TYR R 43 " --> pdb=" O LYS R 39 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU R 65 " --> pdb=" O ARG R 61 " (cutoff:3.500A) Processing helix chain 'R' and resid 82 through 110 removed outlier: 3.544A pdb=" N MET R 86 " --> pdb=" O SER R 82 " (cutoff:3.500A) Processing helix chain 'R' and resid 113 through 145 removed outlier: 3.873A pdb=" N ALA R 117 " --> pdb=" O ASP R 113 " (cutoff:3.500A) Processing helix chain 'R' and resid 145 through 151 Processing helix chain 'S' and resid 4 through 36 removed outlier: 3.508A pdb=" N GLY S 36 " --> pdb=" O GLN S 32 " (cutoff:3.500A) Processing helix chain 'S' and resid 37 through 65 removed outlier: 3.519A pdb=" N TYR S 43 " --> pdb=" O LYS S 39 " (cutoff:3.500A) Processing helix chain 'S' and resid 82 through 110 removed outlier: 3.569A pdb=" N MET S 86 " --> pdb=" O SER S 82 " (cutoff:3.500A) Processing helix chain 'S' and resid 113 through 145 removed outlier: 3.860A pdb=" N ALA S 117 " --> pdb=" O ASP S 113 " (cutoff:3.500A) Processing helix chain 'S' and resid 145 through 151 Processing helix chain 'T' and resid 4 through 35 Processing helix chain 'T' and resid 37 through 65 removed outlier: 3.520A pdb=" N LEU T 65 " --> pdb=" O ARG T 61 " (cutoff:3.500A) Processing helix chain 'T' and resid 82 through 110 removed outlier: 3.549A pdb=" N MET T 86 " --> pdb=" O SER T 82 " (cutoff:3.500A) Processing helix chain 'T' and resid 113 through 145 removed outlier: 3.905A pdb=" N ALA T 117 " --> pdb=" O ASP T 113 " (cutoff:3.500A) Processing helix chain 'T' and resid 145 through 151 Processing helix chain 'U' and resid 4 through 35 removed outlier: 3.542A pdb=" N LYS U 35 " --> pdb=" O LEU U 31 " (cutoff:3.500A) Processing helix chain 'U' and resid 37 through 65 removed outlier: 3.608A pdb=" N TYR U 43 " --> pdb=" O LYS U 39 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU U 65 " --> pdb=" O ARG U 61 " (cutoff:3.500A) Processing helix chain 'U' and resid 82 through 110 Processing helix chain 'U' and resid 113 through 145 removed outlier: 3.903A pdb=" N ALA U 117 " --> pdb=" O ASP U 113 " (cutoff:3.500A) Processing helix chain 'U' and resid 145 through 151 Processing helix chain 'V' and resid 4 through 35 removed outlier: 3.541A pdb=" N ILE V 8 " --> pdb=" O ASP V 4 " (cutoff:3.500A) Processing helix chain 'V' and resid 37 through 65 Processing helix chain 'V' and resid 82 through 111 Processing helix chain 'V' and resid 113 through 145 removed outlier: 3.711A pdb=" N ALA V 117 " --> pdb=" O ASP V 113 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASP V 126 " --> pdb=" O ALA V 122 " (cutoff:3.500A) Processing helix chain 'V' and resid 145 through 151 Processing helix chain 'W' and resid 4 through 36 removed outlier: 3.601A pdb=" N GLY W 36 " --> pdb=" O GLN W 32 " (cutoff:3.500A) Processing helix chain 'W' and resid 37 through 65 removed outlier: 3.682A pdb=" N ALA W 41 " --> pdb=" O TRP W 37 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LYS W 42 " --> pdb=" O THR W 38 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N TYR W 43 " --> pdb=" O LYS W 39 " (cutoff:3.500A) Processing helix chain 'W' and resid 82 through 110 removed outlier: 3.553A pdb=" N MET W 86 " --> pdb=" O SER W 82 " (cutoff:3.500A) Processing helix chain 'W' and resid 113 through 145 removed outlier: 3.867A pdb=" N ALA W 117 " --> pdb=" O ASP W 113 " (cutoff:3.500A) Processing helix chain 'W' and resid 145 through 151 Processing helix chain 'X' and resid 4 through 35 Processing helix chain 'X' and resid 37 through 65 removed outlier: 3.570A pdb=" N TYR X 43 " --> pdb=" O LYS X 39 " (cutoff:3.500A) Processing helix chain 'X' and resid 82 through 110 removed outlier: 3.574A pdb=" N MET X 86 " --> pdb=" O SER X 82 " (cutoff:3.500A) Processing helix chain 'X' and resid 113 through 145 removed outlier: 3.879A pdb=" N ALA X 117 " --> pdb=" O ASP X 113 " (cutoff:3.500A) Processing helix chain 'X' and resid 145 through 151 2579 hydrogen bonds defined for protein. 7737 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: 8.98 Time building geometry restraints manager: 8.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.41: 13351 1.41 - 1.59: 18377 1.59 - 1.78: 6 1.78 - 1.96: 186 1.96 - 2.14: 48 Bond restraints: 31968 Sorted by residual: bond pdb=" C GLN W 14 " pdb=" N LEU W 15 " ideal model delta sigma weight residual 1.335 1.407 -0.072 1.31e-02 5.83e+03 3.01e+01 bond pdb=" C GLU W 13 " pdb=" N GLN W 14 " ideal model delta sigma weight residual 1.335 1.405 -0.070 1.31e-02 5.83e+03 2.89e+01 bond pdb=" CB MET Q 52 " pdb=" CG MET Q 52 " ideal model delta sigma weight residual 1.520 1.470 0.050 3.00e-02 1.11e+03 2.79e+00 bond pdb=" CGA HEM C 203 " pdb=" O2A HEM C 203 " ideal model delta sigma weight residual 1.258 1.288 -0.030 2.00e-02 2.50e+03 2.25e+00 bond pdb=" NB HEM S 203 " pdb="FE HEM S 203 " ideal model delta sigma weight residual 2.080 1.975 0.105 7.00e-02 2.04e+02 2.25e+00 ... (remaining 31963 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.37: 43332 6.37 - 12.74: 15 12.74 - 19.12: 2 19.12 - 25.49: 2 25.49 - 31.86: 3 Bond angle restraints: 43354 Sorted by residual: angle pdb=" CB MET C 52 " pdb=" CG MET C 52 " pdb=" SD MET C 52 " ideal model delta sigma weight residual 112.70 83.42 29.28 3.00e+00 1.11e-01 9.52e+01 angle pdb=" CB MET X 52 " pdb=" CG MET X 52 " pdb=" SD MET X 52 " ideal model delta sigma weight residual 112.70 93.08 19.62 3.00e+00 1.11e-01 4.28e+01 angle pdb=" CB MET S 52 " pdb=" CG MET S 52 " pdb=" SD MET S 52 " ideal model delta sigma weight residual 112.70 93.25 19.45 3.00e+00 1.11e-01 4.20e+01 angle pdb=" O GLN W 14 " pdb=" C GLN W 14 " pdb=" N LEU W 15 " ideal model delta sigma weight residual 122.12 115.48 6.64 1.06e+00 8.90e-01 3.92e+01 angle pdb=" CB MET N 52 " pdb=" CG MET N 52 " pdb=" SD MET N 52 " ideal model delta sigma weight residual 112.70 95.16 17.54 3.00e+00 1.11e-01 3.42e+01 ... (remaining 43349 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 16867 17.68 - 35.35: 1827 35.35 - 53.03: 296 53.03 - 70.70: 99 70.70 - 88.38: 29 Dihedral angle restraints: 19118 sinusoidal: 7994 harmonic: 11124 Sorted by residual: dihedral pdb=" C2B HEM S 203 " pdb=" C3B HEM S 203 " pdb=" CAB HEM S 203 " pdb=" CBB HEM S 203 " ideal model delta sinusoidal sigma weight residual 0.00 32.74 -32.74 2 1.00e+01 1.00e-02 1.40e+01 dihedral pdb=" CA GLU Q 51 " pdb=" C GLU Q 51 " pdb=" N MET Q 52 " pdb=" CA MET Q 52 " ideal model delta harmonic sigma weight residual 180.00 161.27 18.73 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" C2B HEM K 203 " pdb=" C3B HEM K 203 " pdb=" CAB HEM K 203 " pdb=" CBB HEM K 203 " ideal model delta sinusoidal sigma weight residual 0.00 -30.74 30.74 2 1.00e+01 1.00e-02 1.25e+01 ... (remaining 19115 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 3785 0.034 - 0.069: 722 0.069 - 0.103: 269 0.103 - 0.137: 28 0.137 - 0.172: 2 Chirality restraints: 4806 Sorted by residual: chirality pdb=" CA MET Q 52 " pdb=" N MET Q 52 " pdb=" C MET Q 52 " pdb=" CB MET Q 52 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.38e-01 chirality pdb=" CA PHE F 49 " pdb=" N PHE F 49 " pdb=" C PHE F 49 " pdb=" CB PHE F 49 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.78e-01 chirality pdb=" CA MET C 52 " pdb=" N MET C 52 " pdb=" C MET C 52 " pdb=" CB MET C 52 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.61e-01 ... (remaining 4803 not shown) Planarity restraints: 5596 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG R 45 " -0.450 9.50e-02 1.11e+02 2.02e-01 2.63e+01 pdb=" NE ARG R 45 " 0.034 2.00e-02 2.50e+03 pdb=" CZ ARG R 45 " -0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG R 45 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG R 45 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 49 " 0.016 2.00e-02 2.50e+03 2.93e-02 1.50e+01 pdb=" CG PHE F 49 " -0.062 2.00e-02 2.50e+03 pdb=" CD1 PHE F 49 " 0.037 2.00e-02 2.50e+03 pdb=" CD2 PHE F 49 " 0.019 2.00e-02 2.50e+03 pdb=" CE1 PHE F 49 " -0.015 2.00e-02 2.50e+03 pdb=" CE2 PHE F 49 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE F 49 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1A HEM C 203 " 0.011 2.00e-02 2.50e+03 2.11e-02 1.00e+01 pdb=" C2A HEM C 203 " 0.028 2.00e-02 2.50e+03 pdb=" C3A HEM C 203 " 0.010 2.00e-02 2.50e+03 pdb=" C4A HEM C 203 " 0.004 2.00e-02 2.50e+03 pdb=" CAA HEM C 203 " -0.032 2.00e-02 2.50e+03 pdb=" CHA HEM C 203 " 0.017 2.00e-02 2.50e+03 pdb=" CHB HEM C 203 " 0.003 2.00e-02 2.50e+03 pdb=" CMA HEM C 203 " 0.001 2.00e-02 2.50e+03 pdb=" NA HEM C 203 " -0.041 2.00e-02 2.50e+03 ... (remaining 5593 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 74 2.43 - 3.04: 19740 3.04 - 3.66: 43843 3.66 - 4.28: 68450 4.28 - 4.90: 115959 Nonbonded interactions: 248066 Sorted by model distance: nonbonded pdb=" OE2 GLU H 94 " pdb="FE FE H 202 " model vdw 1.807 2.260 nonbonded pdb=" OE1 GLU G 127 " pdb="FE FE G 202 " model vdw 1.953 2.260 nonbonded pdb=" OE1 GLU T 127 " pdb="FE FE2 T 203 " model vdw 1.972 3.000 nonbonded pdb=" OE1 GLU F 127 " pdb="FE FE2 F 202 " model vdw 1.974 3.000 nonbonded pdb=" OE1 GLU R 127 " pdb="FE FE R 202 " model vdw 2.031 2.260 ... (remaining 248061 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 156) selection = (chain 'B' and resid 1 through 156) selection = (chain 'C' and resid 1 through 156) selection = (chain 'D' and resid 1 through 156) selection = (chain 'E' and resid 1 through 156) selection = (chain 'F' and resid 1 through 156) selection = (chain 'G' and resid 1 through 156) selection = (chain 'H' and resid 1 through 156) selection = (chain 'I' and resid 1 through 156) selection = (chain 'J' and resid 1 through 156) selection = (chain 'K' and resid 1 through 156) selection = (chain 'L' and resid 1 through 156) selection = (chain 'M' and resid 1 through 156) selection = (chain 'N' and resid 1 through 156) selection = (chain 'O' and resid 1 through 156) selection = (chain 'P' and resid 1 through 156) selection = (chain 'Q' and resid 1 through 156) selection = (chain 'R' and resid 1 through 156) selection = (chain 'S' and resid 1 through 156) selection = (chain 'T' and resid 1 through 156) selection = (chain 'U' and resid 1 through 156) selection = (chain 'V' and resid 1 through 156) selection = (chain 'W' and resid 1 through 156) selection = (chain 'X' and resid 1 through 156) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 1.640 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: 1.120 Check model and map are aligned: 0.220 Set scattering table: 0.250 Process input model: 59.750 Find NCS groups from input model: 1.990 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.666 31999 Z= 0.211 Angle : 0.618 31.860 43354 Z= 0.323 Chirality : 0.033 0.172 4806 Planarity : 0.004 0.202 5596 Dihedral : 15.053 88.377 11862 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.11 (0.13), residues: 3724 helix: 3.83 (0.08), residues: 2999 sheet: None (None), residues: 0 loop : -2.73 (0.19), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 37 HIS 0.003 0.001 HIS U 54 PHE 0.062 0.003 PHE F 49 TYR 0.047 0.001 TYR T 71 ARG 0.019 0.000 ARG R 45 Details of bonding type rmsd hydrogen bonds : bond 0.13535 ( 2579) hydrogen bonds : angle 4.25600 ( 7737) covalent geometry : bond 0.00317 (31968) covalent geometry : angle 0.61805 (43354) Misc. bond : bond 0.25639 ( 31) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 712 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 712 time to evaluate : 3.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 1 MET cc_start: 0.5264 (mtm) cc_final: 0.5011 (mtm) REVERT: L 129 HIS cc_start: 0.7173 (m-70) cc_final: 0.6954 (m90) REVERT: S 146 GLU cc_start: 0.8364 (mt-10) cc_final: 0.8137 (mm-30) outliers start: 0 outliers final: 0 residues processed: 712 average time/residue: 1.4385 time to fit residues: 1203.3959 Evaluate side-chains 655 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 655 time to evaluate : 3.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 303 optimal weight: 0.7980 chunk 272 optimal weight: 0.9980 chunk 151 optimal weight: 6.9990 chunk 93 optimal weight: 2.9990 chunk 184 optimal weight: 9.9990 chunk 145 optimal weight: 9.9990 chunk 282 optimal weight: 8.9990 chunk 109 optimal weight: 0.8980 chunk 171 optimal weight: 0.0870 chunk 210 optimal weight: 9.9990 chunk 326 optimal weight: 7.9990 overall best weight: 1.1560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 112 HIS D 156 GLN ** H 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 112 HIS ** M 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 156 GLN Q 112 HIS T 70 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.162134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.156549 restraints weight = 25809.926| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 0.32 r_work: 0.3497 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3380 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.459 31999 Z= 0.165 Angle : 0.517 11.350 43354 Z= 0.247 Chirality : 0.032 0.132 4806 Planarity : 0.003 0.086 5596 Dihedral : 6.890 83.297 4204 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 0.94 % Allowed : 7.66 % Favored : 91.40 % 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: 4.69 (0.13), residues: 3724 helix: 4.18 (0.08), residues: 3024 sheet: None (None), residues: 0 loop : -2.49 (0.20), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 37 HIS 0.004 0.000 HIS Q 129 PHE 0.039 0.002 PHE F 49 TYR 0.041 0.001 TYR T 71 ARG 0.003 0.000 ARG F 45 Details of bonding type rmsd hydrogen bonds : bond 0.08735 ( 2579) hydrogen bonds : angle 3.45109 ( 7737) covalent geometry : bond 0.00292 (31968) covalent geometry : angle 0.51732 (43354) Misc. bond : bond 0.13943 ( 31) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 686 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 655 time to evaluate : 3.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7816 (mt-10) REVERT: L 155 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7843 (mt-10) REVERT: V 155 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7722 (mt-10) outliers start: 31 outliers final: 1 residues processed: 659 average time/residue: 1.6265 time to fit residues: 1254.5589 Evaluate side-chains 629 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 628 time to evaluate : 4.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 60 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 302 optimal weight: 7.9990 chunk 335 optimal weight: 30.0000 chunk 73 optimal weight: 0.9990 chunk 273 optimal weight: 0.9980 chunk 308 optimal weight: 5.9990 chunk 314 optimal weight: 10.0000 chunk 350 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 310 optimal weight: 10.0000 chunk 2 optimal weight: 8.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 112 HIS ** H 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 88 GLN ** M 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 156 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.156801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.151240 restraints weight = 25703.214| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 0.31 r_work: 0.3429 rms_B_bonded: 1.29 restraints_weight: 0.5000 r_work: 0.3313 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.458 31999 Z= 0.175 Angle : 0.536 21.690 43354 Z= 0.249 Chirality : 0.032 0.117 4806 Planarity : 0.003 0.070 5596 Dihedral : 7.035 87.080 4204 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 1.87 % Allowed : 8.27 % Favored : 89.86 % 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: 4.74 (0.13), residues: 3724 helix: 4.22 (0.08), residues: 3024 sheet: None (None), residues: 0 loop : -2.49 (0.19), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 37 HIS 0.003 0.000 HIS Q 129 PHE 0.023 0.002 PHE O 120 TYR 0.029 0.001 TYR T 71 ARG 0.003 0.000 ARG F 45 Details of bonding type rmsd hydrogen bonds : bond 0.09514 ( 2579) hydrogen bonds : angle 3.42807 ( 7737) covalent geometry : bond 0.00310 (31968) covalent geometry : angle 0.53629 (43354) Misc. bond : bond 0.16038 ( 31) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 703 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 641 time to evaluate : 3.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ASP cc_start: 0.8179 (t0) cc_final: 0.7915 (t0) REVERT: B 81 GLN cc_start: 0.8019 (OUTLIER) cc_final: 0.7589 (mt0) REVERT: C 66 ASP cc_start: 0.8209 (t0) cc_final: 0.7950 (t0) REVERT: F 81 GLN cc_start: 0.8191 (OUTLIER) cc_final: 0.7535 (mt0) REVERT: H 66 ASP cc_start: 0.8193 (t0) cc_final: 0.7928 (t0) REVERT: L 155 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7704 (mt-10) REVERT: N 81 GLN cc_start: 0.8309 (mt0) cc_final: 0.8061 (mt0) REVERT: P 66 ASP cc_start: 0.8139 (t0) cc_final: 0.7891 (t0) REVERT: S 81 GLN cc_start: 0.8195 (OUTLIER) cc_final: 0.7545 (mt0) REVERT: U 66 ASP cc_start: 0.8111 (t70) cc_final: 0.7814 (t0) outliers start: 62 outliers final: 6 residues processed: 646 average time/residue: 1.6096 time to fit residues: 1209.1442 Evaluate side-chains 630 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 621 time to evaluate : 3.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain M residue 60 ASP Chi-restraints excluded: chain O residue 35 LYS Chi-restraints excluded: chain P residue 60 ASP Chi-restraints excluded: chain S residue 81 GLN Chi-restraints excluded: chain V residue 60 ASP Chi-restraints excluded: chain X residue 35 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 71 optimal weight: 9.9990 chunk 324 optimal weight: 7.9990 chunk 93 optimal weight: 0.9990 chunk 201 optimal weight: 6.9990 chunk 189 optimal weight: 4.9990 chunk 341 optimal weight: 4.9990 chunk 176 optimal weight: 0.0970 chunk 355 optimal weight: 10.0000 chunk 333 optimal weight: 0.0070 chunk 47 optimal weight: 9.9990 chunk 290 optimal weight: 0.9980 overall best weight: 1.4200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 88 GLN ** M 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 156 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.159002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.153252 restraints weight = 25839.530| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 0.33 r_work: 0.3498 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.3391 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.447 31999 Z= 0.165 Angle : 0.504 20.792 43354 Z= 0.238 Chirality : 0.031 0.115 4806 Planarity : 0.002 0.055 5596 Dihedral : 7.035 81.402 4204 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 1.63 % Allowed : 10.35 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.88 (0.13), residues: 3724 helix: 4.32 (0.08), residues: 3024 sheet: None (None), residues: 0 loop : -2.47 (0.19), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 37 HIS 0.003 0.000 HIS Q 129 PHE 0.020 0.002 PHE O 120 TYR 0.023 0.001 TYR T 71 ARG 0.002 0.000 ARG F 45 Details of bonding type rmsd hydrogen bonds : bond 0.09000 ( 2579) hydrogen bonds : angle 3.34545 ( 7737) covalent geometry : bond 0.00294 (31968) covalent geometry : angle 0.50386 (43354) Misc. bond : bond 0.15575 ( 31) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 698 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 644 time to evaluate : 3.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ASP cc_start: 0.8217 (t0) cc_final: 0.7940 (t0) REVERT: C 66 ASP cc_start: 0.8231 (t0) cc_final: 0.7853 (t0) REVERT: E 81 GLN cc_start: 0.7881 (OUTLIER) cc_final: 0.7428 (mt0) REVERT: G 81 GLN cc_start: 0.7929 (OUTLIER) cc_final: 0.7448 (mt0) REVERT: H 66 ASP cc_start: 0.8258 (t0) cc_final: 0.7802 (t0) REVERT: I 81 GLN cc_start: 0.7953 (OUTLIER) cc_final: 0.7528 (mt0) REVERT: J 81 GLN cc_start: 0.8236 (mt0) cc_final: 0.7978 (mt0) REVERT: L 86 MET cc_start: 0.7179 (mtt) cc_final: 0.6969 (mtt) REVERT: L 155 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7786 (mt-10) REVERT: M 1 MET cc_start: 0.6029 (mmp) cc_final: 0.5663 (mmm) REVERT: N 81 GLN cc_start: 0.8197 (mt0) cc_final: 0.7912 (mt0) REVERT: P 66 ASP cc_start: 0.8139 (t0) cc_final: 0.7861 (t0) REVERT: Q 81 GLN cc_start: 0.8069 (OUTLIER) cc_final: 0.7672 (mt0) REVERT: S 81 GLN cc_start: 0.8135 (OUTLIER) cc_final: 0.7512 (mt0) outliers start: 54 outliers final: 12 residues processed: 648 average time/residue: 1.6351 time to fit residues: 1237.3334 Evaluate side-chains 643 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 626 time to evaluate : 3.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain E residue 81 GLN Chi-restraints excluded: chain F residue 60 ASP Chi-restraints excluded: chain G residue 81 GLN Chi-restraints excluded: chain I residue 60 ASP Chi-restraints excluded: chain I residue 81 GLN Chi-restraints excluded: chain J residue 60 ASP Chi-restraints excluded: chain M residue 35 LYS Chi-restraints excluded: chain M residue 60 ASP Chi-restraints excluded: chain N residue 60 ASP Chi-restraints excluded: chain O residue 35 LYS Chi-restraints excluded: chain P residue 60 ASP Chi-restraints excluded: chain Q residue 81 GLN Chi-restraints excluded: chain S residue 81 GLN Chi-restraints excluded: chain T residue 60 ASP Chi-restraints excluded: chain V residue 60 ASP Chi-restraints excluded: chain X residue 35 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 283 optimal weight: 0.9990 chunk 11 optimal weight: 9.9990 chunk 93 optimal weight: 0.9990 chunk 206 optimal weight: 6.9990 chunk 174 optimal weight: 3.9990 chunk 224 optimal weight: 8.9990 chunk 124 optimal weight: 7.9990 chunk 70 optimal weight: 10.0000 chunk 156 optimal weight: 0.0370 chunk 101 optimal weight: 9.9990 chunk 138 optimal weight: 8.9990 overall best weight: 2.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 54 HIS M 88 GLN ** M 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.142125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.134607 restraints weight = 24009.653| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 0.41 r_work: 0.3264 rms_B_bonded: 1.38 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.449 31999 Z= 0.210 Angle : 0.591 21.428 43354 Z= 0.276 Chirality : 0.033 0.121 4806 Planarity : 0.003 0.057 5596 Dihedral : 7.222 88.576 4204 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 1.42 % Allowed : 11.53 % Favored : 87.05 % 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: 4.77 (0.13), residues: 3724 helix: 4.13 (0.08), residues: 3024 sheet: None (None), residues: 0 loop : -1.89 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 37 HIS 0.004 0.001 HIS Q 129 PHE 0.020 0.002 PHE F 49 TYR 0.030 0.002 TYR T 71 ARG 0.003 0.000 ARG S 45 Details of bonding type rmsd hydrogen bonds : bond 0.11765 ( 2579) hydrogen bonds : angle 3.60247 ( 7737) covalent geometry : bond 0.00379 (31968) covalent geometry : angle 0.59089 (43354) Misc. bond : bond 0.16691 ( 31) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 708 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 661 time to evaluate : 6.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 81 GLN cc_start: 0.8223 (OUTLIER) cc_final: 0.7800 (mt0) REVERT: D 81 GLN cc_start: 0.8464 (mt0) cc_final: 0.8177 (mt0) REVERT: E 81 GLN cc_start: 0.8173 (OUTLIER) cc_final: 0.7720 (mt0) REVERT: G 81 GLN cc_start: 0.8124 (OUTLIER) cc_final: 0.7686 (mt0) REVERT: I 81 GLN cc_start: 0.8211 (OUTLIER) cc_final: 0.7788 (mt0) REVERT: J 81 GLN cc_start: 0.8403 (mt0) cc_final: 0.8060 (mt0) REVERT: L 66 ASP cc_start: 0.8082 (t70) cc_final: 0.7723 (t0) REVERT: M 1 MET cc_start: 0.6219 (mmp) cc_final: 0.5706 (mmm) REVERT: N 1 MET cc_start: 0.5091 (mmm) cc_final: 0.4546 (mtm) REVERT: N 81 GLN cc_start: 0.8366 (mt0) cc_final: 0.8069 (mt0) REVERT: U 81 GLN cc_start: 0.8241 (OUTLIER) cc_final: 0.7839 (mt0) REVERT: W 66 ASP cc_start: 0.8294 (t0) cc_final: 0.7972 (t0) outliers start: 47 outliers final: 4 residues processed: 667 average time/residue: 1.8053 time to fit residues: 1406.5766 Evaluate side-chains 667 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 658 time to evaluate : 4.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain E residue 81 GLN Chi-restraints excluded: chain G residue 81 GLN Chi-restraints excluded: chain I residue 81 GLN Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain T residue 66 ASP Chi-restraints excluded: chain U residue 81 GLN Chi-restraints excluded: chain V residue 60 ASP Chi-restraints excluded: chain W residue 44 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 207 optimal weight: 2.9990 chunk 180 optimal weight: 10.0000 chunk 277 optimal weight: 4.9990 chunk 345 optimal weight: 4.9990 chunk 278 optimal weight: 10.0000 chunk 63 optimal weight: 8.9990 chunk 354 optimal weight: 8.9990 chunk 143 optimal weight: 4.9990 chunk 339 optimal weight: 6.9990 chunk 254 optimal weight: 3.9990 chunk 292 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.132622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.125012 restraints weight = 23728.825| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 0.41 r_work: 0.3130 rms_B_bonded: 1.29 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 2.50 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.455 31999 Z= 0.265 Angle : 0.678 24.691 43354 Z= 0.325 Chirality : 0.037 0.127 4806 Planarity : 0.004 0.065 5596 Dihedral : 7.466 89.657 4204 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.72 % Allowed : 11.62 % Favored : 86.66 % 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: 4.32 (0.13), residues: 3724 helix: 3.82 (0.08), residues: 3024 sheet: None (None), residues: 0 loop : -2.05 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP L 37 HIS 0.006 0.001 HIS H 54 PHE 0.026 0.002 PHE F 49 TYR 0.043 0.002 TYR T 71 ARG 0.005 0.001 ARG S 45 Details of bonding type rmsd hydrogen bonds : bond 0.14650 ( 2579) hydrogen bonds : angle 3.86985 ( 7737) covalent geometry : bond 0.00503 (31968) covalent geometry : angle 0.67762 (43354) Misc. bond : bond 0.16722 ( 31) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 831 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 774 time to evaluate : 6.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 81 GLN cc_start: 0.8319 (OUTLIER) cc_final: 0.7822 (mt0) REVERT: C 4 ASP cc_start: 0.7613 (m-30) cc_final: 0.7366 (t70) REVERT: D 4 ASP cc_start: 0.7618 (m-30) cc_final: 0.7401 (t70) REVERT: D 81 GLN cc_start: 0.8544 (mt0) cc_final: 0.8257 (mt0) REVERT: E 81 GLN cc_start: 0.8239 (OUTLIER) cc_final: 0.7785 (mt0) REVERT: F 4 ASP cc_start: 0.7591 (m-30) cc_final: 0.7387 (t70) REVERT: G 81 GLN cc_start: 0.8218 (OUTLIER) cc_final: 0.7774 (mt0) REVERT: J 81 GLN cc_start: 0.8469 (mt0) cc_final: 0.8155 (mt0) REVERT: K 81 GLN cc_start: 0.8305 (OUTLIER) cc_final: 0.7818 (mt0) REVERT: L 66 ASP cc_start: 0.8367 (t70) cc_final: 0.7873 (t0) REVERT: M 1 MET cc_start: 0.6416 (mmp) cc_final: 0.5902 (mmm) REVERT: M 66 ASP cc_start: 0.8396 (t70) cc_final: 0.7965 (t0) REVERT: N 66 ASP cc_start: 0.8382 (t70) cc_final: 0.7958 (t0) REVERT: N 81 GLN cc_start: 0.8472 (mt0) cc_final: 0.8190 (mt0) REVERT: O 66 ASP cc_start: 0.8230 (t70) cc_final: 0.7729 (t0) REVERT: P 81 GLN cc_start: 0.8269 (OUTLIER) cc_final: 0.7761 (mt0) REVERT: R 155 GLU cc_start: 0.7855 (tt0) cc_final: 0.7653 (tt0) REVERT: S 66 ASP cc_start: 0.8413 (t70) cc_final: 0.7980 (t0) REVERT: T 1 MET cc_start: 0.4828 (OUTLIER) cc_final: 0.4625 (mmm) REVERT: V 66 ASP cc_start: 0.8031 (t0) cc_final: 0.7673 (t0) REVERT: W 81 GLN cc_start: 0.8273 (OUTLIER) cc_final: 0.7575 (mt0) outliers start: 57 outliers final: 8 residues processed: 779 average time/residue: 2.0147 time to fit residues: 1832.2849 Evaluate side-chains 769 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 754 time to evaluate : 3.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain E residue 81 GLN Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain G residue 81 GLN Chi-restraints excluded: chain K residue 81 GLN Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain O residue 4 ASP Chi-restraints excluded: chain P residue 81 GLN Chi-restraints excluded: chain R residue 26 PHE Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 66 ASP Chi-restraints excluded: chain W residue 44 THR Chi-restraints excluded: chain W residue 81 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 336 optimal weight: 0.0980 chunk 284 optimal weight: 8.9990 chunk 72 optimal weight: 0.9980 chunk 321 optimal weight: 5.9990 chunk 351 optimal weight: 6.9990 chunk 75 optimal weight: 10.0000 chunk 155 optimal weight: 3.9990 chunk 143 optimal weight: 3.9990 chunk 221 optimal weight: 9.9990 chunk 300 optimal weight: 10.0000 chunk 241 optimal weight: 1.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.143961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.136539 restraints weight = 24026.056| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 0.41 r_work: 0.3293 rms_B_bonded: 1.26 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 2.52 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.458 31999 Z= 0.201 Angle : 0.605 27.277 43354 Z= 0.276 Chirality : 0.033 0.171 4806 Planarity : 0.003 0.056 5596 Dihedral : 7.402 89.692 4204 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 2.11 % Allowed : 13.64 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.64 (0.13), residues: 3724 helix: 4.04 (0.08), residues: 3024 sheet: None (None), residues: 0 loop : -1.96 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP P 37 HIS 0.004 0.001 HIS Q 129 PHE 0.020 0.001 PHE F 49 TYR 0.024 0.001 TYR T 71 ARG 0.004 0.000 ARG F 45 Details of bonding type rmsd hydrogen bonds : bond 0.11154 ( 2579) hydrogen bonds : angle 3.61548 ( 7737) covalent geometry : bond 0.00369 (31968) covalent geometry : angle 0.60517 (43354) Misc. bond : bond 0.15877 ( 31) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 723 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 653 time to evaluate : 3.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8449 (mt) REVERT: A 81 GLN cc_start: 0.8070 (OUTLIER) cc_final: 0.7426 (mt0) REVERT: B 4 ASP cc_start: 0.7430 (OUTLIER) cc_final: 0.7173 (t70) REVERT: B 68 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8393 (mt) REVERT: B 81 GLN cc_start: 0.8163 (OUTLIER) cc_final: 0.7676 (mt0) REVERT: C 68 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8401 (mt) REVERT: D 68 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8406 (mt) REVERT: D 81 GLN cc_start: 0.8372 (mt0) cc_final: 0.8080 (mt0) REVERT: E 4 ASP cc_start: 0.7473 (OUTLIER) cc_final: 0.7239 (t70) REVERT: E 81 GLN cc_start: 0.8098 (OUTLIER) cc_final: 0.7664 (mt0) REVERT: F 68 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8422 (mt) REVERT: G 4 ASP cc_start: 0.7352 (OUTLIER) cc_final: 0.6973 (t70) REVERT: G 68 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8413 (mt) REVERT: G 81 GLN cc_start: 0.8106 (OUTLIER) cc_final: 0.7682 (mt0) REVERT: H 1 MET cc_start: 0.4614 (OUTLIER) cc_final: 0.4196 (mmm) REVERT: I 4 ASP cc_start: 0.7481 (OUTLIER) cc_final: 0.7275 (t70) REVERT: I 68 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8390 (mt) REVERT: J 68 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8427 (mt) REVERT: J 81 GLN cc_start: 0.8346 (mt0) cc_final: 0.8025 (mt0) REVERT: K 68 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8397 (mt) REVERT: K 81 GLN cc_start: 0.8122 (OUTLIER) cc_final: 0.7664 (mt0) REVERT: L 66 ASP cc_start: 0.8032 (t70) cc_final: 0.7641 (t0) REVERT: M 1 MET cc_start: 0.6312 (mmp) cc_final: 0.5966 (mmm) REVERT: N 66 ASP cc_start: 0.8145 (t70) cc_final: 0.7786 (t0) REVERT: N 81 GLN cc_start: 0.8348 (mt0) cc_final: 0.8057 (mt0) REVERT: P 68 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8447 (mt) REVERT: P 81 GLN cc_start: 0.8138 (OUTLIER) cc_final: 0.7631 (mt0) REVERT: Q 66 ASP cc_start: 0.8185 (t70) cc_final: 0.7809 (t0) REVERT: R 68 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8418 (mt) REVERT: R 155 GLU cc_start: 0.7827 (tt0) cc_final: 0.7616 (tt0) REVERT: T 4 ASP cc_start: 0.7368 (OUTLIER) cc_final: 0.7144 (t70) REVERT: T 81 GLN cc_start: 0.8093 (OUTLIER) cc_final: 0.7461 (mt0) REVERT: U 68 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8441 (mt) REVERT: W 66 ASP cc_start: 0.8270 (t0) cc_final: 0.7919 (t0) REVERT: X 1 MET cc_start: 0.4476 (OUTLIER) cc_final: 0.3884 (mmm) outliers start: 70 outliers final: 4 residues processed: 674 average time/residue: 1.8848 time to fit residues: 1488.1965 Evaluate side-chains 676 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 646 time to evaluate : 3.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain B residue 4 ASP Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain E residue 4 ASP Chi-restraints excluded: chain E residue 81 GLN Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain G residue 4 ASP Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 81 GLN Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain I residue 4 ASP Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 81 GLN Chi-restraints excluded: chain P residue 68 LEU Chi-restraints excluded: chain P residue 81 GLN Chi-restraints excluded: chain R residue 26 PHE Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain S residue 4 ASP Chi-restraints excluded: chain T residue 4 ASP Chi-restraints excluded: chain T residue 66 ASP Chi-restraints excluded: chain T residue 81 GLN Chi-restraints excluded: chain U residue 68 LEU Chi-restraints excluded: chain W residue 44 THR Chi-restraints excluded: chain X residue 1 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 46 optimal weight: 3.9990 chunk 224 optimal weight: 8.9990 chunk 1 optimal weight: 5.9990 chunk 170 optimal weight: 3.9990 chunk 130 optimal weight: 10.0000 chunk 327 optimal weight: 2.9990 chunk 333 optimal weight: 7.9990 chunk 65 optimal weight: 8.9990 chunk 198 optimal weight: 0.7980 chunk 280 optimal weight: 9.9990 chunk 204 optimal weight: 6.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.135456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.127890 restraints weight = 23779.274| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 0.41 r_work: 0.3179 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 2.50 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.562 31999 Z= 0.242 Angle : 0.679 26.709 43354 Z= 0.313 Chirality : 0.035 0.245 4806 Planarity : 0.003 0.032 5596 Dihedral : 7.520 87.334 4204 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.10 % Favored : 98.87 % Rotamer: Outliers : 2.05 % Allowed : 15.48 % Favored : 82.47 % 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: 4.37 (0.13), residues: 3724 helix: 3.86 (0.08), residues: 3024 sheet: None (None), residues: 0 loop : -2.07 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP J 37 HIS 0.005 0.001 HIS H 54 PHE 0.026 0.002 PHE F 49 TYR 0.029 0.002 TYR T 71 ARG 0.005 0.001 ARG G 73 Details of bonding type rmsd hydrogen bonds : bond 0.13428 ( 2579) hydrogen bonds : angle 3.80161 ( 7737) covalent geometry : bond 0.00452 (31968) covalent geometry : angle 0.67926 (43354) Misc. bond : bond 0.17136 ( 31) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 798 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 730 time to evaluate : 7.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 GLN cc_start: 0.8102 (OUTLIER) cc_final: 0.7411 (mt0) REVERT: B 81 GLN cc_start: 0.8241 (OUTLIER) cc_final: 0.7755 (mt0) REVERT: C 81 GLN cc_start: 0.8277 (OUTLIER) cc_final: 0.7852 (mt0) REVERT: D 81 GLN cc_start: 0.8492 (mt0) cc_final: 0.8168 (mt0) REVERT: E 81 GLN cc_start: 0.8201 (OUTLIER) cc_final: 0.7732 (mt0) REVERT: G 81 GLN cc_start: 0.8173 (OUTLIER) cc_final: 0.7699 (mt0) REVERT: H 1 MET cc_start: 0.4655 (OUTLIER) cc_final: 0.4033 (mmm) REVERT: J 68 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8420 (mt) REVERT: J 81 GLN cc_start: 0.8394 (mt0) cc_final: 0.8065 (mt0) REVERT: K 1 MET cc_start: 0.6120 (mtm) cc_final: 0.5820 (mtm) REVERT: K 81 GLN cc_start: 0.8244 (OUTLIER) cc_final: 0.7743 (mt0) REVERT: L 66 ASP cc_start: 0.8253 (t70) cc_final: 0.7825 (t0) REVERT: L 68 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8509 (mt) REVERT: M 1 MET cc_start: 0.6277 (mmp) cc_final: 0.6018 (mmm) REVERT: M 66 ASP cc_start: 0.8408 (t70) cc_final: 0.8015 (t0) REVERT: N 81 GLN cc_start: 0.8417 (mt0) cc_final: 0.8134 (mt0) REVERT: O 66 ASP cc_start: 0.8216 (t70) cc_final: 0.7769 (t0) REVERT: O 68 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8482 (mt) REVERT: P 81 GLN cc_start: 0.8202 (OUTLIER) cc_final: 0.7684 (mt0) REVERT: R 155 GLU cc_start: 0.7888 (tt0) cc_final: 0.7681 (tt0) REVERT: T 81 GLN cc_start: 0.8134 (OUTLIER) cc_final: 0.7464 (mt0) REVERT: V 66 ASP cc_start: 0.8042 (t0) cc_final: 0.7688 (t0) REVERT: V 68 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8481 (mt) REVERT: X 1 MET cc_start: 0.4555 (OUTLIER) cc_final: 0.4011 (mmm) outliers start: 68 outliers final: 9 residues processed: 746 average time/residue: 1.7351 time to fit residues: 1503.2709 Evaluate side-chains 750 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 727 time to evaluate : 3.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain E residue 81 GLN Chi-restraints excluded: chain G residue 81 GLN Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain K residue 81 GLN Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain O residue 6 GLU Chi-restraints excluded: chain O residue 68 LEU Chi-restraints excluded: chain P residue 81 GLN Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain R residue 26 PHE Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 44 THR Chi-restraints excluded: chain T residue 66 ASP Chi-restraints excluded: chain T residue 81 GLN Chi-restraints excluded: chain V residue 68 LEU Chi-restraints excluded: chain W residue 44 THR Chi-restraints excluded: chain X residue 1 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 88 optimal weight: 0.9980 chunk 172 optimal weight: 4.9990 chunk 96 optimal weight: 8.9990 chunk 82 optimal weight: 0.9990 chunk 327 optimal weight: 3.9990 chunk 182 optimal weight: 10.0000 chunk 245 optimal weight: 5.9990 chunk 163 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 chunk 303 optimal weight: 3.9990 chunk 237 optimal weight: 5.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.146616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.139279 restraints weight = 24237.904| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 0.41 r_work: 0.3325 rms_B_bonded: 1.34 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.647 31999 Z= 0.194 Angle : 0.645 35.629 43354 Z= 0.280 Chirality : 0.033 0.295 4806 Planarity : 0.003 0.031 5596 Dihedral : 7.517 88.992 4204 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.09 % Allowed : 15.54 % Favored : 83.37 % 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: 4.67 (0.13), residues: 3724 helix: 4.08 (0.08), residues: 3024 sheet: None (None), residues: 0 loop : -2.07 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP H 37 HIS 0.003 0.001 HIS Q 129 PHE 0.018 0.001 PHE F 49 TYR 0.019 0.001 TYR T 71 ARG 0.003 0.000 ARG G 73 Details of bonding type rmsd hydrogen bonds : bond 0.10531 ( 2579) hydrogen bonds : angle 3.58089 ( 7737) covalent geometry : bond 0.00362 (31968) covalent geometry : angle 0.64512 (43354) Misc. bond : bond 0.18093 ( 31) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 679 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 643 time to evaluate : 3.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 GLN cc_start: 0.8000 (OUTLIER) cc_final: 0.7355 (mt0) REVERT: B 81 GLN cc_start: 0.8167 (OUTLIER) cc_final: 0.7689 (mt0) REVERT: C 81 GLN cc_start: 0.8217 (OUTLIER) cc_final: 0.7808 (mt0) REVERT: D 81 GLN cc_start: 0.8328 (mt0) cc_final: 0.8034 (mt0) REVERT: E 66 ASP cc_start: 0.8195 (t0) cc_final: 0.7927 (t70) REVERT: E 81 GLN cc_start: 0.8056 (OUTLIER) cc_final: 0.7615 (mt0) REVERT: G 1 MET cc_start: 0.5990 (mtm) cc_final: 0.5677 (mtm) REVERT: H 1 MET cc_start: 0.4562 (OUTLIER) cc_final: 0.4044 (mmm) REVERT: J 81 GLN cc_start: 0.8310 (mt0) cc_final: 0.8005 (mt0) REVERT: K 81 GLN cc_start: 0.8143 (OUTLIER) cc_final: 0.7676 (mt0) REVERT: L 66 ASP cc_start: 0.8062 (t70) cc_final: 0.7696 (t0) REVERT: M 1 MET cc_start: 0.6270 (mmp) cc_final: 0.5959 (mmm) REVERT: N 4 ASP cc_start: 0.7491 (OUTLIER) cc_final: 0.7137 (t70) REVERT: N 81 GLN cc_start: 0.8320 (mt0) cc_final: 0.8049 (mt0) REVERT: P 81 GLN cc_start: 0.8074 (OUTLIER) cc_final: 0.7581 (mt0) REVERT: R 155 GLU cc_start: 0.7852 (tt0) cc_final: 0.7633 (tt0) REVERT: S 4 ASP cc_start: 0.7468 (OUTLIER) cc_final: 0.7173 (t70) REVERT: T 81 GLN cc_start: 0.8010 (OUTLIER) cc_final: 0.7365 (mt0) REVERT: W 4 ASP cc_start: 0.7483 (OUTLIER) cc_final: 0.7169 (t70) REVERT: X 4 ASP cc_start: 0.7483 (OUTLIER) cc_final: 0.7117 (t70) outliers start: 36 outliers final: 4 residues processed: 656 average time/residue: 1.5036 time to fit residues: 1151.6616 Evaluate side-chains 659 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 643 time to evaluate : 3.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain E residue 81 GLN Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain K residue 81 GLN Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain N residue 4 ASP Chi-restraints excluded: chain P residue 81 GLN Chi-restraints excluded: chain R residue 26 PHE Chi-restraints excluded: chain S residue 4 ASP Chi-restraints excluded: chain T residue 66 ASP Chi-restraints excluded: chain T residue 81 GLN Chi-restraints excluded: chain W residue 4 ASP Chi-restraints excluded: chain X residue 4 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 33 optimal weight: 2.9990 chunk 279 optimal weight: 4.9990 chunk 307 optimal weight: 4.9990 chunk 354 optimal weight: 0.9990 chunk 220 optimal weight: 9.9990 chunk 181 optimal weight: 1.9990 chunk 130 optimal weight: 10.0000 chunk 20 optimal weight: 0.9990 chunk 107 optimal weight: 7.9990 chunk 342 optimal weight: 3.9990 chunk 232 optimal weight: 5.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.144583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.137212 restraints weight = 24123.921| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 0.40 r_work: 0.3297 rms_B_bonded: 1.34 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.662 31999 Z= 0.202 Angle : 0.730 39.779 43354 Z= 0.301 Chirality : 0.033 0.272 4806 Planarity : 0.003 0.031 5596 Dihedral : 7.610 88.574 4204 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 0.69 % Allowed : 16.75 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 4.66 (0.13), residues: 3724 helix: 4.06 (0.08), residues: 3024 sheet: None (None), residues: 0 loop : -1.96 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP P 37 HIS 0.003 0.001 HIS Q 129 PHE 0.024 0.001 PHE F 49 TYR 0.021 0.001 TYR T 71 ARG 0.004 0.000 ARG E 73 Details of bonding type rmsd hydrogen bonds : bond 0.11013 ( 2579) hydrogen bonds : angle 3.62987 ( 7737) covalent geometry : bond 0.00369 (31968) covalent geometry : angle 0.72957 (43354) Misc. bond : bond 0.19425 ( 31) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 668 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 645 time to evaluate : 3.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 GLN cc_start: 0.8013 (OUTLIER) cc_final: 0.7309 (mt0) REVERT: B 81 GLN cc_start: 0.8157 (OUTLIER) cc_final: 0.7687 (mt0) REVERT: C 81 GLN cc_start: 0.8236 (OUTLIER) cc_final: 0.7839 (mt0) REVERT: D 81 GLN cc_start: 0.8352 (mt0) cc_final: 0.8024 (mt0) REVERT: E 81 GLN cc_start: 0.8153 (OUTLIER) cc_final: 0.7692 (mt0) REVERT: G 1 MET cc_start: 0.6097 (mtm) cc_final: 0.5732 (mtt) REVERT: G 4 ASP cc_start: 0.7501 (OUTLIER) cc_final: 0.7071 (t70) REVERT: H 1 MET cc_start: 0.4538 (OUTLIER) cc_final: 0.3935 (mmm) REVERT: J 66 ASP cc_start: 0.8230 (t0) cc_final: 0.8020 (t0) REVERT: J 81 GLN cc_start: 0.8322 (mt0) cc_final: 0.8004 (mt0) REVERT: K 1 MET cc_start: 0.6084 (mtm) cc_final: 0.5772 (mtm) REVERT: L 66 ASP cc_start: 0.8098 (t70) cc_final: 0.7741 (t0) REVERT: N 81 GLN cc_start: 0.8323 (mt0) cc_final: 0.8037 (mt0) REVERT: P 81 GLN cc_start: 0.8134 (OUTLIER) cc_final: 0.7621 (mt0) REVERT: R 155 GLU cc_start: 0.7828 (tt0) cc_final: 0.7618 (tt0) REVERT: T 81 GLN cc_start: 0.8085 (OUTLIER) cc_final: 0.7436 (mt0) REVERT: U 1 MET cc_start: 0.6087 (mtm) cc_final: 0.5802 (mtt) REVERT: W 4 ASP cc_start: 0.7491 (OUTLIER) cc_final: 0.7182 (t70) REVERT: W 66 ASP cc_start: 0.8141 (t0) cc_final: 0.7800 (t0) outliers start: 23 outliers final: 5 residues processed: 651 average time/residue: 1.5473 time to fit residues: 1175.0541 Evaluate side-chains 659 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 645 time to evaluate : 3.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain E residue 81 GLN Chi-restraints excluded: chain G residue 4 ASP Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain P residue 81 GLN Chi-restraints excluded: chain R residue 26 PHE Chi-restraints excluded: chain T residue 66 ASP Chi-restraints excluded: chain T residue 81 GLN Chi-restraints excluded: chain W residue 4 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 195 optimal weight: 1.9990 chunk 256 optimal weight: 4.9990 chunk 65 optimal weight: 20.0000 chunk 247 optimal weight: 0.0980 chunk 324 optimal weight: 6.9990 chunk 273 optimal weight: 0.5980 chunk 119 optimal weight: 0.1980 chunk 268 optimal weight: 0.9990 chunk 47 optimal weight: 10.0000 chunk 125 optimal weight: 30.0000 chunk 209 optimal weight: 5.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.167223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.161878 restraints weight = 26215.317| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 0.32 r_work: 0.3553 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3433 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.712 31999 Z= 0.148 Angle : 0.634 34.940 43354 Z= 0.265 Chirality : 0.032 0.185 4806 Planarity : 0.002 0.032 5596 Dihedral : 7.420 89.972 4204 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Rotamer: Outliers : 0.51 % Allowed : 16.78 % Favored : 82.71 % 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: 4.87 (0.13), residues: 3724 helix: 4.30 (0.08), residues: 3024 sheet: None (None), residues: 0 loop : -2.37 (0.19), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 37 HIS 0.002 0.000 HIS Q 129 PHE 0.023 0.001 PHE F 49 TYR 0.012 0.001 TYR T 71 ARG 0.004 0.000 ARG N 53 Details of bonding type rmsd hydrogen bonds : bond 0.07342 ( 2579) hydrogen bonds : angle 3.27711 ( 7737) covalent geometry : bond 0.00276 (31968) covalent geometry : angle 0.63416 (43354) Misc. bond : bond 0.18310 ( 31) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 27115.08 seconds wall clock time: 478 minutes 28.91 seconds (28708.91 seconds total)