Starting phenix.real_space_refine on Thu Jun 26 14:46:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y6p_33645/06_2025/7y6p_33645_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y6p_33645/06_2025/7y6p_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7y6p_33645/06_2025/7y6p_33645.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y6p_33645/06_2025/7y6p_33645.map" model { file = "/net/cci-nas-00/data/ceres_data/7y6p_33645/06_2025/7y6p_33645_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y6p_33645/06_2025/7y6p_33645_trim.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 17.16, per 1000 atoms: 0.55 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: 8.07 Conformation dependent library (CDL) restraints added in 3.5 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: 2.11 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: 9.47 Time building geometry restraints manager: 9.43 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: 1.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 1.190 Check model and map are aligned: 0.220 Set scattering table: 0.280 Process input model: 62.600 Find NCS groups from input model: 2.040 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.420 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.006 0.001 TRP H 37 HIS 0.004 0.001 HIS Q 129 PHE 0.048 0.003 PHE V 120 TYR 0.044 0.001 TYR T 71 ARG 0.003 0.000 ARG F 53 Details of bonding type rmsd hydrogen bonds : bond 0.14135 ( 2551) hydrogen bonds : angle 4.61119 ( 7653) covalent geometry : bond 0.00520 (31968) covalent geometry : angle 0.65664 (43354) 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 : 3.120 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: 0.4479 time to fit residues: 219.5441 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 : 3.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 303 optimal weight: 0.8980 chunk 272 optimal weight: 5.9990 chunk 151 optimal weight: 9.9990 chunk 93 optimal weight: 0.7980 chunk 184 optimal weight: 3.9990 chunk 145 optimal weight: 3.9990 chunk 282 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 chunk 171 optimal weight: 4.9990 chunk 210 optimal weight: 10.0000 chunk 326 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 = 0.3351 r_free = 0.3351 target = 0.132272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.122591 restraints weight = 28543.390| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 0.64 r_work: 0.3110 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.472 31998 Z= 0.156 Angle : 0.540 16.739 43354 Z= 0.245 Chirality : 0.032 0.125 4806 Planarity : 0.003 0.069 5596 Dihedral : 7.013 86.541 4204 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Rotamer: Outliers : 0.03 % Allowed : 2.72 % Favored : 97.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.48 (0.13), residues: 3724 helix: 4.00 (0.08), residues: 3014 sheet: None (None), residues: 0 loop : -2.28 (0.21), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP P 37 HIS 0.002 0.000 HIS H 130 PHE 0.023 0.002 PHE N 26 TYR 0.022 0.001 TYR T 71 ARG 0.005 0.000 ARG F 45 Details of bonding type rmsd hydrogen bonds : bond 0.08486 ( 2551) hydrogen bonds : angle 3.47361 ( 7653) covalent geometry : bond 0.00302 (31968) covalent geometry : angle 0.53980 (43354) Misc. bond : bond 0.13797 ( 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 389 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 388 time to evaluate : 3.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASP cc_start: 0.8565 (t0) cc_final: 0.8335 (t70) REVERT: D 99 ASP cc_start: 0.8537 (t0) cc_final: 0.8311 (t70) REVERT: E 99 ASP cc_start: 0.8544 (t0) cc_final: 0.8330 (t70) REVERT: F 50 ASP cc_start: 0.8587 (m-30) cc_final: 0.8376 (m-30) REVERT: F 53 ARG cc_start: 0.7935 (mtt90) cc_final: 0.7010 (mtp-110) REVERT: G 99 ASP cc_start: 0.8518 (t0) cc_final: 0.8304 (t70) REVERT: H 99 ASP cc_start: 0.8474 (t0) cc_final: 0.8249 (t70) REVERT: M 66 ASP cc_start: 0.8172 (t70) cc_final: 0.7908 (t0) REVERT: N 81 GLN cc_start: 0.8448 (mt0) cc_final: 0.8211 (mt0) REVERT: N 99 ASP cc_start: 0.8488 (t0) cc_final: 0.8232 (t70) REVERT: O 1 MET cc_start: 0.6922 (mtm) cc_final: 0.6470 (mtm) REVERT: P 1 MET cc_start: 0.7511 (mtm) cc_final: 0.7297 (mtm) REVERT: R 99 ASP cc_start: 0.8538 (t0) cc_final: 0.8318 (t70) REVERT: S 99 ASP cc_start: 0.8592 (t0) cc_final: 0.8376 (t70) REVERT: V 66 ASP cc_start: 0.8101 (t70) cc_final: 0.7756 (t0) REVERT: W 99 ASP cc_start: 0.8572 (t0) cc_final: 0.8347 (t70) outliers start: 1 outliers final: 0 residues processed: 388 average time/residue: 0.4543 time to fit residues: 279.3472 Evaluate side-chains 359 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 359 time to evaluate : 3.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 335 optimal weight: 10.0000 chunk 73 optimal weight: 1.9990 chunk 273 optimal weight: 0.9980 chunk 308 optimal weight: 0.9980 chunk 314 optimal weight: 0.7980 chunk 350 optimal weight: 5.9990 chunk 68 optimal weight: 10.0000 chunk 103 optimal weight: 3.9990 chunk 310 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 220 optimal weight: 9.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.138836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.130538 restraints weight = 28199.086| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 0.55 r_work: 0.3178 rms_B_bonded: 1.44 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.450 31998 Z= 0.154 Angle : 0.523 20.587 43354 Z= 0.230 Chirality : 0.032 0.123 4806 Planarity : 0.003 0.060 5596 Dihedral : 6.914 87.142 4204 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 0.33 % Allowed : 3.80 % Favored : 95.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.65 (0.13), residues: 3724 helix: 4.13 (0.08), residues: 3014 sheet: None (None), residues: 0 loop : -2.25 (0.21), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP G 37 HIS 0.003 0.000 HIS H 54 PHE 0.019 0.002 PHE N 26 TYR 0.035 0.001 TYR T 71 ARG 0.004 0.000 ARG F 45 Details of bonding type rmsd hydrogen bonds : bond 0.08534 ( 2551) hydrogen bonds : angle 3.35660 ( 7653) covalent geometry : bond 0.00302 (31968) covalent geometry : angle 0.52290 (43354) Misc. bond : bond 0.12810 ( 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 373 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 362 time to evaluate : 3.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 50 ASP cc_start: 0.8555 (m-30) cc_final: 0.8182 (m-30) REVERT: I 99 ASP cc_start: 0.8542 (t0) cc_final: 0.8306 (t70) REVERT: J 99 ASP cc_start: 0.8552 (t0) cc_final: 0.8301 (t70) REVERT: N 52 MET cc_start: 0.7127 (OUTLIER) cc_final: 0.6801 (mtt) REVERT: O 1 MET cc_start: 0.6813 (mtm) cc_final: 0.6388 (mtm) REVERT: Q 99 ASP cc_start: 0.8527 (t0) cc_final: 0.8323 (t70) REVERT: V 66 ASP cc_start: 0.8205 (t70) cc_final: 0.7911 (t0) outliers start: 11 outliers final: 10 residues processed: 372 average time/residue: 0.4695 time to fit residues: 281.7811 Evaluate side-chains 358 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 347 time to evaluate : 3.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 N residue 52 MET 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 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 93 optimal weight: 1.9990 chunk 201 optimal weight: 2.9990 chunk 189 optimal weight: 5.9990 chunk 341 optimal weight: 10.0000 chunk 176 optimal weight: 20.0000 chunk 355 optimal weight: 0.9990 chunk 333 optimal weight: 7.9990 chunk 47 optimal weight: 8.9990 chunk 290 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 331 optimal weight: 9.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 156 GLN ** U 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 156 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.118774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.109647 restraints weight = 28777.523| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 0.58 r_work: 0.2966 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.0969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.438 31998 Z= 0.209 Angle : 0.592 20.472 43354 Z= 0.267 Chirality : 0.034 0.137 4806 Planarity : 0.003 0.070 5596 Dihedral : 7.032 89.879 4204 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 0.69 % Allowed : 6.22 % Favored : 93.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.28 (0.13), residues: 3724 helix: 3.80 (0.08), residues: 3037 sheet: None (None), residues: 0 loop : -2.28 (0.21), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP F 37 HIS 0.005 0.001 HIS H 54 PHE 0.019 0.002 PHE N 120 TYR 0.052 0.001 TYR T 71 ARG 0.005 0.000 ARG F 45 Details of bonding type rmsd hydrogen bonds : bond 0.11401 ( 2551) hydrogen bonds : angle 3.68119 ( 7653) covalent geometry : bond 0.00448 (31968) covalent geometry : angle 0.59160 (43354) Misc. bond : bond 0.11958 ( 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 387 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 364 time to evaluate : 3.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 52 MET cc_start: 0.6752 (mtt) cc_final: 0.6442 (mtt) REVERT: D 99 ASP cc_start: 0.8551 (t0) cc_final: 0.8320 (t70) REVERT: F 50 ASP cc_start: 0.8557 (m-30) cc_final: 0.8301 (m-30) REVERT: N 52 MET cc_start: 0.7187 (OUTLIER) cc_final: 0.6797 (mtt) REVERT: T 71 TYR cc_start: 0.8189 (m-80) cc_final: 0.7534 (m-80) REVERT: T 99 ASP cc_start: 0.8656 (t0) cc_final: 0.8435 (t70) REVERT: V 66 ASP cc_start: 0.8505 (t70) cc_final: 0.8171 (t0) outliers start: 23 outliers final: 22 residues processed: 386 average time/residue: 0.4224 time to fit residues: 260.4285 Evaluate side-chains 358 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 335 time to evaluate : 4.154 ------------------------------------------------------------------------------- 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 206 optimal weight: 5.9990 chunk 174 optimal weight: 4.9990 chunk 224 optimal weight: 5.9990 chunk 124 optimal weight: 8.9990 chunk 70 optimal weight: 6.9990 chunk 156 optimal weight: 0.0770 chunk 101 optimal weight: 10.0000 chunk 138 optimal weight: 8.9990 chunk 160 optimal weight: 8.9990 chunk 42 optimal weight: 2.9990 chunk 177 optimal weight: 2.9990 overall best weight: 3.4146 ------------------------------------------------------------------------------- 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 = 0.3200 r_free = 0.3200 target = 0.119587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.110001 restraints weight = 28488.933| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 0.62 r_work: 0.2946 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.1036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.434 31998 Z= 0.202 Angle : 0.580 20.186 43354 Z= 0.264 Chirality : 0.033 0.131 4806 Planarity : 0.003 0.067 5596 Dihedral : 7.038 87.268 4204 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 0.75 % Allowed : 6.82 % Favored : 92.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.17 (0.13), residues: 3724 helix: 3.74 (0.08), residues: 3037 sheet: None (None), residues: 0 loop : -2.35 (0.21), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP F 37 HIS 0.004 0.001 HIS H 54 PHE 0.015 0.002 PHE S 26 TYR 0.039 0.001 TYR T 71 ARG 0.005 0.000 ARG F 45 Details of bonding type rmsd hydrogen bonds : bond 0.11074 ( 2551) hydrogen bonds : angle 3.63512 ( 7653) covalent geometry : bond 0.00432 (31968) covalent geometry : angle 0.58022 (43354) Misc. bond : bond 0.12326 ( 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 369 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 344 time to evaluate : 3.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 52 MET cc_start: 0.6779 (mtt) cc_final: 0.6525 (mtt) REVERT: F 50 ASP cc_start: 0.8569 (m-30) cc_final: 0.8300 (m-30) REVERT: G 99 ASP cc_start: 0.8594 (t0) cc_final: 0.8372 (t70) REVERT: N 52 MET cc_start: 0.7271 (OUTLIER) cc_final: 0.6949 (mtt) REVERT: R 99 ASP cc_start: 0.8577 (t0) cc_final: 0.8349 (t70) REVERT: V 66 ASP cc_start: 0.8537 (t70) cc_final: 0.8159 (t0) REVERT: W 99 ASP cc_start: 0.8620 (t0) cc_final: 0.8408 (t70) outliers start: 25 outliers final: 24 residues processed: 366 average time/residue: 0.4164 time to fit residues: 246.7736 Evaluate side-chains 350 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 325 time to evaluate : 3.336 ------------------------------------------------------------------------------- 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 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 278 optimal weight: 2.9990 chunk 63 optimal weight: 8.9990 chunk 354 optimal weight: 10.0000 chunk 143 optimal weight: 1.9990 chunk 339 optimal weight: 8.9990 chunk 254 optimal weight: 6.9990 chunk 292 optimal weight: 0.4980 chunk 113 optimal weight: 2.9990 chunk 312 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 chunk 41 optimal weight: 9.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- 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 = 0.3328 r_free = 0.3328 target = 0.130277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.120572 restraints weight = 28410.800| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 0.64 r_work: 0.3090 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.401 31998 Z= 0.157 Angle : 0.517 18.799 43354 Z= 0.236 Chirality : 0.032 0.127 4806 Planarity : 0.002 0.058 5596 Dihedral : 6.958 87.151 4204 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 0.69 % Allowed : 7.54 % Favored : 91.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.52 (0.13), residues: 3724 helix: 4.05 (0.08), residues: 3014 sheet: None (None), residues: 0 loop : -2.38 (0.20), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP M 37 HIS 0.002 0.000 HIS H 54 PHE 0.016 0.001 PHE N 26 TYR 0.054 0.001 TYR T 71 ARG 0.005 0.000 ARG F 45 Details of bonding type rmsd hydrogen bonds : bond 0.08718 ( 2551) hydrogen bonds : angle 3.32747 ( 7653) covalent geometry : bond 0.00312 (31968) covalent geometry : angle 0.51725 (43354) Misc. bond : bond 0.12668 ( 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 386 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 363 time to evaluate : 3.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 99 ASP cc_start: 0.8462 (t0) cc_final: 0.8227 (t70) REVERT: E 99 ASP cc_start: 0.8487 (t0) cc_final: 0.8255 (t70) REVERT: F 50 ASP cc_start: 0.8421 (m-30) cc_final: 0.8178 (m-30) REVERT: F 53 ARG cc_start: 0.7784 (mtt90) cc_final: 0.6860 (mtm110) REVERT: F 99 ASP cc_start: 0.8525 (t0) cc_final: 0.8284 (t70) REVERT: H 99 ASP cc_start: 0.8424 (t0) cc_final: 0.8189 (t70) REVERT: I 99 ASP cc_start: 0.8519 (t0) cc_final: 0.8287 (t70) REVERT: J 99 ASP cc_start: 0.8533 (t0) cc_final: 0.8300 (t70) REVERT: K 99 ASP cc_start: 0.8522 (t0) cc_final: 0.8292 (t70) REVERT: N 52 MET cc_start: 0.7067 (OUTLIER) cc_final: 0.6833 (mtt) REVERT: Q 99 ASP cc_start: 0.8495 (t0) cc_final: 0.8286 (t70) REVERT: S 99 ASP cc_start: 0.8555 (t0) cc_final: 0.8336 (t70) REVERT: T 99 ASP cc_start: 0.8572 (t0) cc_final: 0.8347 (t70) REVERT: U 99 ASP cc_start: 0.8539 (t0) cc_final: 0.8323 (t70) REVERT: V 66 ASP cc_start: 0.8328 (t70) cc_final: 0.7989 (t0) outliers start: 23 outliers final: 21 residues processed: 382 average time/residue: 0.4225 time to fit residues: 259.6101 Evaluate side-chains 372 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 350 time to evaluate : 3.231 ------------------------------------------------------------------------------- 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 I residue 79 VAL Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain L 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 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 75 optimal weight: 10.0000 chunk 155 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 chunk 221 optimal weight: 9.9990 chunk 300 optimal weight: 10.0000 chunk 241 optimal weight: 2.9990 chunk 202 optimal weight: 5.9990 chunk 257 optimal weight: 6.9990 chunk 275 optimal weight: 0.9980 chunk 346 optimal weight: 10.0000 chunk 191 optimal weight: 8.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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 = 0.3197 r_free = 0.3197 target = 0.119703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.110696 restraints weight = 28650.786| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 0.57 r_work: 0.2981 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.419 31998 Z= 0.201 Angle : 0.579 21.841 43354 Z= 0.262 Chirality : 0.034 0.133 4806 Planarity : 0.003 0.068 5596 Dihedral : 6.976 89.686 4204 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.88 % Allowed : 7.51 % Favored : 91.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.25 (0.13), residues: 3724 helix: 3.80 (0.08), residues: 3037 sheet: None (None), residues: 0 loop : -2.39 (0.21), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP U 37 HIS 0.004 0.001 HIS H 54 PHE 0.014 0.001 PHE S 26 TYR 0.049 0.001 TYR T 71 ARG 0.005 0.000 ARG F 45 Details of bonding type rmsd hydrogen bonds : bond 0.11030 ( 2551) hydrogen bonds : angle 3.60033 ( 7653) covalent geometry : bond 0.00431 (31968) covalent geometry : angle 0.57915 (43354) Misc. bond : bond 0.12311 ( 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 362 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 333 time to evaluate : 3.567 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 52 MET cc_start: 0.7204 (OUTLIER) cc_final: 0.6891 (mtt) REVERT: T 71 TYR cc_start: 0.8193 (m-80) cc_final: 0.7635 (m-80) REVERT: V 66 ASP cc_start: 0.8510 (t70) cc_final: 0.8125 (t0) outliers start: 29 outliers final: 27 residues processed: 358 average time/residue: 0.4199 time to fit residues: 242.6185 Evaluate side-chains 337 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 309 time to evaluate : 3.620 ------------------------------------------------------------------------------- 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 H residue 79 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 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 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 333 optimal weight: 6.9990 chunk 65 optimal weight: 0.9990 chunk 198 optimal weight: 3.9990 chunk 280 optimal weight: 1.9990 chunk 204 optimal weight: 7.9990 chunk 253 optimal weight: 0.7980 chunk 291 optimal weight: 2.9990 chunk 225 optimal weight: 10.0000 chunk 69 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 252 optimal weight: 1.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 156 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.135049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.125323 restraints weight = 28394.682| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 0.64 r_work: 0.3154 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.436 31998 Z= 0.145 Angle : 0.522 18.728 43354 Z= 0.231 Chirality : 0.031 0.148 4806 Planarity : 0.002 0.057 5596 Dihedral : 6.912 87.882 4204 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 0.57 % Allowed : 8.00 % Favored : 91.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.62 (0.13), residues: 3724 helix: 4.12 (0.08), residues: 3014 sheet: None (None), residues: 0 loop : -2.37 (0.21), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP O 37 HIS 0.002 0.000 HIS L 129 PHE 0.017 0.001 PHE N 26 TYR 0.035 0.001 TYR T 71 ARG 0.005 0.000 ARG F 45 Details of bonding type rmsd hydrogen bonds : bond 0.07817 ( 2551) hydrogen bonds : angle 3.22794 ( 7653) covalent geometry : bond 0.00289 (31968) covalent geometry : angle 0.52179 (43354) Misc. bond : bond 0.13493 ( 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 374 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 355 time to evaluate : 3.310 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 99 ASP cc_start: 0.8538 (t0) cc_final: 0.8301 (t70) REVERT: D 99 ASP cc_start: 0.8518 (t0) cc_final: 0.8264 (t70) REVERT: E 99 ASP cc_start: 0.8526 (t0) cc_final: 0.8274 (t70) REVERT: F 53 ARG cc_start: 0.7639 (mtt90) cc_final: 0.6778 (mtm110) REVERT: G 99 ASP cc_start: 0.8511 (t0) cc_final: 0.8258 (t70) REVERT: H 99 ASP cc_start: 0.8424 (t0) cc_final: 0.8199 (t70) REVERT: I 99 ASP cc_start: 0.8542 (t0) cc_final: 0.8313 (t70) REVERT: J 99 ASP cc_start: 0.8541 (t0) cc_final: 0.8313 (t70) REVERT: N 52 MET cc_start: 0.7077 (OUTLIER) cc_final: 0.6858 (mtt) REVERT: N 132 ASP cc_start: 0.9014 (t70) cc_final: 0.8788 (t0) REVERT: Q 99 ASP cc_start: 0.8499 (t0) cc_final: 0.8289 (t70) REVERT: R 99 ASP cc_start: 0.8487 (t0) cc_final: 0.8247 (t70) REVERT: S 53 ARG cc_start: 0.7953 (mtt180) cc_final: 0.7143 (mtm110) REVERT: T 71 TYR cc_start: 0.8081 (m-80) cc_final: 0.7288 (m-80) REVERT: T 99 ASP cc_start: 0.8625 (t0) cc_final: 0.8420 (t70) REVERT: U 99 ASP cc_start: 0.8600 (t0) cc_final: 0.8350 (t70) REVERT: W 99 ASP cc_start: 0.8564 (t0) cc_final: 0.8340 (t70) outliers start: 19 outliers final: 17 residues processed: 369 average time/residue: 0.4976 time to fit residues: 289.6464 Evaluate side-chains 369 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 351 time to evaluate : 3.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain J 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 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 X residue 79 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 163 optimal weight: 0.9990 chunk 81 optimal weight: 0.0040 chunk 303 optimal weight: 4.9990 chunk 237 optimal weight: 1.9990 chunk 272 optimal weight: 9.9990 chunk 216 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 151 optimal weight: 10.0000 chunk 85 optimal weight: 9.9990 chunk 110 optimal weight: 2.9990 overall best weight: 0.9596 ------------------------------------------------------------------------------- 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 = 0.3514 r_free = 0.3514 target = 0.146152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.136542 restraints weight = 28423.352| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 0.65 r_work: 0.3297 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.550 31998 Z= 0.125 Angle : 0.509 19.088 43354 Z= 0.221 Chirality : 0.031 0.155 4806 Planarity : 0.002 0.048 5596 Dihedral : 6.747 86.814 4204 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 0.54 % Allowed : 7.94 % Favored : 91.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.87 (0.13), residues: 3724 helix: 4.29 (0.08), residues: 3014 sheet: None (None), residues: 0 loop : -2.24 (0.21), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP L 37 HIS 0.003 0.000 HIS Q 54 PHE 0.018 0.001 PHE R 26 TYR 0.033 0.001 TYR T 71 ARG 0.006 0.000 ARG F 45 Details of bonding type rmsd hydrogen bonds : bond 0.06353 ( 2551) hydrogen bonds : angle 3.00020 ( 7653) covalent geometry : bond 0.00244 (31968) covalent geometry : angle 0.50899 (43354) Misc. bond : bond 0.15488 ( 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 371 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 353 time to evaluate : 3.523 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 53 ARG cc_start: 0.7479 (mtt90) cc_final: 0.6542 (mtm110) REVERT: I 132 ASP cc_start: 0.8916 (t70) cc_final: 0.8706 (t0) REVERT: K 66 ASP cc_start: 0.8733 (t70) cc_final: 0.8524 (t0) REVERT: N 52 MET cc_start: 0.6920 (OUTLIER) cc_final: 0.6714 (mtt) REVERT: R 132 ASP cc_start: 0.8971 (t70) cc_final: 0.8768 (t0) REVERT: S 53 ARG cc_start: 0.7866 (mtt180) cc_final: 0.7665 (mtm-85) REVERT: S 99 ASP cc_start: 0.8539 (t0) cc_final: 0.8320 (t70) REVERT: T 71 TYR cc_start: 0.7987 (m-80) cc_final: 0.7197 (m-80) REVERT: V 99 ASP cc_start: 0.8346 (t0) cc_final: 0.8084 (t70) outliers start: 18 outliers final: 15 residues processed: 369 average time/residue: 0.4611 time to fit residues: 266.9338 Evaluate side-chains 356 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 340 time to evaluate : 3.777 ------------------------------------------------------------------------------- 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 G residue 79 VAL Chi-restraints excluded: chain H 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 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 R residue 26 PHE Chi-restraints excluded: chain T residue 79 VAL Chi-restraints excluded: chain U residue 79 VAL Chi-restraints excluded: chain X residue 79 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 20 optimal weight: 5.9990 chunk 107 optimal weight: 9.9990 chunk 342 optimal weight: 9.9990 chunk 232 optimal weight: 7.9990 chunk 25 optimal weight: 4.9990 chunk 204 optimal weight: 6.9990 chunk 318 optimal weight: 2.9990 chunk 347 optimal weight: 7.9990 chunk 325 optimal weight: 10.0000 chunk 198 optimal weight: 1.9990 chunk 249 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 = 0.3149 r_free = 0.3149 target = 0.115723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.106549 restraints weight = 28735.685| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 0.58 r_work: 0.2925 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.1166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.615 31998 Z= 0.239 Angle : 0.688 24.872 43354 Z= 0.308 Chirality : 0.036 0.196 4806 Planarity : 0.003 0.075 5596 Dihedral : 6.928 87.547 4204 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.78 % Allowed : 8.27 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.28 (0.13), residues: 3724 helix: 3.72 (0.08), residues: 3037 sheet: None (None), residues: 0 loop : -1.84 (0.24), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP S 37 HIS 0.005 0.001 HIS Q 129 PHE 0.034 0.002 PHE R 26 TYR 0.053 0.001 TYR T 71 ARG 0.006 0.000 ARG F 45 Details of bonding type rmsd hydrogen bonds : bond 0.12410 ( 2551) hydrogen bonds : angle 3.75157 ( 7653) covalent geometry : bond 0.00542 (31968) covalent geometry : angle 0.68801 (43354) Misc. bond : bond 0.17264 ( 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 330 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 304 time to evaluate : 6.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 1 MET cc_start: 0.7340 (mtm) cc_final: 0.7121 (mtm) outliers start: 26 outliers final: 24 residues processed: 327 average time/residue: 0.5568 time to fit residues: 298.5196 Evaluate side-chains 316 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 292 time to evaluate : 3.250 ------------------------------------------------------------------------------- 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 G residue 83 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 J residue 79 VAL Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 83 VAL 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 Q residue 83 VAL Chi-restraints excluded: chain R residue 26 PHE Chi-restraints excluded: chain T residue 79 VAL Chi-restraints excluded: chain U residue 79 VAL Chi-restraints excluded: chain W residue 79 VAL Chi-restraints excluded: chain X residue 79 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 47 optimal weight: 5.9990 chunk 125 optimal weight: 50.0000 chunk 209 optimal weight: 0.9990 chunk 92 optimal weight: 4.9990 chunk 138 optimal weight: 0.3980 chunk 158 optimal weight: 2.9990 chunk 142 optimal weight: 9.9990 chunk 43 optimal weight: 0.8980 chunk 183 optimal weight: 4.9990 chunk 117 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 2 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.136668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.126902 restraints weight = 28232.123| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 0.64 r_work: 0.3198 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.793 31998 Z= 0.151 Angle : 0.600 20.098 43354 Z= 0.262 Chirality : 0.032 0.235 4806 Planarity : 0.003 0.063 5596 Dihedral : 6.902 87.344 4204 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 0.24 % Allowed : 8.75 % Favored : 91.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.60 (0.13), residues: 3724 helix: 4.11 (0.08), residues: 3014 sheet: None (None), residues: 0 loop : -2.35 (0.21), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP O 37 HIS 0.005 0.000 HIS Q 54 PHE 0.032 0.001 PHE R 26 TYR 0.034 0.001 TYR T 71 ARG 0.006 0.000 ARG F 45 Details of bonding type rmsd hydrogen bonds : bond 0.07609 ( 2551) hydrogen bonds : angle 3.23086 ( 7653) covalent geometry : bond 0.00298 (31968) covalent geometry : angle 0.60025 (43354) Misc. bond : bond 0.20558 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12967.12 seconds wall clock time: 225 minutes 16.08 seconds (13516.08 seconds total)