Starting phenix.real_space_refine on Thu Jan 15 23:34:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y6p_33645/01_2026/7y6p_33645_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y6p_33645/01_2026/7y6p_33645.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7y6p_33645/01_2026/7y6p_33645_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y6p_33645/01_2026/7y6p_33645_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7y6p_33645/01_2026/7y6p_33645.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y6p_33645/01_2026/7y6p_33645.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.009 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 60 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 98 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31428 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: 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: "K" 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: "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: 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: "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: 6.90, per 1000 atoms: 0.22 Number of scatterers: 31428 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 60 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=30, symmetry=0 Number of additional bonds: simple=30, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.04 Conformation dependent library (CDL) restraints added in 1.4 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 82.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 4 through 35 removed outlier: 3.504A pdb=" N LYS A 35 " --> pdb=" O LEU A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 65 removed outlier: 3.506A pdb=" N ALA A 41 " --> pdb=" O TRP A 37 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A 65 " --> pdb=" O ARG A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 110 Processing helix chain 'A' and resid 113 through 145 removed outlier: 3.986A 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 35 removed outlier: 3.516A pdb=" N LYS B 35 " --> pdb=" O LEU B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 65 removed outlier: 3.830A pdb=" N TYR B 43 " --> pdb=" O LYS B 39 " (cutoff:3.500A) removed outlier: 3.540A 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: 4.008A 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: 3.502A pdb=" N ALA C 41 " --> pdb=" O TRP C 37 " (cutoff:3.500A) removed outlier: 3.527A 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: 4.010A 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 35 removed outlier: 3.511A pdb=" N LYS D 35 " --> pdb=" O LEU D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 65 removed outlier: 3.710A pdb=" N TYR D 43 " --> pdb=" O LYS D 39 " (cutoff:3.500A) removed outlier: 3.544A 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 114 through 145 Processing helix chain 'D' and resid 145 through 151 Processing helix chain 'E' and resid 4 through 35 removed outlier: 3.505A pdb=" N LYS E 35 " --> pdb=" O LEU E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 65 removed outlier: 3.506A pdb=" N ALA E 41 " --> pdb=" O TRP E 37 " (cutoff:3.500A) removed outlier: 3.520A 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: 4.013A 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 35 removed outlier: 3.500A pdb=" N LYS F 35 " --> pdb=" O LEU F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 37 through 65 removed outlier: 3.670A pdb=" N TYR F 43 " --> pdb=" O LYS F 39 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU F 65 " --> pdb=" O ARG F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 110 Processing helix chain 'F' and resid 113 through 145 removed outlier: 3.986A 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: 3.504A pdb=" N ALA G 41 " --> pdb=" O TRP G 37 " (cutoff:3.500A) 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: 4.024A 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 removed outlier: 3.511A pdb=" N LYS H 35 " --> pdb=" O LEU H 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 65 removed outlier: 3.510A 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: 4.017A 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 removed outlier: 3.510A pdb=" N LYS I 35 " --> pdb=" O LEU I 31 " (cutoff:3.500A) Processing helix chain 'I' and resid 37 through 65 removed outlier: 3.506A pdb=" N ALA I 41 " --> pdb=" O TRP I 37 " (cutoff:3.500A) removed outlier: 3.525A 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: 4.034A 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: 3.536A pdb=" N GLY J 36 " --> pdb=" O GLN J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 37 through 65 removed outlier: 3.518A pdb=" N ALA J 41 " --> pdb=" O TRP J 37 " (cutoff:3.500A) removed outlier: 3.540A 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: 4.034A 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 removed outlier: 3.516A pdb=" N LYS K 35 " --> pdb=" O LEU K 31 " (cutoff:3.500A) Processing helix chain 'K' and resid 37 through 65 removed outlier: 3.816A 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: 3.996A 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 Processing helix chain 'L' and resid 37 through 65 removed outlier: 3.556A pdb=" N GLU L 56 " --> pdb=" O MET L 52 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU L 65 " --> pdb=" O ARG L 61 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 111 removed outlier: 3.570A pdb=" N LYS L 111 " --> pdb=" O VAL L 107 " (cutoff:3.500A) Processing helix chain 'L' and resid 113 through 145 removed outlier: 3.989A 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: 3.650A 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: 3.591A pdb=" N LYS M 111 " --> pdb=" O VAL M 107 " (cutoff:3.500A) Processing helix chain 'M' and resid 113 through 145 removed outlier: 3.881A pdb=" N ALA M 117 " --> pdb=" O ASP M 113 " (cutoff:3.500A) removed outlier: 3.827A 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 removed outlier: 3.507A pdb=" N LYS N 35 " --> pdb=" O LEU N 31 " (cutoff:3.500A) Processing helix chain 'N' and resid 37 through 65 removed outlier: 3.519A pdb=" N LEU N 65 " --> pdb=" O ARG N 61 " (cutoff:3.500A) Processing helix chain 'N' and resid 82 through 110 Processing helix chain 'N' and resid 113 through 145 removed outlier: 3.987A 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 removed outlier: 3.596A pdb=" N ILE O 8 " --> pdb=" O ASP O 4 " (cutoff:3.500A) Processing helix chain 'O' and resid 37 through 65 Processing helix chain 'O' and resid 82 through 110 Processing helix chain 'O' and resid 113 through 145 removed outlier: 3.975A 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: 3.827A pdb=" N TYR P 43 " --> pdb=" O LYS P 39 " (cutoff:3.500A) removed outlier: 3.554A 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: 4.011A 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: 3.514A pdb=" N ALA Q 41 " --> pdb=" O TRP Q 37 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU Q 65 " --> pdb=" O ARG Q 61 " (cutoff:3.500A) Processing helix chain 'Q' and resid 82 through 110 Processing helix chain 'Q' and resid 113 through 145 removed outlier: 4.046A 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 35 Processing helix chain 'R' and resid 37 through 65 removed outlier: 3.728A pdb=" N TYR R 43 " --> pdb=" O LYS R 39 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU R 65 " --> pdb=" O ARG R 61 " (cutoff:3.500A) Processing helix chain 'R' and resid 83 through 110 Processing helix chain 'R' and resid 113 through 145 removed outlier: 4.005A 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 35 removed outlier: 3.507A pdb=" N LYS S 35 " --> pdb=" O LEU S 31 " (cutoff:3.500A) Processing helix chain 'S' and resid 37 through 65 removed outlier: 3.693A pdb=" N TYR S 43 " --> pdb=" O LYS S 39 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU S 65 " --> pdb=" O ARG S 61 " (cutoff:3.500A) Processing helix chain 'S' and resid 83 through 110 Processing helix chain 'S' and resid 113 through 145 removed outlier: 3.980A 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 removed outlier: 3.503A pdb=" N LYS T 35 " --> pdb=" O LEU T 31 " (cutoff:3.500A) Processing helix chain 'T' and resid 37 through 65 removed outlier: 3.501A pdb=" N ALA T 41 " --> pdb=" O TRP T 37 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU T 65 " --> pdb=" O ARG T 61 " (cutoff:3.500A) Processing helix chain 'T' and resid 83 through 110 Processing helix chain 'T' and resid 113 through 145 removed outlier: 4.011A 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: 3.557A pdb=" N LYS U 35 " --> pdb=" O LEU U 31 " (cutoff:3.500A) Processing helix chain 'U' and resid 37 through 65 removed outlier: 3.826A pdb=" N TYR U 43 " --> pdb=" O LYS U 39 " (cutoff:3.500A) removed outlier: 3.556A 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: 4.018A 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: 3.644A 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 removed outlier: 3.601A pdb=" N LYS V 111 " --> pdb=" O VAL V 107 " (cutoff:3.500A) Processing helix chain 'V' and resid 113 through 145 removed outlier: 3.903A pdb=" N ALA V 117 " --> pdb=" O ASP V 113 " (cutoff:3.500A) removed outlier: 3.811A 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: 3.545A pdb=" N GLY W 36 " --> pdb=" O GLN W 32 " (cutoff:3.500A) Processing helix chain 'W' and resid 37 through 65 removed outlier: 3.613A pdb=" N ALA W 41 " --> pdb=" O TRP W 37 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS W 42 " --> pdb=" O THR W 38 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N TYR W 43 " --> pdb=" O LYS W 39 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU W 65 " --> pdb=" O ARG W 61 " (cutoff:3.500A) Processing helix chain 'W' and resid 83 through 110 Processing helix chain 'W' and resid 113 through 145 removed outlier: 3.989A 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 removed outlier: 3.512A pdb=" N LYS X 35 " --> pdb=" O LEU X 31 " (cutoff:3.500A) Processing helix chain 'X' and resid 37 through 65 removed outlier: 3.712A pdb=" N TYR X 43 " --> pdb=" O LYS X 39 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU X 65 " --> pdb=" O ARG X 61 " (cutoff:3.500A) Processing helix chain 'X' and resid 83 through 110 Processing helix chain 'X' and resid 113 through 145 removed outlier: 4.003A pdb=" N ALA X 117 " --> pdb=" O ASP X 113 " (cutoff:3.500A) Processing helix chain 'X' and resid 145 through 151 2551 hydrogen bonds defined for protein. 7653 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: 5.62 Time building geometry restraints manager: 4.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.40: 13355 1.40 - 1.58: 18373 1.58 - 1.76: 1 1.76 - 1.94: 191 1.94 - 2.12: 48 Bond restraints: 31968 Sorted by residual: bond pdb=" CB MET N 52 " pdb=" CG MET N 52 " ideal model delta sigma weight residual 1.520 1.466 0.054 3.00e-02 1.11e+03 3.22e+00 bond pdb=" CG MET F 52 " pdb=" SD MET F 52 " ideal model delta sigma weight residual 1.803 1.763 0.040 2.50e-02 1.60e+03 2.51e+00 bond pdb=" CGA HEM C 203 " pdb=" O2A HEM C 203 " ideal model delta sigma weight residual 1.258 1.289 -0.031 2.00e-02 2.50e+03 2.39e+00 bond pdb=" CB MET C 52 " pdb=" CG MET C 52 " ideal model delta sigma weight residual 1.520 1.476 0.044 3.00e-02 1.11e+03 2.15e+00 bond pdb=" NA HEM F 203 " pdb="FE HEM F 203 " ideal model delta sigma weight residual 2.080 1.990 0.090 7.00e-02 2.04e+02 1.66e+00 ... (remaining 31963 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.16: 43306 5.16 - 10.33: 36 10.33 - 15.49: 7 15.49 - 20.66: 3 20.66 - 25.82: 2 Bond angle restraints: 43354 Sorted by residual: angle pdb=" CB MET X 52 " pdb=" CG MET X 52 " pdb=" SD MET X 52 " ideal model delta sigma weight residual 112.70 86.88 25.82 3.00e+00 1.11e-01 7.41e+01 angle pdb=" CA MET F 52 " pdb=" CB MET F 52 " pdb=" CG MET F 52 " ideal model delta sigma weight residual 114.10 127.35 -13.25 2.00e+00 2.50e-01 4.39e+01 angle pdb=" CB MET Q 52 " pdb=" CG MET Q 52 " pdb=" SD MET Q 52 " ideal model delta sigma weight residual 112.70 93.53 19.17 3.00e+00 1.11e-01 4.08e+01 angle pdb=" CB MET C 52 " pdb=" CG MET C 52 " pdb=" SD MET C 52 " ideal model delta sigma weight residual 112.70 94.86 17.84 3.00e+00 1.11e-01 3.54e+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 97.53 15.17 3.00e+00 1.11e-01 2.56e+01 ... (remaining 43349 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 16841 17.87 - 35.75: 1820 35.75 - 53.62: 326 53.62 - 71.49: 101 71.49 - 89.37: 30 Dihedral angle restraints: 19118 sinusoidal: 7994 harmonic: 11124 Sorted by residual: dihedral pdb=" CA GLU F 51 " pdb=" C GLU F 51 " pdb=" N MET F 52 " pdb=" CA MET F 52 " ideal model delta harmonic sigma weight residual 180.00 156.95 23.05 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" C2D HEM F 203 " pdb=" C3D HEM F 203 " pdb=" CAD HEM F 203 " pdb=" CBD HEM F 203 " ideal model delta sinusoidal sigma weight residual 180.00 91.69 88.31 2 2.00e+01 2.50e-03 1.20e+01 dihedral pdb=" C1A HEM F 203 " pdb=" C2A HEM F 203 " pdb=" CAA HEM F 203 " pdb=" CBA HEM F 203 " ideal model delta sinusoidal sigma weight residual 180.00 96.11 83.89 2 2.00e+01 2.50e-03 1.19e+01 ... (remaining 19115 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 4443 0.060 - 0.120: 337 0.120 - 0.181: 25 0.181 - 0.241: 0 0.241 - 0.301: 1 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 2.21 0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" CG LEU P 19 " pdb=" CB LEU P 19 " pdb=" CD1 LEU P 19 " pdb=" CD2 LEU P 19 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.91e-01 chirality pdb=" CA PHE M 120 " pdb=" N PHE M 120 " pdb=" C PHE M 120 " pdb=" CB PHE M 120 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.36e-01 ... (remaining 4803 not shown) Planarity restraints: 5596 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1A HEM F 203 " 0.003 2.00e-02 2.50e+03 2.04e-02 9.35e+00 pdb=" C2A HEM F 203 " 0.002 2.00e-02 2.50e+03 pdb=" C3A HEM F 203 " 0.003 2.00e-02 2.50e+03 pdb=" C4A HEM F 203 " -0.051 2.00e-02 2.50e+03 pdb=" CAA HEM F 203 " -0.004 2.00e-02 2.50e+03 pdb=" CHA HEM F 203 " 0.012 2.00e-02 2.50e+03 pdb=" CHB HEM F 203 " 0.029 2.00e-02 2.50e+03 pdb=" CMA HEM F 203 " 0.007 2.00e-02 2.50e+03 pdb=" NA HEM F 203 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR T 71 " 0.015 2.00e-02 2.50e+03 2.00e-02 8.00e+00 pdb=" CG TYR T 71 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 TYR T 71 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR T 71 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR T 71 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR T 71 " 0.012 2.00e-02 2.50e+03 pdb=" CZ TYR T 71 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR T 71 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE V 120 " 0.024 2.00e-02 2.50e+03 2.10e-02 7.70e+00 pdb=" CG PHE V 120 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 PHE V 120 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE V 120 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE V 120 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE V 120 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE V 120 " 0.004 2.00e-02 2.50e+03 ... (remaining 5593 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 89 2.49 - 3.10: 21796 3.10 - 3.70: 43728 3.70 - 4.30: 66828 4.30 - 4.90: 114740 Nonbonded interactions: 247181 Sorted by model distance: nonbonded pdb=" OE2 GLU H 94 " pdb="FE FE H 202 " model vdw 1.892 2.260 nonbonded pdb=" OE1 GLU M 94 " pdb="FE FE M 202 " model vdw 1.953 2.260 nonbonded pdb=" OE2 GLU M 94 " pdb="FE FE M 202 " model vdw 2.025 2.260 nonbonded pdb=" OE1 GLU R 127 " pdb="FE FE R 202 " model vdw 2.054 2.260 nonbonded pdb=" OE2 GLU J 51 " pdb="FE FE J 202 " model vdw 2.056 2.260 ... (remaining 247176 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 156) selection = (chain 'B' and resid 1 through 156) selection = (chain 'C' and resid 1 through 156) selection = (chain 'D' and resid 1 through 156) selection = (chain 'E' and resid 1 through 156) selection = (chain 'F' and resid 1 through 156) selection = (chain 'G' and resid 1 through 156) selection = (chain 'H' and resid 1 through 156) selection = (chain 'I' and resid 1 through 156) selection = (chain 'J' and resid 1 through 156) selection = (chain 'K' and resid 1 through 156) selection = (chain 'L' and resid 1 through 156) selection = (chain 'M' and resid 1 through 156) selection = (chain 'N' and resid 1 through 156) selection = (chain 'O' and resid 1 through 156) selection = (chain 'P' and resid 1 through 156) selection = (chain 'Q' and resid 1 through 156) selection = (chain 'R' and resid 1 through 156) selection = (chain 'S' and resid 1 through 156) selection = (chain 'T' and resid 1 through 156) selection = (chain 'U' and resid 1 through 156) selection = (chain 'V' and resid 1 through 156) selection = (chain 'W' and resid 1 through 156) selection = (chain 'X' and resid 1 through 156) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.820 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: 0.050 Extract box with map and model: 0.500 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 28.490 Find NCS groups from input model: 0.980 Set up NCS constraints: 0.050 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: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 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 0.965 31998 Z= 0.618 Angle : 0.657 25.824 43354 Z= 0.323 Chirality : 0.036 0.301 4806 Planarity : 0.003 0.063 5596 Dihedral : 15.544 89.366 11862 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.00 % Allowed : 0.03 % Favored : 99.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.78 (0.13), residues: 3724 helix: 3.44 (0.08), residues: 2994 sheet: None (None), residues: 0 loop : -1.98 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 53 TYR 0.044 0.001 TYR T 71 PHE 0.048 0.003 PHE V 120 TRP 0.006 0.001 TRP H 37 HIS 0.004 0.001 HIS Q 129 Details of bonding type rmsd covalent geometry : bond 0.00520 (31968) covalent geometry : angle 0.65664 (43354) hydrogen bonds : bond 0.14135 ( 2551) hydrogen bonds : angle 4.61119 ( 7653) Misc. bond : bond 0.23895 ( 30) *********************** 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 309 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 309 time to evaluate : 1.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 1 MET cc_start: 0.7085 (mtm) cc_final: 0.6558 (mtm) outliers start: 0 outliers final: 0 residues processed: 309 average time/residue: 0.2146 time to fit residues: 104.9939 Evaluate side-chains 263 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 263 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.7980 chunk 298 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 2 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.143137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.133575 restraints weight = 28741.491| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 0.64 r_work: 0.3262 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.479 31998 Z= 0.136 Angle : 0.530 16.894 43354 Z= 0.239 Chirality : 0.032 0.120 4806 Planarity : 0.003 0.067 5596 Dihedral : 7.042 88.009 4204 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Rotamer: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.66 (0.13), residues: 3724 helix: 4.12 (0.08), residues: 3014 sheet: None (None), residues: 0 loop : -2.19 (0.21), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 45 TYR 0.019 0.001 TYR T 71 PHE 0.024 0.002 PHE N 26 TRP 0.010 0.001 TRP P 37 HIS 0.002 0.000 HIS L 112 Details of bonding type rmsd covalent geometry : bond 0.00263 (31968) covalent geometry : angle 0.52985 (43354) hydrogen bonds : bond 0.06704 ( 2551) hydrogen bonds : angle 3.24205 ( 7653) Misc. bond : bond 0.14362 ( 30) *********************** 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 376 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 376 time to evaluate : 1.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASP cc_start: 0.8491 (t0) cc_final: 0.8244 (t70) REVERT: E 99 ASP cc_start: 0.8486 (t0) cc_final: 0.8278 (t70) REVERT: F 50 ASP cc_start: 0.8454 (m-30) cc_final: 0.8211 (m-30) REVERT: F 53 ARG cc_start: 0.7855 (mtt90) cc_final: 0.6911 (mtm110) REVERT: F 99 ASP cc_start: 0.8466 (t0) cc_final: 0.8237 (t70) REVERT: G 99 ASP cc_start: 0.8437 (t0) cc_final: 0.8228 (t70) REVERT: H 99 ASP cc_start: 0.8424 (t0) cc_final: 0.8208 (t70) REVERT: L 99 ASP cc_start: 0.8386 (t0) cc_final: 0.8176 (t70) REVERT: M 66 ASP cc_start: 0.7833 (t70) cc_final: 0.7587 (t0) REVERT: M 99 ASP cc_start: 0.8458 (t0) cc_final: 0.8210 (t70) REVERT: N 99 ASP cc_start: 0.8401 (t0) cc_final: 0.8151 (t70) REVERT: O 99 ASP cc_start: 0.8464 (t0) cc_final: 0.8261 (t70) REVERT: P 99 ASP cc_start: 0.8459 (t0) cc_final: 0.8247 (t70) REVERT: R 99 ASP cc_start: 0.8452 (t0) cc_final: 0.8238 (t70) REVERT: S 99 ASP cc_start: 0.8477 (t0) cc_final: 0.8252 (t70) REVERT: V 66 ASP cc_start: 0.7823 (t70) cc_final: 0.7511 (t0) REVERT: V 99 ASP cc_start: 0.8296 (t0) cc_final: 0.8089 (t70) outliers start: 0 outliers final: 0 residues processed: 376 average time/residue: 0.2189 time to fit residues: 130.0865 Evaluate side-chains 356 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 356 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 162 optimal weight: 1.9990 chunk 11 optimal weight: 10.0000 chunk 266 optimal weight: 9.9990 chunk 93 optimal weight: 6.9990 chunk 34 optimal weight: 6.9990 chunk 278 optimal weight: 5.9990 chunk 242 optimal weight: 10.0000 chunk 80 optimal weight: 3.9990 chunk 62 optimal weight: 9.9990 chunk 164 optimal weight: 0.8980 chunk 136 optimal weight: 7.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 156 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.118794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.109686 restraints weight = 28938.198| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 0.58 r_work: 0.2929 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.0872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.447 31998 Z= 0.221 Angle : 0.613 20.669 43354 Z= 0.276 Chirality : 0.034 0.157 4806 Planarity : 0.003 0.072 5596 Dihedral : 7.001 88.097 4204 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 0.75 % Allowed : 3.59 % Favored : 95.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.23 (0.13), residues: 3724 helix: 3.78 (0.08), residues: 3037 sheet: None (None), residues: 0 loop : -2.31 (0.21), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 45 TYR 0.043 0.001 TYR T 71 PHE 0.024 0.002 PHE W 120 TRP 0.004 0.001 TRP S 37 HIS 0.005 0.001 HIS H 54 Details of bonding type rmsd covalent geometry : bond 0.00487 (31968) covalent geometry : angle 0.61321 (43354) hydrogen bonds : bond 0.11715 ( 2551) hydrogen bonds : angle 3.74259 ( 7653) Misc. bond : bond 0.12345 ( 30) *********************** 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 406 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 381 time to evaluate : 1.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 99 ASP cc_start: 0.8582 (t0) cc_final: 0.8359 (t70) REVERT: M 66 ASP cc_start: 0.8547 (t70) cc_final: 0.8239 (t0) REVERT: Q 1 MET cc_start: 0.7434 (ptt) cc_final: 0.7184 (ptt) REVERT: V 66 ASP cc_start: 0.8477 (t70) cc_final: 0.8124 (t0) REVERT: V 99 ASP cc_start: 0.8488 (t0) cc_final: 0.8278 (t70) outliers start: 25 outliers final: 24 residues processed: 405 average time/residue: 0.2089 time to fit residues: 135.2833 Evaluate side-chains 378 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 354 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain J residue 79 VAL Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain O residue 57 VAL Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain Q residue 79 VAL Chi-restraints excluded: chain Q residue 83 VAL Chi-restraints excluded: chain R residue 79 VAL Chi-restraints excluded: chain S residue 79 VAL Chi-restraints excluded: chain T residue 79 VAL Chi-restraints excluded: chain U residue 79 VAL Chi-restraints excluded: chain V residue 79 VAL Chi-restraints excluded: chain W residue 79 VAL Chi-restraints excluded: chain X residue 79 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 55 optimal weight: 6.9990 chunk 325 optimal weight: 3.9990 chunk 157 optimal weight: 3.9990 chunk 175 optimal weight: 9.9990 chunk 21 optimal weight: 6.9990 chunk 264 optimal weight: 9.9990 chunk 278 optimal weight: 5.9990 chunk 188 optimal weight: 3.9990 chunk 272 optimal weight: 0.9980 chunk 336 optimal weight: 0.0060 chunk 39 optimal weight: 1.9990 overall best weight: 2.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.125927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.117098 restraints weight = 28544.130| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 0.56 r_work: 0.3125 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.431 31998 Z= 0.169 Angle : 0.538 19.015 43354 Z= 0.245 Chirality : 0.032 0.145 4806 Planarity : 0.003 0.059 5596 Dihedral : 6.943 88.233 4204 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 0.15 % Allowed : 6.25 % Favored : 93.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.44 (0.13), residues: 3724 helix: 3.99 (0.08), residues: 3014 sheet: None (None), residues: 0 loop : -2.36 (0.20), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 45 TYR 0.048 0.001 TYR T 71 PHE 0.017 0.001 PHE N 26 TRP 0.003 0.001 TRP G 37 HIS 0.003 0.000 HIS H 54 Details of bonding type rmsd covalent geometry : bond 0.00338 (31968) covalent geometry : angle 0.53774 (43354) hydrogen bonds : bond 0.09447 ( 2551) hydrogen bonds : angle 3.44675 ( 7653) Misc. bond : bond 0.12531 ( 30) *********************** 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 379 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 374 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 52 MET cc_start: 0.6915 (mtt) cc_final: 0.6581 (mtt) REVERT: D 99 ASP cc_start: 0.8531 (t0) cc_final: 0.8306 (t70) REVERT: M 66 ASP cc_start: 0.8454 (t70) cc_final: 0.8165 (t0) REVERT: N 52 MET cc_start: 0.7208 (OUTLIER) cc_final: 0.6856 (mtt) REVERT: N 99 ASP cc_start: 0.8581 (t0) cc_final: 0.8355 (t70) REVERT: O 66 ASP cc_start: 0.8205 (t0) cc_final: 0.8005 (t0) REVERT: T 71 TYR cc_start: 0.8213 (m-80) cc_final: 0.7456 (m-80) REVERT: T 73 ARG cc_start: 0.8717 (mtm-85) cc_final: 0.8455 (mtm180) REVERT: T 99 ASP cc_start: 0.8653 (t0) cc_final: 0.8427 (t70) REVERT: V 66 ASP cc_start: 0.8388 (t70) cc_final: 0.8007 (t0) REVERT: W 99 ASP cc_start: 0.8613 (t0) cc_final: 0.8400 (t70) outliers start: 5 outliers final: 4 residues processed: 377 average time/residue: 0.2131 time to fit residues: 127.3235 Evaluate side-chains 363 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 358 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain N residue 52 MET Chi-restraints excluded: chain O residue 57 VAL Chi-restraints excluded: chain R residue 26 PHE Chi-restraints excluded: chain W residue 79 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 251 optimal weight: 6.9990 chunk 243 optimal weight: 9.9990 chunk 233 optimal weight: 9.9990 chunk 143 optimal weight: 3.9990 chunk 357 optimal weight: 2.9990 chunk 190 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 197 optimal weight: 0.9980 chunk 61 optimal weight: 10.0000 chunk 36 optimal weight: 6.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 156 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.118836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.109836 restraints weight = 28704.325| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 0.57 r_work: 0.2944 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.1045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.435 31998 Z= 0.207 Angle : 0.583 20.695 43354 Z= 0.266 Chirality : 0.034 0.138 4806 Planarity : 0.003 0.068 5596 Dihedral : 6.985 89.609 4204 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 0.54 % Allowed : 6.85 % Favored : 92.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.16 (0.13), residues: 3724 helix: 3.74 (0.08), residues: 3037 sheet: None (None), residues: 0 loop : -2.38 (0.21), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 45 TYR 0.038 0.001 TYR T 71 PHE 0.015 0.002 PHE N 120 TRP 0.003 0.001 TRP H 37 HIS 0.005 0.001 HIS H 54 Details of bonding type rmsd covalent geometry : bond 0.00447 (31968) covalent geometry : angle 0.58335 (43354) hydrogen bonds : bond 0.11263 ( 2551) hydrogen bonds : angle 3.64715 ( 7653) Misc. bond : bond 0.11935 ( 30) *********************** 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 374 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 356 time to evaluate : 1.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 52 MET cc_start: 0.6829 (mtt) cc_final: 0.6617 (mtt) REVERT: I 99 ASP cc_start: 0.8557 (t0) cc_final: 0.8331 (t70) REVERT: M 66 ASP cc_start: 0.8568 (t70) cc_final: 0.8248 (t0) REVERT: N 52 MET cc_start: 0.7132 (OUTLIER) cc_final: 0.6811 (mtt) REVERT: V 66 ASP cc_start: 0.8506 (t70) cc_final: 0.8115 (t0) outliers start: 18 outliers final: 17 residues processed: 371 average time/residue: 0.2021 time to fit residues: 120.3557 Evaluate side-chains 353 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 335 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain J residue 79 VAL Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain N residue 52 MET Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain O residue 57 VAL Chi-restraints excluded: chain Q residue 83 VAL Chi-restraints excluded: chain R residue 26 PHE Chi-restraints excluded: chain R residue 79 VAL Chi-restraints excluded: chain S residue 79 VAL Chi-restraints excluded: chain T residue 79 VAL Chi-restraints excluded: chain V residue 79 VAL Chi-restraints excluded: chain W residue 79 VAL Chi-restraints excluded: chain X residue 79 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 290 optimal weight: 5.9990 chunk 129 optimal weight: 2.9990 chunk 142 optimal weight: 9.9990 chunk 308 optimal weight: 9.9990 chunk 344 optimal weight: 3.9990 chunk 317 optimal weight: 9.9990 chunk 209 optimal weight: 1.9990 chunk 238 optimal weight: 5.9990 chunk 253 optimal weight: 0.9990 chunk 166 optimal weight: 4.9990 chunk 40 optimal weight: 10.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.121188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.111428 restraints weight = 28398.349| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 0.63 r_work: 0.2966 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.1174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.415 31998 Z= 0.190 Angle : 0.558 20.561 43354 Z= 0.255 Chirality : 0.033 0.143 4806 Planarity : 0.003 0.064 5596 Dihedral : 6.972 86.342 4204 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 0.84 % Allowed : 7.03 % Favored : 92.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.23 (0.13), residues: 3724 helix: 3.85 (0.08), residues: 3014 sheet: None (None), residues: 0 loop : -2.50 (0.20), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 45 TYR 0.056 0.001 TYR T 71 PHE 0.015 0.001 PHE N 26 TRP 0.002 0.001 TRP U 37 HIS 0.004 0.000 HIS H 54 Details of bonding type rmsd covalent geometry : bond 0.00398 (31968) covalent geometry : angle 0.55777 (43354) hydrogen bonds : bond 0.10552 ( 2551) hydrogen bonds : angle 3.56203 ( 7653) Misc. bond : bond 0.12848 ( 30) *********************** 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 380 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 352 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 99 ASP cc_start: 0.8503 (t0) cc_final: 0.8269 (t70) REVERT: E 99 ASP cc_start: 0.8528 (t0) cc_final: 0.8306 (t70) REVERT: G 99 ASP cc_start: 0.8548 (t0) cc_final: 0.8327 (t70) REVERT: J 99 ASP cc_start: 0.8567 (t0) cc_final: 0.8347 (t70) REVERT: M 66 ASP cc_start: 0.8570 (t70) cc_final: 0.8244 (t0) REVERT: N 52 MET cc_start: 0.7108 (OUTLIER) cc_final: 0.6844 (mtt) REVERT: T 99 ASP cc_start: 0.8614 (t0) cc_final: 0.8396 (t70) REVERT: V 66 ASP cc_start: 0.8510 (t70) cc_final: 0.8117 (t0) outliers start: 28 outliers final: 26 residues processed: 376 average time/residue: 0.2132 time to fit residues: 127.5629 Evaluate side-chains 350 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 323 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain N residue 52 MET Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain O residue 57 VAL Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain P residue 83 VAL Chi-restraints excluded: chain Q residue 79 VAL Chi-restraints excluded: chain Q residue 83 VAL Chi-restraints excluded: chain R residue 26 PHE Chi-restraints excluded: chain R residue 79 VAL Chi-restraints excluded: chain S residue 79 VAL Chi-restraints excluded: chain T residue 79 VAL Chi-restraints excluded: chain U residue 79 VAL Chi-restraints excluded: chain V residue 79 VAL Chi-restraints excluded: chain W residue 79 VAL Chi-restraints excluded: chain X residue 79 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 237 optimal weight: 1.9990 chunk 167 optimal weight: 10.0000 chunk 105 optimal weight: 4.9990 chunk 86 optimal weight: 10.0000 chunk 173 optimal weight: 8.9990 chunk 202 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 132 optimal weight: 0.9990 chunk 168 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 chunk 63 optimal weight: 8.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.118301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.109272 restraints weight = 28764.097| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 0.57 r_work: 0.2954 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.1103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.420 31998 Z= 0.207 Angle : 0.592 22.178 43354 Z= 0.267 Chirality : 0.034 0.140 4806 Planarity : 0.003 0.071 5596 Dihedral : 6.999 87.189 4204 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.00 % Allowed : 7.27 % Favored : 91.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.09 (0.13), residues: 3724 helix: 3.74 (0.08), residues: 3019 sheet: None (None), residues: 0 loop : -2.56 (0.20), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 45 TYR 0.050 0.001 TYR T 71 PHE 0.014 0.001 PHE S 26 TRP 0.003 0.001 TRP U 37 HIS 0.005 0.001 HIS H 54 Details of bonding type rmsd covalent geometry : bond 0.00449 (31968) covalent geometry : angle 0.59164 (43354) hydrogen bonds : bond 0.11322 ( 2551) hydrogen bonds : angle 3.65382 ( 7653) Misc. bond : bond 0.12856 ( 30) *********************** 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 357 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 324 time to evaluate : 1.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASP cc_start: 0.8584 (t0) cc_final: 0.8360 (t70) REVERT: B 99 ASP cc_start: 0.8551 (t0) cc_final: 0.8335 (t70) REVERT: H 99 ASP cc_start: 0.8519 (t0) cc_final: 0.8309 (t70) REVERT: I 99 ASP cc_start: 0.8585 (t0) cc_final: 0.8363 (t70) REVERT: M 66 ASP cc_start: 0.8602 (t70) cc_final: 0.8395 (t0) REVERT: N 52 MET cc_start: 0.7155 (OUTLIER) cc_final: 0.6883 (mtt) REVERT: T 71 TYR cc_start: 0.8252 (m-80) cc_final: 0.7502 (m-80) REVERT: V 66 ASP cc_start: 0.8555 (t70) cc_final: 0.8179 (t0) REVERT: W 99 ASP cc_start: 0.8619 (t0) cc_final: 0.8406 (t70) outliers start: 33 outliers final: 31 residues processed: 353 average time/residue: 0.2058 time to fit residues: 116.0960 Evaluate side-chains 345 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 313 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain J residue 79 VAL Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain N residue 52 MET Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain O residue 57 VAL Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain P residue 83 VAL Chi-restraints excluded: chain Q residue 79 VAL Chi-restraints excluded: chain Q residue 83 VAL Chi-restraints excluded: chain R residue 26 PHE Chi-restraints excluded: chain R residue 79 VAL Chi-restraints excluded: chain S residue 79 VAL Chi-restraints excluded: chain T residue 79 VAL Chi-restraints excluded: chain U residue 79 VAL Chi-restraints excluded: chain V residue 79 VAL Chi-restraints excluded: chain W residue 79 VAL Chi-restraints excluded: chain X residue 79 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 173 optimal weight: 0.9990 chunk 149 optimal weight: 3.9990 chunk 245 optimal weight: 1.9990 chunk 330 optimal weight: 10.0000 chunk 94 optimal weight: 0.9990 chunk 169 optimal weight: 8.9990 chunk 302 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 318 optimal weight: 6.9990 chunk 214 optimal weight: 0.9990 chunk 306 optimal weight: 0.0770 overall best weight: 0.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 2 GLN X 156 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.144156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.134537 restraints weight = 28468.348| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 0.65 r_work: 0.3277 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.367 31998 Z= 0.130 Angle : 0.508 17.655 43354 Z= 0.224 Chirality : 0.031 0.144 4806 Planarity : 0.002 0.057 5596 Dihedral : 6.944 87.153 4204 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Rotamer: Outliers : 0.42 % Allowed : 7.94 % Favored : 91.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.68 (0.13), residues: 3724 helix: 4.17 (0.08), residues: 3014 sheet: None (None), residues: 0 loop : -2.37 (0.21), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 45 TYR 0.032 0.001 TYR T 71 PHE 0.018 0.001 PHE N 26 TRP 0.007 0.001 TRP M 37 HIS 0.002 0.000 HIS H 54 Details of bonding type rmsd covalent geometry : bond 0.00252 (31968) covalent geometry : angle 0.50784 (43354) hydrogen bonds : bond 0.06358 ( 2551) hydrogen bonds : angle 3.07886 ( 7653) Misc. bond : bond 0.13353 ( 30) *********************** 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 380 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 366 time to evaluate : 1.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 99 ASP cc_start: 0.8440 (t0) cc_final: 0.8167 (t70) REVERT: D 99 ASP cc_start: 0.8417 (t0) cc_final: 0.8171 (t70) REVERT: E 99 ASP cc_start: 0.8475 (t0) cc_final: 0.8207 (t70) REVERT: E 132 ASP cc_start: 0.8974 (t70) cc_final: 0.8750 (t0) REVERT: F 53 ARG cc_start: 0.7537 (mtt90) cc_final: 0.6661 (mtm110) REVERT: G 99 ASP cc_start: 0.8492 (t0) cc_final: 0.8236 (t70) REVERT: H 99 ASP cc_start: 0.8390 (t0) cc_final: 0.8129 (t70) REVERT: I 99 ASP cc_start: 0.8497 (t0) cc_final: 0.8239 (t70) REVERT: J 99 ASP cc_start: 0.8495 (t0) cc_final: 0.8226 (t70) REVERT: N 52 MET cc_start: 0.6945 (OUTLIER) cc_final: 0.6721 (mtt) REVERT: P 132 ASP cc_start: 0.8954 (t70) cc_final: 0.8749 (t0) REVERT: Q 99 ASP cc_start: 0.8448 (t0) cc_final: 0.8203 (t70) REVERT: S 53 ARG cc_start: 0.7890 (mtt180) cc_final: 0.7009 (mtm110) REVERT: T 71 TYR cc_start: 0.7983 (m-80) cc_final: 0.7282 (m-80) REVERT: T 99 ASP cc_start: 0.8583 (t0) cc_final: 0.8327 (t70) REVERT: V 66 ASP cc_start: 0.7988 (t70) cc_final: 0.7752 (t0) REVERT: W 99 ASP cc_start: 0.8490 (t0) cc_final: 0.8256 (t70) REVERT: X 1 MET cc_start: 0.7526 (mtm) cc_final: 0.7319 (mtm) REVERT: X 132 ASP cc_start: 0.8996 (t70) cc_final: 0.8795 (t0) outliers start: 14 outliers final: 11 residues processed: 377 average time/residue: 0.2202 time to fit residues: 130.2531 Evaluate side-chains 367 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 355 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain N residue 52 MET Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain Q residue 79 VAL Chi-restraints excluded: chain R residue 26 PHE Chi-restraints excluded: chain R residue 79 VAL Chi-restraints excluded: chain T residue 79 VAL Chi-restraints excluded: chain U residue 79 VAL Chi-restraints excluded: chain V residue 79 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 100 optimal weight: 4.9990 chunk 346 optimal weight: 5.9990 chunk 232 optimal weight: 6.9990 chunk 172 optimal weight: 0.2980 chunk 354 optimal weight: 8.9990 chunk 120 optimal weight: 10.0000 chunk 334 optimal weight: 5.9990 chunk 163 optimal weight: 0.9980 chunk 159 optimal weight: 1.9990 chunk 318 optimal weight: 3.9990 chunk 201 optimal weight: 0.6980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.136101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.126330 restraints weight = 28550.690| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 0.65 r_work: 0.3168 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.363 31998 Z= 0.145 Angle : 0.522 21.910 43354 Z= 0.229 Chirality : 0.032 0.148 4806 Planarity : 0.002 0.053 5596 Dihedral : 6.807 85.718 4204 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 0.54 % Allowed : 8.51 % Favored : 90.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.69 (0.13), residues: 3724 helix: 4.18 (0.08), residues: 3014 sheet: None (None), residues: 0 loop : -2.36 (0.21), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 45 TYR 0.033 0.001 TYR T 71 PHE 0.019 0.001 PHE R 26 TRP 0.004 0.001 TRP L 37 HIS 0.002 0.000 HIS K 130 Details of bonding type rmsd covalent geometry : bond 0.00289 (31968) covalent geometry : angle 0.52151 (43354) hydrogen bonds : bond 0.07762 ( 2551) hydrogen bonds : angle 3.17052 ( 7653) Misc. bond : bond 0.13513 ( 30) *********************** 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 372 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 354 time to evaluate : 1.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASP cc_start: 0.8531 (t0) cc_final: 0.8305 (t70) REVERT: F 53 ARG cc_start: 0.7658 (mtt90) cc_final: 0.6738 (mtm110) REVERT: F 99 ASP cc_start: 0.8553 (t0) cc_final: 0.8344 (t70) REVERT: N 52 MET cc_start: 0.6868 (OUTLIER) cc_final: 0.6639 (mtt) REVERT: N 99 ASP cc_start: 0.8479 (t0) cc_final: 0.8235 (t70) REVERT: S 53 ARG cc_start: 0.8020 (mtt180) cc_final: 0.7150 (mtm110) REVERT: S 99 ASP cc_start: 0.8613 (t0) cc_final: 0.8407 (t70) REVERT: T 71 TYR cc_start: 0.8104 (m-80) cc_final: 0.7385 (m-80) REVERT: V 66 ASP cc_start: 0.8163 (t70) cc_final: 0.7917 (t0) outliers start: 18 outliers final: 16 residues processed: 369 average time/residue: 0.2119 time to fit residues: 123.8720 Evaluate side-chains 364 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 347 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain J residue 79 VAL Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain N residue 52 MET Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain Q residue 79 VAL Chi-restraints excluded: chain R residue 26 PHE Chi-restraints excluded: chain R residue 79 VAL Chi-restraints excluded: chain T residue 79 VAL Chi-restraints excluded: chain U residue 79 VAL Chi-restraints excluded: chain V residue 79 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 173 optimal weight: 3.9990 chunk 232 optimal weight: 7.9990 chunk 243 optimal weight: 0.8980 chunk 59 optimal weight: 7.9990 chunk 236 optimal weight: 0.6980 chunk 202 optimal weight: 9.9990 chunk 45 optimal weight: 10.0000 chunk 124 optimal weight: 0.9990 chunk 51 optimal weight: 0.5980 chunk 72 optimal weight: 7.9990 chunk 331 optimal weight: 9.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.136931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.127208 restraints weight = 28501.881| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 0.65 r_work: 0.3176 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.463 31998 Z= 0.142 Angle : 0.529 21.624 43354 Z= 0.231 Chirality : 0.032 0.214 4806 Planarity : 0.002 0.050 5596 Dihedral : 6.750 86.712 4204 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 0.51 % Allowed : 8.51 % Favored : 90.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.72 (0.13), residues: 3724 helix: 4.19 (0.08), residues: 3014 sheet: None (None), residues: 0 loop : -2.33 (0.21), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Q 53 TYR 0.034 0.001 TYR T 71 PHE 0.027 0.001 PHE R 26 TRP 0.005 0.001 TRP M 37 HIS 0.002 0.000 HIS F 54 Details of bonding type rmsd covalent geometry : bond 0.00277 (31968) covalent geometry : angle 0.52910 (43354) hydrogen bonds : bond 0.07592 ( 2551) hydrogen bonds : angle 3.15726 ( 7653) Misc. bond : bond 0.15132 ( 30) ********************** 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 363 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 346 time to evaluate : 1.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASP cc_start: 0.8551 (t0) cc_final: 0.8329 (t70) REVERT: B 99 ASP cc_start: 0.8515 (t0) cc_final: 0.8271 (t70) REVERT: D 99 ASP cc_start: 0.8499 (t0) cc_final: 0.8251 (t70) REVERT: E 99 ASP cc_start: 0.8552 (t0) cc_final: 0.8335 (t70) REVERT: F 53 ARG cc_start: 0.7496 (mtt90) cc_final: 0.6594 (mtm110) REVERT: G 99 ASP cc_start: 0.8545 (t0) cc_final: 0.8329 (t70) REVERT: I 99 ASP cc_start: 0.8552 (t0) cc_final: 0.8311 (t70) REVERT: N 52 MET cc_start: 0.6887 (OUTLIER) cc_final: 0.6640 (mtt) REVERT: N 99 ASP cc_start: 0.8479 (t0) cc_final: 0.8239 (t70) REVERT: S 53 ARG cc_start: 0.7883 (mtt180) cc_final: 0.7072 (mtm110) REVERT: S 99 ASP cc_start: 0.8628 (t0) cc_final: 0.8424 (t70) REVERT: T 71 TYR cc_start: 0.8107 (m-80) cc_final: 0.7263 (m-80) REVERT: V 66 ASP cc_start: 0.8195 (t70) cc_final: 0.7957 (t0) REVERT: W 99 ASP cc_start: 0.8613 (t0) cc_final: 0.8388 (t70) outliers start: 17 outliers final: 15 residues processed: 360 average time/residue: 0.2127 time to fit residues: 121.9138 Evaluate side-chains 358 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 342 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain N residue 52 MET Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain Q residue 79 VAL Chi-restraints excluded: chain R residue 26 PHE Chi-restraints excluded: chain S residue 79 VAL Chi-restraints excluded: chain T residue 79 VAL Chi-restraints excluded: chain U residue 79 VAL Chi-restraints excluded: chain V residue 79 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 338 optimal weight: 4.9990 chunk 160 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 chunk 1 optimal weight: 10.0000 chunk 82 optimal weight: 10.0000 chunk 225 optimal weight: 10.0000 chunk 323 optimal weight: 2.9990 chunk 146 optimal weight: 7.9990 chunk 178 optimal weight: 2.9990 chunk 354 optimal weight: 7.9990 chunk 246 optimal weight: 0.9980 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.121737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.112778 restraints weight = 28767.986| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 0.57 r_work: 0.2986 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.553 31998 Z= 0.197 Angle : 0.621 24.569 43354 Z= 0.275 Chirality : 0.034 0.247 4806 Planarity : 0.003 0.067 5596 Dihedral : 6.856 88.835 4204 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.63 % Allowed : 8.51 % Favored : 90.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.38 (0.13), residues: 3724 helix: 3.91 (0.08), residues: 3032 sheet: None (None), residues: 0 loop : -2.36 (0.21), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Q 53 TYR 0.045 0.001 TYR T 71 PHE 0.037 0.002 PHE R 26 TRP 0.003 0.001 TRP U 37 HIS 0.003 0.001 HIS Q 129 Details of bonding type rmsd covalent geometry : bond 0.00421 (31968) covalent geometry : angle 0.62096 (43354) hydrogen bonds : bond 0.10605 ( 2551) hydrogen bonds : angle 3.52255 ( 7653) Misc. bond : bond 0.16065 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5960.07 seconds wall clock time: 103 minutes 8.95 seconds (6188.95 seconds total)