Starting phenix.real_space_refine on Wed May 28 06:24:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y6g_33640/05_2025/7y6g_33640_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y6g_33640/05_2025/7y6g_33640.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7y6g_33640/05_2025/7y6g_33640.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y6g_33640/05_2025/7y6g_33640.map" model { file = "/net/cci-nas-00/data/ceres_data/7y6g_33640/05_2025/7y6g_33640_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y6g_33640/05_2025/7y6g_33640_trim.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 19.40, per 1000 atoms: 0.62 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: 8.85 Conformation dependent library (CDL) restraints added in 3.7 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: 2.05 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: 9.17 Time building geometry restraints manager: 10.00 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.800 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: 0.040 Extract box with map and model: 1.480 Check model and map are aligned: 0.260 Set scattering table: 0.360 Process input model: 65.840 Find NCS groups from input model: 2.030 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6037 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 474 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 474 time to evaluate : 3.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 474 average time/residue: 0.4632 time to fit residues: 343.0891 Evaluate side-chains 208 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 3.941 ------------------------------------------------------------------------------- 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: 10.0000 chunk 272 optimal weight: 5.9990 chunk 151 optimal weight: 10.0000 chunk 93 optimal weight: 20.0000 chunk 184 optimal weight: 5.9990 chunk 145 optimal weight: 0.8980 chunk 282 optimal weight: 7.9990 chunk 109 optimal weight: 6.9990 chunk 171 optimal weight: 3.9990 chunk 210 optimal weight: 30.0000 chunk 326 optimal weight: 9.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 81 GLN J 112 HIS M 137 GLN ** M 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 112 HIS S 81 GLN U 156 GLN W 81 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.035599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.028921 restraints weight = 205584.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.029961 restraints weight = 127956.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.030768 restraints weight = 91248.975| |-----------------------------------------------------------------------------| r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.301 31999 Z= 0.157 Angle : 0.639 14.540 43354 Z= 0.300 Chirality : 0.032 0.129 4806 Planarity : 0.003 0.078 5596 Dihedral : 6.855 79.272 4204 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Rotamer: Outliers : 0.42 % Allowed : 8.27 % Favored : 91.31 % 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: 4.53 (0.13), residues: 3724 helix: 3.98 (0.08), residues: 3062 sheet: None (None), residues: 0 loop : -2.46 (0.20), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 37 HIS 0.004 0.001 HIS V 112 PHE 0.033 0.002 PHE F 49 TYR 0.028 0.001 TYR T 71 ARG 0.006 0.000 ARG P 53 Details of bonding type rmsd hydrogen bonds : bond 0.06757 ( 2579) hydrogen bonds : angle 3.77523 ( 7737) covalent geometry : bond 0.00359 (31968) covalent geometry : angle 0.63894 (43354) Misc. bond : bond 0.08712 ( 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 288 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 274 time to evaluate : 3.618 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 59 THR cc_start: 0.9344 (m) cc_final: 0.9087 (p) REVERT: E 53 ARG cc_start: 0.9017 (mtt90) cc_final: 0.8777 (mtm-85) REVERT: G 59 THR cc_start: 0.9414 (m) cc_final: 0.9131 (p) REVERT: H 52 MET cc_start: 0.7371 (mtm) cc_final: 0.6871 (mtm) REVERT: I 59 THR cc_start: 0.9364 (m) cc_final: 0.9117 (p) REVERT: J 53 ARG cc_start: 0.9006 (mtt90) cc_final: 0.8685 (mtm-85) REVERT: K 52 MET cc_start: 0.7860 (mtm) cc_final: 0.7533 (mtp) REVERT: L 52 MET cc_start: 0.7597 (mtm) cc_final: 0.7371 (mtm) REVERT: L 108 MET cc_start: 0.9123 (mtm) cc_final: 0.8921 (mtp) REVERT: M 53 ARG cc_start: 0.8966 (mtt90) cc_final: 0.8760 (mtm-85) REVERT: M 86 MET cc_start: 0.9469 (mtt) cc_final: 0.9237 (mtt) REVERT: M 105 ILE cc_start: 0.9603 (tt) cc_final: 0.9359 (mt) REVERT: M 108 MET cc_start: 0.8912 (mtm) cc_final: 0.8705 (mtp) REVERT: O 59 THR cc_start: 0.9377 (m) cc_final: 0.9145 (p) REVERT: V 108 MET cc_start: 0.9171 (mtm) cc_final: 0.8940 (mtp) REVERT: W 52 MET cc_start: 0.6750 (mtm) cc_final: 0.6481 (mtm) outliers start: 14 outliers final: 3 residues processed: 277 average time/residue: 0.3586 time to fit residues: 171.1997 Evaluate side-chains 202 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 199 time to evaluate : 3.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 8 ILE Chi-restraints excluded: chain P residue 98 ILE Chi-restraints excluded: chain Q residue 52 MET 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: 40.0000 chunk 73 optimal weight: 10.0000 chunk 273 optimal weight: 6.9990 chunk 308 optimal weight: 8.9990 chunk 314 optimal weight: 6.9990 chunk 350 optimal weight: 5.9990 chunk 68 optimal weight: 20.0000 chunk 103 optimal weight: 9.9990 chunk 310 optimal weight: 30.0000 chunk 2 optimal weight: 8.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN B 130 HIS H 130 HIS I 130 HIS ** M 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 130 HIS P 130 HIS Q 130 HIS R 130 HIS T 81 GLN T 130 HIS U 130 HIS X 130 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.034108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2626 r_free = 0.2626 target = 0.027295 restraints weight = 213600.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.028344 restraints weight = 136395.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.029136 restraints weight = 96969.102| |-----------------------------------------------------------------------------| r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8986 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.300 31999 Z= 0.185 Angle : 0.637 15.573 43354 Z= 0.298 Chirality : 0.033 0.121 4806 Planarity : 0.003 0.053 5596 Dihedral : 6.976 86.978 4204 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 0.84 % Allowed : 9.57 % Favored : 89.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.41 (0.13), residues: 3724 helix: 3.85 (0.08), residues: 3072 sheet: None (None), residues: 0 loop : -2.36 (0.20), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 37 HIS 0.003 0.001 HIS L 54 PHE 0.021 0.002 PHE S 26 TYR 0.040 0.001 TYR T 71 ARG 0.004 0.001 ARG P 53 Details of bonding type rmsd hydrogen bonds : bond 0.06952 ( 2579) hydrogen bonds : angle 3.88667 ( 7737) covalent geometry : bond 0.00413 (31968) covalent geometry : angle 0.63745 (43354) Misc. bond : bond 0.07621 ( 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 234 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 206 time to evaluate : 3.788 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 59 THR cc_start: 0.9368 (m) cc_final: 0.9110 (p) REVERT: A 86 MET cc_start: 0.9408 (mtt) cc_final: 0.8861 (mpp) REVERT: C 59 THR cc_start: 0.9299 (m) cc_final: 0.9050 (p) REVERT: D 86 MET cc_start: 0.9428 (mtt) cc_final: 0.9227 (mtt) REVERT: E 53 ARG cc_start: 0.8997 (mtt90) cc_final: 0.8587 (mtm-85) REVERT: F 59 THR cc_start: 0.9406 (m) cc_final: 0.9157 (p) REVERT: F 86 MET cc_start: 0.9401 (mtt) cc_final: 0.8866 (mpp) REVERT: G 59 THR cc_start: 0.9380 (m) cc_final: 0.9125 (p) REVERT: H 52 MET cc_start: 0.7649 (mtm) cc_final: 0.7111 (mtm) REVERT: I 59 THR cc_start: 0.9380 (m) cc_final: 0.9131 (p) REVERT: J 53 ARG cc_start: 0.8962 (mtt90) cc_final: 0.8626 (mtm-85) REVERT: K 52 MET cc_start: 0.7957 (mtm) cc_final: 0.7636 (mtp) REVERT: M 53 ARG cc_start: 0.8905 (mtt90) cc_final: 0.8562 (mtm-85) REVERT: M 108 MET cc_start: 0.8987 (mtm) cc_final: 0.8779 (mtp) REVERT: O 59 THR cc_start: 0.9388 (m) cc_final: 0.9141 (p) REVERT: R 86 MET cc_start: 0.9391 (mtt) cc_final: 0.8850 (mpp) REVERT: S 86 MET cc_start: 0.9410 (mtt) cc_final: 0.8878 (mpp) REVERT: T 86 MET cc_start: 0.9400 (mtt) cc_final: 0.8852 (mpp) REVERT: W 86 MET cc_start: 0.9406 (mtt) cc_final: 0.8852 (mpp) REVERT: X 86 MET cc_start: 0.9412 (mtt) cc_final: 0.8886 (mpp) outliers start: 28 outliers final: 20 residues processed: 207 average time/residue: 0.3888 time to fit residues: 139.1377 Evaluate side-chains 197 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 177 time to evaluate : 3.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain G residue 98 ILE Chi-restraints excluded: chain H residue 98 ILE Chi-restraints excluded: chain I residue 98 ILE Chi-restraints excluded: chain J residue 98 ILE Chi-restraints excluded: chain K residue 98 ILE Chi-restraints excluded: chain M residue 8 ILE Chi-restraints excluded: chain N residue 98 ILE Chi-restraints excluded: chain P residue 98 ILE Chi-restraints excluded: chain Q residue 52 MET Chi-restraints excluded: chain R residue 98 ILE Chi-restraints excluded: chain S residue 98 ILE Chi-restraints excluded: chain T residue 98 ILE Chi-restraints excluded: chain U residue 98 ILE Chi-restraints excluded: chain W residue 98 ILE Chi-restraints excluded: chain X residue 98 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 71 optimal weight: 3.9990 chunk 324 optimal weight: 20.0000 chunk 93 optimal weight: 20.0000 chunk 201 optimal weight: 20.0000 chunk 189 optimal weight: 9.9990 chunk 341 optimal weight: 3.9990 chunk 176 optimal weight: 30.0000 chunk 355 optimal weight: 6.9990 chunk 333 optimal weight: 0.2980 chunk 47 optimal weight: 9.9990 chunk 290 optimal weight: 9.9990 overall best weight: 5.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 130 HIS H 130 HIS I 130 HIS ** M 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 130 HIS P 130 HIS R 130 HIS T 130 HIS U 130 HIS X 130 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.034735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.028014 restraints weight = 216755.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.029075 restraints weight = 138025.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.029871 restraints weight = 98060.451| |-----------------------------------------------------------------------------| r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8961 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.332 31999 Z= 0.147 Angle : 0.587 14.564 43354 Z= 0.274 Chirality : 0.032 0.121 4806 Planarity : 0.002 0.042 5596 Dihedral : 6.980 89.108 4204 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 0.48 % Allowed : 10.35 % Favored : 89.17 % 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: 4.54 (0.13), residues: 3724 helix: 3.93 (0.08), residues: 3067 sheet: None (None), residues: 0 loop : -2.14 (0.20), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 37 HIS 0.002 0.001 HIS L 54 PHE 0.019 0.001 PHE S 26 TYR 0.031 0.001 TYR T 71 ARG 0.003 0.000 ARG F 45 Details of bonding type rmsd hydrogen bonds : bond 0.06095 ( 2579) hydrogen bonds : angle 3.69060 ( 7737) covalent geometry : bond 0.00329 (31968) covalent geometry : angle 0.58709 (43354) Misc. bond : bond 0.09541 ( 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 208 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 192 time to evaluate : 3.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 THR cc_start: 0.9317 (m) cc_final: 0.9033 (p) REVERT: B 59 THR cc_start: 0.9392 (m) cc_final: 0.9116 (p) REVERT: B 108 MET cc_start: 0.8766 (ptm) cc_final: 0.8448 (ppp) REVERT: C 59 THR cc_start: 0.9251 (m) cc_final: 0.8991 (p) REVERT: E 53 ARG cc_start: 0.8976 (mtt90) cc_final: 0.8557 (mtm-85) REVERT: E 59 THR cc_start: 0.9390 (m) cc_final: 0.9126 (p) REVERT: F 59 THR cc_start: 0.9368 (m) cc_final: 0.9081 (p) REVERT: F 108 MET cc_start: 0.8837 (ptm) cc_final: 0.8515 (ppp) REVERT: G 59 THR cc_start: 0.9320 (m) cc_final: 0.9033 (p) REVERT: H 52 MET cc_start: 0.7496 (mtm) cc_final: 0.7113 (mtm) REVERT: H 108 MET cc_start: 0.8825 (ptm) cc_final: 0.8487 (ppp) REVERT: I 59 THR cc_start: 0.9351 (m) cc_final: 0.9067 (p) REVERT: J 53 ARG cc_start: 0.8936 (mtt90) cc_final: 0.8600 (mtm-85) REVERT: K 52 MET cc_start: 0.8039 (mtm) cc_final: 0.7744 (mtp) REVERT: K 59 THR cc_start: 0.9394 (m) cc_final: 0.9133 (p) REVERT: M 53 ARG cc_start: 0.8894 (mtt90) cc_final: 0.8691 (mtm-85) REVERT: O 59 THR cc_start: 0.9354 (m) cc_final: 0.9085 (p) REVERT: O 108 MET cc_start: 0.9415 (OUTLIER) cc_final: 0.9011 (ppp) REVERT: R 59 THR cc_start: 0.9384 (m) cc_final: 0.9116 (p) REVERT: R 108 MET cc_start: 0.8730 (ptm) cc_final: 0.8239 (ppp) REVERT: S 59 THR cc_start: 0.9384 (m) cc_final: 0.9120 (p) REVERT: W 59 THR cc_start: 0.9475 (m) cc_final: 0.9207 (p) REVERT: W 108 MET cc_start: 0.8772 (ptm) cc_final: 0.8478 (ppp) REVERT: X 108 MET cc_start: 0.8759 (ptm) cc_final: 0.8492 (ppp) outliers start: 16 outliers final: 4 residues processed: 197 average time/residue: 0.3857 time to fit residues: 130.2782 Evaluate side-chains 182 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 177 time to evaluate : 3.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain M residue 8 ILE Chi-restraints excluded: chain O residue 108 MET Chi-restraints excluded: chain Q residue 52 MET Chi-restraints excluded: chain V residue 79 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 283 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 chunk 93 optimal weight: 5.9990 chunk 206 optimal weight: 9.9990 chunk 174 optimal weight: 8.9990 chunk 224 optimal weight: 7.9990 chunk 124 optimal weight: 20.0000 chunk 70 optimal weight: 9.9990 chunk 156 optimal weight: 0.9980 chunk 101 optimal weight: 10.0000 chunk 138 optimal weight: 20.0000 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 156 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.034357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.027655 restraints weight = 218052.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.028707 restraints weight = 138872.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.029498 restraints weight = 98832.710| |-----------------------------------------------------------------------------| r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8975 moved from start: 0.3733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.679 31999 Z= 0.152 Angle : 0.576 16.600 43354 Z= 0.266 Chirality : 0.032 0.119 4806 Planarity : 0.002 0.038 5596 Dihedral : 6.989 89.497 4204 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 0.69 % Allowed : 10.26 % Favored : 89.05 % 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: 4.50 (0.13), residues: 3724 helix: 3.86 (0.08), residues: 3065 sheet: None (None), residues: 0 loop : -1.92 (0.21), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 37 HIS 0.002 0.001 HIS J 34 PHE 0.019 0.001 PHE S 26 TYR 0.032 0.001 TYR T 71 ARG 0.003 0.000 ARG F 45 Details of bonding type rmsd hydrogen bonds : bond 0.06029 ( 2579) hydrogen bonds : angle 3.64813 ( 7737) covalent geometry : bond 0.00334 (31968) covalent geometry : angle 0.57584 (43354) Misc. bond : bond 0.14828 ( 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 209 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 186 time to evaluate : 3.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.8641 (ptm) cc_final: 0.8373 (ppp) REVERT: B 59 THR cc_start: 0.9391 (m) cc_final: 0.9118 (p) REVERT: B 108 MET cc_start: 0.8687 (ptm) cc_final: 0.8418 (ppp) REVERT: D 108 MET cc_start: 0.8684 (ptm) cc_final: 0.8380 (ppp) REVERT: E 53 ARG cc_start: 0.8949 (mtt90) cc_final: 0.8508 (mtm-85) REVERT: E 108 MET cc_start: 0.8836 (ptm) cc_final: 0.8490 (ppp) REVERT: F 59 THR cc_start: 0.9365 (m) cc_final: 0.9078 (p) REVERT: F 108 MET cc_start: 0.8742 (ptm) cc_final: 0.8508 (ppp) REVERT: G 108 MET cc_start: 0.8677 (ptm) cc_final: 0.8382 (ppp) REVERT: H 52 MET cc_start: 0.7461 (mtm) cc_final: 0.7147 (ttm) REVERT: H 108 MET cc_start: 0.8768 (ptm) cc_final: 0.8543 (ppp) REVERT: I 59 THR cc_start: 0.9364 (m) cc_final: 0.9076 (p) REVERT: I 108 MET cc_start: 0.8649 (ptm) cc_final: 0.8400 (ppp) REVERT: J 53 ARG cc_start: 0.8909 (mtt90) cc_final: 0.8492 (mtm-85) REVERT: K 59 THR cc_start: 0.9398 (m) cc_final: 0.9132 (p) REVERT: K 108 MET cc_start: 0.8627 (ptm) cc_final: 0.8387 (ppp) REVERT: L 108 MET cc_start: 0.9229 (ptp) cc_final: 0.9019 (ptm) REVERT: M 53 ARG cc_start: 0.8887 (mtt90) cc_final: 0.8509 (mtm-85) REVERT: N 108 MET cc_start: 0.9063 (tmm) cc_final: 0.8740 (ppp) REVERT: O 59 THR cc_start: 0.9348 (m) cc_final: 0.9072 (p) REVERT: O 108 MET cc_start: 0.9355 (OUTLIER) cc_final: 0.8963 (ppp) REVERT: P 108 MET cc_start: 0.8596 (ptm) cc_final: 0.8324 (ppp) REVERT: Q 108 MET cc_start: 0.8714 (ptm) cc_final: 0.8383 (ppp) REVERT: R 59 THR cc_start: 0.9378 (m) cc_final: 0.9103 (p) REVERT: R 108 MET cc_start: 0.8704 (ptm) cc_final: 0.8251 (ppp) REVERT: S 59 THR cc_start: 0.9398 (m) cc_final: 0.9134 (p) REVERT: S 108 MET cc_start: 0.8757 (ptm) cc_final: 0.8485 (ppp) REVERT: T 108 MET cc_start: 0.8798 (ptm) cc_final: 0.8308 (ppp) REVERT: U 108 MET cc_start: 0.8762 (ptm) cc_final: 0.8422 (ppp) REVERT: V 86 MET cc_start: 0.9356 (mtt) cc_final: 0.8782 (mpp) REVERT: W 59 THR cc_start: 0.9473 (m) cc_final: 0.9224 (p) REVERT: W 108 MET cc_start: 0.8683 (ptm) cc_final: 0.8431 (ppp) REVERT: X 108 MET cc_start: 0.8751 (ptm) cc_final: 0.8532 (ppp) outliers start: 23 outliers final: 8 residues processed: 201 average time/residue: 0.3986 time to fit residues: 134.4057 Evaluate side-chains 184 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 175 time to evaluate : 3.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain M residue 8 ILE Chi-restraints excluded: chain M residue 79 VAL Chi-restraints excluded: chain N residue 98 ILE Chi-restraints excluded: chain O residue 108 MET Chi-restraints excluded: chain P residue 98 ILE Chi-restraints excluded: chain Q residue 52 MET Chi-restraints excluded: chain V residue 79 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 207 optimal weight: 5.9990 chunk 180 optimal weight: 30.0000 chunk 277 optimal weight: 7.9990 chunk 345 optimal weight: 0.2980 chunk 278 optimal weight: 4.9990 chunk 63 optimal weight: 9.9990 chunk 354 optimal weight: 8.9990 chunk 143 optimal weight: 10.0000 chunk 339 optimal weight: 10.0000 chunk 254 optimal weight: 5.9990 chunk 292 optimal weight: 20.0000 overall best weight: 5.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 130 HIS H 130 HIS I 130 HIS O 130 HIS P 130 HIS T 130 HIS X 130 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.034520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.027822 restraints weight = 219924.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.028868 restraints weight = 139857.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.029647 restraints weight = 99267.760| |-----------------------------------------------------------------------------| r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8973 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.694 31999 Z= 0.145 Angle : 0.597 14.132 43354 Z= 0.273 Chirality : 0.032 0.145 4806 Planarity : 0.002 0.029 5596 Dihedral : 6.919 86.958 4204 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.63 % Allowed : 10.89 % Favored : 88.47 % 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: 4.56 (0.13), residues: 3724 helix: 3.87 (0.08), residues: 3065 sheet: None (None), residues: 0 loop : -1.75 (0.22), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 37 HIS 0.002 0.001 HIS Q 34 PHE 0.018 0.001 PHE N 26 TYR 0.027 0.001 TYR T 71 ARG 0.003 0.000 ARG T 73 Details of bonding type rmsd hydrogen bonds : bond 0.05825 ( 2579) hydrogen bonds : angle 3.59961 ( 7737) covalent geometry : bond 0.00320 (31968) covalent geometry : angle 0.59665 (43354) Misc. bond : bond 0.15159 ( 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 198 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 177 time to evaluate : 3.579 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 108 MET cc_start: 0.8593 (ptm) cc_final: 0.8389 (ppp) REVERT: B 108 MET cc_start: 0.8645 (ptm) cc_final: 0.8434 (ppp) REVERT: D 108 MET cc_start: 0.8594 (ptm) cc_final: 0.8373 (ppp) REVERT: E 53 ARG cc_start: 0.8938 (mtt90) cc_final: 0.8509 (mtm-85) REVERT: E 108 MET cc_start: 0.8736 (ptm) cc_final: 0.8472 (ppp) REVERT: G 108 MET cc_start: 0.8585 (ptm) cc_final: 0.8328 (ppp) REVERT: H 52 MET cc_start: 0.7509 (mtm) cc_final: 0.7250 (mtm) REVERT: H 108 MET cc_start: 0.8748 (ptm) cc_final: 0.8532 (ppp) REVERT: I 108 MET cc_start: 0.8559 (ptm) cc_final: 0.8356 (ppp) REVERT: J 53 ARG cc_start: 0.8888 (mtt90) cc_final: 0.8575 (mtm-85) REVERT: J 86 MET cc_start: 0.9401 (mtt) cc_final: 0.8833 (mpp) REVERT: J 108 MET cc_start: 0.8686 (ptm) cc_final: 0.8373 (ppp) REVERT: K 59 THR cc_start: 0.9383 (m) cc_final: 0.9103 (p) REVERT: M 53 ARG cc_start: 0.8873 (mtt90) cc_final: 0.8502 (mtm-85) REVERT: N 86 MET cc_start: 0.9392 (mtt) cc_final: 0.8829 (mpp) REVERT: N 108 MET cc_start: 0.9095 (tmm) cc_final: 0.8762 (ppp) REVERT: O 59 THR cc_start: 0.9319 (m) cc_final: 0.9033 (p) REVERT: O 108 MET cc_start: 0.9347 (OUTLIER) cc_final: 0.8967 (ppp) REVERT: P 108 MET cc_start: 0.8536 (ptm) cc_final: 0.8324 (ppp) REVERT: Q 108 MET cc_start: 0.8636 (ptm) cc_final: 0.8391 (ppp) REVERT: R 59 THR cc_start: 0.9363 (m) cc_final: 0.9077 (p) REVERT: R 108 MET cc_start: 0.8700 (ptm) cc_final: 0.8261 (ppp) REVERT: S 59 THR cc_start: 0.9395 (m) cc_final: 0.9117 (p) REVERT: S 108 MET cc_start: 0.8722 (ptm) cc_final: 0.8468 (ppp) REVERT: T 108 MET cc_start: 0.8718 (ptm) cc_final: 0.8246 (ppp) REVERT: U 108 MET cc_start: 0.8671 (ptm) cc_final: 0.8362 (ppp) REVERT: V 108 MET cc_start: 0.9191 (ptp) cc_final: 0.8968 (ptm) REVERT: W 59 THR cc_start: 0.9432 (m) cc_final: 0.9166 (p) REVERT: W 108 MET cc_start: 0.8638 (ptm) cc_final: 0.8433 (ppp) outliers start: 21 outliers final: 8 residues processed: 191 average time/residue: 0.3932 time to fit residues: 126.3583 Evaluate side-chains 181 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 172 time to evaluate : 3.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain G residue 98 ILE Chi-restraints excluded: chain M residue 8 ILE Chi-restraints excluded: chain M residue 79 VAL Chi-restraints excluded: chain O residue 108 MET Chi-restraints excluded: chain Q residue 52 MET Chi-restraints excluded: chain R residue 26 PHE Chi-restraints excluded: chain V residue 79 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 336 optimal weight: 1.9990 chunk 284 optimal weight: 5.9990 chunk 72 optimal weight: 6.9990 chunk 321 optimal weight: 9.9990 chunk 351 optimal weight: 9.9990 chunk 75 optimal weight: 30.0000 chunk 155 optimal weight: 10.0000 chunk 143 optimal weight: 20.0000 chunk 221 optimal weight: 0.4980 chunk 300 optimal weight: 30.0000 chunk 241 optimal weight: 20.0000 overall best weight: 5.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 130 HIS H 130 HIS O 130 HIS P 130 HIS X 130 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.034557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.027861 restraints weight = 216866.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.028895 restraints weight = 138808.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.029657 restraints weight = 99412.024| |-----------------------------------------------------------------------------| r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8973 moved from start: 0.4036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.731 31999 Z= 0.144 Angle : 0.581 13.825 43354 Z= 0.265 Chirality : 0.032 0.115 4806 Planarity : 0.002 0.032 5596 Dihedral : 6.853 83.477 4204 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 0.54 % Allowed : 11.16 % Favored : 88.29 % 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: 4.57 (0.13), residues: 3724 helix: 3.85 (0.08), residues: 3065 sheet: None (None), residues: 0 loop : -1.61 (0.22), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP O 37 HIS 0.002 0.001 HIS D 34 PHE 0.018 0.001 PHE S 26 TYR 0.027 0.001 TYR T 71 ARG 0.004 0.000 ARG H 73 Details of bonding type rmsd hydrogen bonds : bond 0.05767 ( 2579) hydrogen bonds : angle 3.55903 ( 7737) covalent geometry : bond 0.00316 (31968) covalent geometry : angle 0.58052 (43354) Misc. bond : bond 0.16606 ( 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 192 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 174 time to evaluate : 4.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 86 MET cc_start: 0.9386 (mtt) cc_final: 0.8811 (mpp) REVERT: D 108 MET cc_start: 0.8586 (ptm) cc_final: 0.8385 (ppp) REVERT: E 53 ARG cc_start: 0.8954 (mtt90) cc_final: 0.8517 (mtm-85) REVERT: E 108 MET cc_start: 0.8768 (ptm) cc_final: 0.8527 (ppp) REVERT: F 86 MET cc_start: 0.9326 (mtt) cc_final: 0.8827 (mpp) REVERT: G 108 MET cc_start: 0.8570 (ptm) cc_final: 0.8352 (ppp) REVERT: H 52 MET cc_start: 0.7654 (mtm) cc_final: 0.7329 (mtm) REVERT: H 108 MET cc_start: 0.8730 (ptm) cc_final: 0.8506 (ppp) REVERT: J 53 ARG cc_start: 0.8894 (mtt90) cc_final: 0.8487 (mtm-85) REVERT: J 108 MET cc_start: 0.8666 (ptm) cc_final: 0.8429 (ppp) REVERT: K 59 THR cc_start: 0.9380 (m) cc_final: 0.9099 (p) REVERT: L 108 MET cc_start: 0.8780 (ptm) cc_final: 0.8451 (ppp) REVERT: M 53 ARG cc_start: 0.8857 (mtt90) cc_final: 0.8532 (mtm-85) REVERT: M 108 MET cc_start: 0.8713 (ptm) cc_final: 0.8443 (ppp) REVERT: N 108 MET cc_start: 0.9073 (tmm) cc_final: 0.8728 (ppp) REVERT: O 59 THR cc_start: 0.9309 (m) cc_final: 0.9024 (p) REVERT: O 108 MET cc_start: 0.9351 (OUTLIER) cc_final: 0.8951 (ppp) REVERT: Q 108 MET cc_start: 0.8635 (ptm) cc_final: 0.8425 (ppp) REVERT: R 86 MET cc_start: 0.9325 (mtt) cc_final: 0.8823 (mpp) REVERT: R 108 MET cc_start: 0.8685 (ptm) cc_final: 0.8266 (ppp) REVERT: S 59 THR cc_start: 0.9404 (m) cc_final: 0.9123 (p) REVERT: S 86 MET cc_start: 0.9320 (mtt) cc_final: 0.8833 (mpp) REVERT: S 108 MET cc_start: 0.8713 (ptm) cc_final: 0.8496 (ppp) REVERT: T 86 MET cc_start: 0.9336 (mtt) cc_final: 0.8825 (mpp) REVERT: T 108 MET cc_start: 0.8723 (ptm) cc_final: 0.8272 (ppp) REVERT: U 108 MET cc_start: 0.8656 (ptm) cc_final: 0.8394 (ppp) REVERT: V 86 MET cc_start: 0.9333 (mtt) cc_final: 0.8736 (mpp) REVERT: V 108 MET cc_start: 0.9207 (ptp) cc_final: 0.8983 (ptm) REVERT: W 59 THR cc_start: 0.9433 (m) cc_final: 0.9165 (p) REVERT: W 86 MET cc_start: 0.9311 (mtt) cc_final: 0.8790 (mpp) REVERT: X 86 MET cc_start: 0.9332 (mtt) cc_final: 0.8838 (mpp) outliers start: 18 outliers final: 12 residues processed: 184 average time/residue: 0.3922 time to fit residues: 123.0704 Evaluate side-chains 183 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 170 time to evaluate : 3.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain G residue 98 ILE Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain M residue 8 ILE Chi-restraints excluded: chain M residue 79 VAL Chi-restraints excluded: chain N residue 98 ILE Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 108 MET Chi-restraints excluded: chain Q residue 52 MET Chi-restraints excluded: chain R residue 26 PHE Chi-restraints excluded: chain R residue 98 ILE Chi-restraints excluded: chain V residue 79 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 46 optimal weight: 7.9990 chunk 224 optimal weight: 6.9990 chunk 1 optimal weight: 8.9990 chunk 170 optimal weight: 5.9990 chunk 130 optimal weight: 10.0000 chunk 327 optimal weight: 10.0000 chunk 333 optimal weight: 9.9990 chunk 65 optimal weight: 40.0000 chunk 198 optimal weight: 20.0000 chunk 280 optimal weight: 6.9990 chunk 204 optimal weight: 5.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 HIS C 130 HIS N 130 HIS U 130 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.033804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2618 r_free = 0.2618 target = 0.027092 restraints weight = 215894.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2650 r_free = 0.2650 target = 0.028097 restraints weight = 138845.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.028859 restraints weight = 99725.121| |-----------------------------------------------------------------------------| r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9007 moved from start: 0.4050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.764 31999 Z= 0.172 Angle : 0.605 14.239 43354 Z= 0.281 Chirality : 0.033 0.113 4806 Planarity : 0.002 0.033 5596 Dihedral : 6.856 81.594 4204 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.60 % Allowed : 11.56 % Favored : 87.84 % 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: 4.49 (0.13), residues: 3724 helix: 3.79 (0.08), residues: 3065 sheet: None (None), residues: 0 loop : -1.59 (0.22), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP O 37 HIS 0.003 0.001 HIS B 34 PHE 0.019 0.001 PHE S 26 TYR 0.028 0.001 TYR T 71 ARG 0.005 0.000 ARG J 73 Details of bonding type rmsd hydrogen bonds : bond 0.06319 ( 2579) hydrogen bonds : angle 3.69250 ( 7737) covalent geometry : bond 0.00378 (31968) covalent geometry : angle 0.60450 (43354) Misc. bond : bond 0.17273 ( 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 191 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 171 time to evaluate : 3.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 MET cc_start: 0.9097 (mtm) cc_final: 0.8753 (mpp) REVERT: D 86 MET cc_start: 0.9410 (mtt) cc_final: 0.8839 (mpp) REVERT: D 108 MET cc_start: 0.8651 (ptm) cc_final: 0.8389 (ppp) REVERT: E 53 ARG cc_start: 0.8940 (mtt90) cc_final: 0.8516 (mtm-85) REVERT: E 108 MET cc_start: 0.8826 (ptm) cc_final: 0.8518 (ppp) REVERT: F 86 MET cc_start: 0.9384 (mtt) cc_final: 0.8864 (mpp) REVERT: G 108 MET cc_start: 0.8640 (ptm) cc_final: 0.8385 (ppp) REVERT: H 52 MET cc_start: 0.7678 (mtm) cc_final: 0.7303 (mtm) REVERT: H 108 MET cc_start: 0.8779 (ptm) cc_final: 0.8374 (ppp) REVERT: J 53 ARG cc_start: 0.8880 (mtt90) cc_final: 0.8554 (mtm-85) REVERT: J 86 MET cc_start: 0.9408 (mtt) cc_final: 0.8804 (mpp) REVERT: J 108 MET cc_start: 0.8733 (ptm) cc_final: 0.8407 (ppp) REVERT: K 59 THR cc_start: 0.9410 (m) cc_final: 0.9135 (p) REVERT: L 108 MET cc_start: 0.8871 (ptm) cc_final: 0.8477 (ppp) REVERT: M 53 ARG cc_start: 0.8856 (mtt90) cc_final: 0.8541 (mtm-85) REVERT: M 108 MET cc_start: 0.8757 (ptm) cc_final: 0.8487 (ppp) REVERT: O 59 THR cc_start: 0.9350 (m) cc_final: 0.9074 (p) REVERT: O 108 MET cc_start: 0.9356 (OUTLIER) cc_final: 0.9136 (ptm) REVERT: Q 108 MET cc_start: 0.8682 (ptm) cc_final: 0.8405 (ppp) REVERT: R 86 MET cc_start: 0.9368 (mtt) cc_final: 0.8852 (mpp) REVERT: R 108 MET cc_start: 0.8734 (ptm) cc_final: 0.8327 (ppp) REVERT: S 59 THR cc_start: 0.9422 (m) cc_final: 0.9151 (p) REVERT: S 86 MET cc_start: 0.9384 (mtt) cc_final: 0.8885 (mpp) REVERT: S 108 MET cc_start: 0.8772 (ptm) cc_final: 0.8533 (ppp) REVERT: T 86 MET cc_start: 0.9394 (mtt) cc_final: 0.8858 (mpp) REVERT: T 108 MET cc_start: 0.8749 (ptm) cc_final: 0.8309 (ppp) REVERT: U 108 MET cc_start: 0.8713 (ptm) cc_final: 0.8425 (ppp) REVERT: V 86 MET cc_start: 0.9356 (mtt) cc_final: 0.8757 (mpp) REVERT: V 108 MET cc_start: 0.9239 (ptp) cc_final: 0.9021 (ptm) REVERT: W 59 THR cc_start: 0.9461 (m) cc_final: 0.9202 (p) REVERT: X 86 MET cc_start: 0.9375 (mtt) cc_final: 0.8854 (mpp) outliers start: 20 outliers final: 18 residues processed: 176 average time/residue: 0.3767 time to fit residues: 114.4817 Evaluate side-chains 186 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 167 time to evaluate : 3.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain G residue 98 ILE Chi-restraints excluded: chain H residue 98 ILE Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain M residue 8 ILE Chi-restraints excluded: chain M residue 79 VAL Chi-restraints excluded: chain N residue 98 ILE Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 108 MET Chi-restraints excluded: chain P residue 98 ILE Chi-restraints excluded: chain Q residue 52 MET Chi-restraints excluded: chain R residue 26 PHE Chi-restraints excluded: chain R residue 98 ILE Chi-restraints excluded: chain S residue 98 ILE Chi-restraints excluded: chain V residue 79 VAL Chi-restraints excluded: chain W residue 98 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 88 optimal weight: 9.9990 chunk 172 optimal weight: 30.0000 chunk 96 optimal weight: 20.0000 chunk 82 optimal weight: 7.9990 chunk 327 optimal weight: 10.0000 chunk 182 optimal weight: 20.0000 chunk 245 optimal weight: 5.9990 chunk 163 optimal weight: 20.0000 chunk 81 optimal weight: 0.7980 chunk 303 optimal weight: 10.0000 chunk 237 optimal weight: 6.9990 overall best weight: 6.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 HIS B 130 HIS C 130 HIS H 130 HIS O 130 HIS P 130 HIS U 130 HIS X 130 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.033732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2620 r_free = 0.2620 target = 0.026929 restraints weight = 208702.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.027925 restraints weight = 135047.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.028676 restraints weight = 97163.322| |-----------------------------------------------------------------------------| r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9001 moved from start: 0.4105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.753 31999 Z= 0.164 Angle : 0.611 14.563 43354 Z= 0.282 Chirality : 0.032 0.117 4806 Planarity : 0.002 0.031 5596 Dihedral : 6.856 82.342 4204 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.72 % Allowed : 11.80 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.43 (0.13), residues: 3724 helix: 3.74 (0.08), residues: 3088 sheet: None (None), residues: 0 loop : -1.74 (0.23), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP O 37 HIS 0.002 0.001 HIS P 34 PHE 0.018 0.001 PHE S 26 TYR 0.027 0.001 TYR T 71 ARG 0.004 0.000 ARG J 73 Details of bonding type rmsd hydrogen bonds : bond 0.06217 ( 2579) hydrogen bonds : angle 3.65625 ( 7737) covalent geometry : bond 0.00361 (31968) covalent geometry : angle 0.61084 (43354) Misc. bond : bond 0.16892 ( 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 193 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 169 time to evaluate : 3.885 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 86 MET cc_start: 0.9117 (mtm) cc_final: 0.8758 (mpp) REVERT: D 108 MET cc_start: 0.8631 (ptm) cc_final: 0.8393 (ppp) REVERT: E 53 ARG cc_start: 0.8935 (mtt90) cc_final: 0.8502 (mtm-85) REVERT: E 108 MET cc_start: 0.8809 (ptm) cc_final: 0.8543 (ppp) REVERT: F 86 MET cc_start: 0.9360 (mtt) cc_final: 0.8842 (mpp) REVERT: G 108 MET cc_start: 0.8619 (ptm) cc_final: 0.8227 (ppp) REVERT: H 52 MET cc_start: 0.7685 (mtm) cc_final: 0.7316 (mtm) REVERT: H 108 MET cc_start: 0.8766 (ptm) cc_final: 0.8377 (ppp) REVERT: J 53 ARG cc_start: 0.8876 (mtt90) cc_final: 0.8550 (mtm-85) REVERT: J 108 MET cc_start: 0.8711 (ptm) cc_final: 0.8411 (ppp) REVERT: L 108 MET cc_start: 0.8856 (ptm) cc_final: 0.8484 (ppp) REVERT: M 53 ARG cc_start: 0.8863 (mtt90) cc_final: 0.8543 (mtm-85) REVERT: M 108 MET cc_start: 0.8755 (ptm) cc_final: 0.8513 (ppp) REVERT: O 59 THR cc_start: 0.9340 (m) cc_final: 0.9064 (p) REVERT: O 108 MET cc_start: 0.9362 (OUTLIER) cc_final: 0.9145 (ptm) REVERT: Q 108 MET cc_start: 0.8661 (ptm) cc_final: 0.8418 (ppp) REVERT: R 86 MET cc_start: 0.9363 (mtt) cc_final: 0.8850 (mpp) REVERT: R 108 MET cc_start: 0.8710 (ptm) cc_final: 0.8302 (ppp) REVERT: S 59 THR cc_start: 0.9414 (m) cc_final: 0.9146 (p) REVERT: S 86 MET cc_start: 0.9362 (mtt) cc_final: 0.8865 (mpp) REVERT: S 108 MET cc_start: 0.8749 (ptm) cc_final: 0.8541 (ppp) REVERT: T 86 MET cc_start: 0.9387 (mtt) cc_final: 0.8857 (mpp) REVERT: T 108 MET cc_start: 0.8743 (ptm) cc_final: 0.8337 (ppp) REVERT: U 108 MET cc_start: 0.8698 (ptm) cc_final: 0.8427 (ppp) REVERT: V 86 MET cc_start: 0.9358 (mtt) cc_final: 0.8758 (mpp) REVERT: V 108 MET cc_start: 0.9224 (ptp) cc_final: 0.9019 (ptm) REVERT: W 59 THR cc_start: 0.9444 (m) cc_final: 0.9184 (p) REVERT: X 86 MET cc_start: 0.9367 (mtt) cc_final: 0.8864 (mpp) outliers start: 24 outliers final: 22 residues processed: 174 average time/residue: 0.3677 time to fit residues: 110.3921 Evaluate side-chains 188 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 165 time to evaluate : 3.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain G residue 98 ILE Chi-restraints excluded: chain H residue 98 ILE Chi-restraints excluded: chain I residue 98 ILE Chi-restraints excluded: chain J residue 98 ILE Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain M residue 8 ILE Chi-restraints excluded: chain M residue 79 VAL Chi-restraints excluded: chain N residue 98 ILE Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 108 MET Chi-restraints excluded: chain P residue 98 ILE Chi-restraints excluded: chain Q residue 52 MET Chi-restraints excluded: chain R residue 26 PHE Chi-restraints excluded: chain R residue 98 ILE Chi-restraints excluded: chain S residue 98 ILE Chi-restraints excluded: chain U residue 98 ILE Chi-restraints excluded: chain V residue 79 VAL Chi-restraints excluded: chain W residue 98 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 33 optimal weight: 0.4980 chunk 279 optimal weight: 7.9990 chunk 307 optimal weight: 7.9990 chunk 354 optimal weight: 6.9990 chunk 220 optimal weight: 10.0000 chunk 181 optimal weight: 9.9990 chunk 130 optimal weight: 5.9990 chunk 20 optimal weight: 20.0000 chunk 107 optimal weight: 6.9990 chunk 342 optimal weight: 3.9990 chunk 232 optimal weight: 9.9990 overall best weight: 4.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 130 HIS N 130 HIS O 130 HIS P 130 HIS X 130 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.034554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.027893 restraints weight = 214101.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.028908 restraints weight = 137868.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.029672 restraints weight = 98793.198| |-----------------------------------------------------------------------------| r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8973 moved from start: 0.4207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.730 31999 Z= 0.142 Angle : 0.599 14.407 43354 Z= 0.273 Chirality : 0.032 0.139 4806 Planarity : 0.002 0.026 5596 Dihedral : 6.864 83.783 4204 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.51 % Allowed : 12.01 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.53 (0.13), residues: 3724 helix: 3.80 (0.08), residues: 3088 sheet: None (None), residues: 0 loop : -1.69 (0.23), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP W 37 HIS 0.003 0.001 HIS F 54 PHE 0.016 0.001 PHE S 26 TYR 0.024 0.001 TYR T 71 ARG 0.004 0.000 ARG J 73 Details of bonding type rmsd hydrogen bonds : bond 0.05720 ( 2579) hydrogen bonds : angle 3.54366 ( 7737) covalent geometry : bond 0.00314 (31968) covalent geometry : angle 0.59913 (43354) Misc. bond : bond 0.16449 ( 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 190 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 173 time to evaluate : 3.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 MET cc_start: 0.9050 (mtm) cc_final: 0.8732 (mpp) REVERT: D 108 MET cc_start: 0.8573 (ptm) cc_final: 0.8363 (ppp) REVERT: E 53 ARG cc_start: 0.8922 (mtt90) cc_final: 0.8531 (mtm-85) REVERT: E 108 MET cc_start: 0.8752 (ptm) cc_final: 0.8498 (ppp) REVERT: F 86 MET cc_start: 0.9324 (mtt) cc_final: 0.8816 (mpp) REVERT: H 52 MET cc_start: 0.7685 (mtm) cc_final: 0.7329 (mtm) REVERT: H 108 MET cc_start: 0.8696 (ptm) cc_final: 0.8331 (ppp) REVERT: J 53 ARG cc_start: 0.8885 (mtt90) cc_final: 0.8478 (mtm-85) REVERT: J 108 MET cc_start: 0.8658 (ptm) cc_final: 0.8415 (ppp) REVERT: L 108 MET cc_start: 0.8808 (ptm) cc_final: 0.8460 (ppp) REVERT: M 53 ARG cc_start: 0.8861 (mtt90) cc_final: 0.8522 (mtm-85) REVERT: N 86 MET cc_start: 0.9336 (mtm) cc_final: 0.8825 (mpp) REVERT: O 108 MET cc_start: 0.9344 (OUTLIER) cc_final: 0.9121 (ptm) REVERT: Q 108 MET cc_start: 0.8616 (ptm) cc_final: 0.8390 (ppp) REVERT: R 86 MET cc_start: 0.9339 (mtt) cc_final: 0.8841 (mpp) REVERT: R 108 MET cc_start: 0.8674 (ptm) cc_final: 0.8273 (ppp) REVERT: S 59 THR cc_start: 0.9398 (m) cc_final: 0.9111 (p) REVERT: S 86 MET cc_start: 0.9335 (mtt) cc_final: 0.8849 (mpp) REVERT: T 86 MET cc_start: 0.9343 (mtt) cc_final: 0.8837 (mpp) REVERT: T 108 MET cc_start: 0.8685 (ptm) cc_final: 0.8281 (ppp) REVERT: U 108 MET cc_start: 0.8626 (ptm) cc_final: 0.8409 (ppp) REVERT: V 86 MET cc_start: 0.9333 (mtt) cc_final: 0.8743 (mpp) REVERT: W 59 THR cc_start: 0.9422 (m) cc_final: 0.9154 (p) REVERT: W 86 MET cc_start: 0.9327 (mtt) cc_final: 0.8796 (mpp) REVERT: X 86 MET cc_start: 0.9328 (mtt) cc_final: 0.8821 (mpp) outliers start: 17 outliers final: 16 residues processed: 178 average time/residue: 0.3751 time to fit residues: 116.1685 Evaluate side-chains 179 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 162 time to evaluate : 3.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain G residue 98 ILE Chi-restraints excluded: chain H residue 98 ILE Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain M residue 8 ILE Chi-restraints excluded: chain M residue 79 VAL Chi-restraints excluded: chain N residue 98 ILE Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 108 MET Chi-restraints excluded: chain P residue 98 ILE Chi-restraints excluded: chain Q residue 52 MET Chi-restraints excluded: chain R residue 26 PHE Chi-restraints excluded: chain R residue 98 ILE Chi-restraints excluded: chain V residue 79 VAL Chi-restraints excluded: chain W residue 98 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 195 optimal weight: 10.0000 chunk 256 optimal weight: 5.9990 chunk 65 optimal weight: 50.0000 chunk 247 optimal weight: 8.9990 chunk 324 optimal weight: 6.9990 chunk 273 optimal weight: 10.0000 chunk 119 optimal weight: 6.9990 chunk 268 optimal weight: 6.9990 chunk 47 optimal weight: 6.9990 chunk 125 optimal weight: 50.0000 chunk 209 optimal weight: 5.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 HIS C 130 HIS D 130 HIS F 130 HIS U 130 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.033707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2623 r_free = 0.2623 target = 0.026917 restraints weight = 207194.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.027902 restraints weight = 134498.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.028650 restraints weight = 97049.215| |-----------------------------------------------------------------------------| r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9003 moved from start: 0.4193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.756 31999 Z= 0.169 Angle : 0.623 14.806 43354 Z= 0.287 Chirality : 0.033 0.128 4806 Planarity : 0.002 0.031 5596 Dihedral : 6.865 83.097 4204 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.60 % Allowed : 11.95 % Favored : 87.45 % 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: 4.39 (0.13), residues: 3724 helix: 3.71 (0.08), residues: 3088 sheet: None (None), residues: 0 loop : -1.76 (0.23), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP W 37 HIS 0.003 0.001 HIS D 34 PHE 0.017 0.001 PHE U 26 TYR 0.027 0.001 TYR T 71 ARG 0.003 0.000 ARG A 73 Details of bonding type rmsd hydrogen bonds : bond 0.06210 ( 2579) hydrogen bonds : angle 3.68074 ( 7737) covalent geometry : bond 0.00370 (31968) covalent geometry : angle 0.62257 (43354) Misc. bond : bond 0.16854 ( 31) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6560.93 seconds wall clock time: 117 minutes 25.32 seconds (7045.32 seconds total)