Starting phenix.real_space_refine on Sun Jul 5 21:53:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y6p_33645/07_2026/7y6p_33645_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y6p_33645/07_2026/7y6p_33645.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7y6p_33645/07_2026/7y6p_33645_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y6p_33645/07_2026/7y6p_33645_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7y6p_33645/07_2026/7y6p_33645.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y6p_33645/07_2026/7y6p_33645.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 60 7.16 5 S 96 5.16 5 C 19886 2.51 5 N 5356 2.21 5 O 6030 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 98 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31428 Number of models: 1 Model: "" Number of chains: 48 Chain: "A" Number of atoms: 1290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1290 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 155} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 1280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1280 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 2, 'TRANS': 153} Chain: "D" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 1290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1290 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 155} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 1290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1290 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 155} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "J" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "M" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "N" Number of atoms: 1290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1290 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 155} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "O" Number of atoms: 1287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1287 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 2, 'TRANS': 154} Chain: "P" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "Q" Number of atoms: 1287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1287 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 2, 'TRANS': 154} Chain: "R" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "U" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "V" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "W" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "X" Number of atoms: 1290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1290 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 155} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 43 Ad-hoc single atom residues: {'FE2': 1, ' FE': 1} Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {'FE2': 1, ' FE': 1} Chain breaks: 2 Chain: "C" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 43 Ad-hoc single atom residues: {'FE2': 1, ' FE': 1} Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {'FE2': 1, ' FE': 1} Chain breaks: 2 Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {'FE2': 1, ' FE': 1} Chain breaks: 2 Chain: "F" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 43 Ad-hoc single atom residues: {' FE': 1, 'FE2': 1} Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "G" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 43 Ad-hoc single atom residues: {'FE2': 1, ' FE': 1} Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "H" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 43 Ad-hoc single atom residues: {'FE2': 1, ' FE': 1} Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' FE': 1, 'FE2': 1} Chain breaks: 2 Chain: "J" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 43 Ad-hoc single atom residues: {'FE2': 1, ' FE': 1} Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {'FE2': 1, ' FE': 1} Chain breaks: 2 Chain: "L" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 43 Ad-hoc single atom residues: {'FE2': 1, ' FE': 1} Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "M" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {'FE2': 1, ' FE': 1} Chain breaks: 2 Chain: "N" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' FE': 1, 'FE2': 1} Chain breaks: 2 Chain: "O" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' FE': 1, 'FE2': 1} Chain breaks: 2 Chain: "P" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 43 Ad-hoc single atom residues: {'FE2': 1, ' FE': 1} Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "Q" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 43 Ad-hoc single atom residues: {'FE2': 1, ' FE': 1} Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "R" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {'FE2': 1, ' FE': 1} Chain breaks: 2 Chain: "S" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 43 Ad-hoc single atom residues: {'FE2': 1, ' FE': 1} Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "T" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 43 Ad-hoc single atom residues: {' FE': 1, 'FE2': 1} Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "U" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {'FE2': 1, ' FE': 1} Chain breaks: 2 Chain: "V" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' FE': 1, 'FE2': 1} Chain breaks: 2 Chain: "W" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 43 Ad-hoc single atom residues: {'FE2': 1, ' FE': 1} Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "X" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' FE': 1, 'FE2': 1} Chain breaks: 2 Time building chain proxies: 7.12, per 1000 atoms: 0.23 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: 2.27 Conformation dependent library (CDL) restraints added in 1.0 seconds 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7256 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 0 sheets defined 82.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 4 through 35 removed outlier: 3.504A pdb=" N LYS A 35 " --> pdb=" O LEU A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 65 removed outlier: 3.506A pdb=" N ALA A 41 " --> pdb=" O TRP A 37 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A 65 " --> pdb=" O ARG A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 110 Processing helix chain 'A' and resid 113 through 145 removed outlier: 3.986A pdb=" N ALA A 117 " --> pdb=" O ASP A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 151 Processing helix chain 'B' and resid 4 through 35 removed outlier: 3.516A pdb=" N LYS B 35 " --> pdb=" O LEU B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 65 removed outlier: 3.830A pdb=" N TYR B 43 " --> pdb=" O LYS B 39 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU B 65 " --> pdb=" O ARG B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 110 Processing helix chain 'B' and resid 113 through 145 removed outlier: 4.008A pdb=" N ALA B 117 " --> pdb=" O ASP B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 151 Processing helix chain 'C' and resid 4 through 35 Processing helix chain 'C' and resid 37 through 65 removed outlier: 3.502A pdb=" N ALA C 41 " --> pdb=" O TRP C 37 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU C 65 " --> pdb=" O ARG C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 110 Processing helix chain 'C' and resid 113 through 145 removed outlier: 4.010A pdb=" N ALA C 117 " --> pdb=" O ASP C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 151 Processing helix chain 'D' and resid 4 through 35 removed outlier: 3.511A pdb=" N LYS D 35 " --> pdb=" O LEU D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 65 removed outlier: 3.710A pdb=" N TYR D 43 " --> pdb=" O LYS D 39 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU D 65 " --> pdb=" O ARG D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 110 Processing helix chain 'D' and resid 114 through 145 Processing helix chain 'D' and resid 145 through 151 Processing helix chain 'E' and resid 4 through 35 removed outlier: 3.505A pdb=" N LYS E 35 " --> pdb=" O LEU E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 65 removed outlier: 3.506A pdb=" N ALA E 41 " --> pdb=" O TRP E 37 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU E 65 " --> pdb=" O ARG E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 110 Processing helix chain 'E' and resid 113 through 145 removed outlier: 4.013A pdb=" N ALA E 117 " --> pdb=" O ASP E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 151 Processing helix chain 'F' and resid 4 through 35 removed outlier: 3.500A pdb=" N LYS F 35 " --> pdb=" O LEU F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 37 through 65 removed outlier: 3.670A pdb=" N TYR F 43 " --> pdb=" O LYS F 39 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU F 65 " --> pdb=" O ARG F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 110 Processing helix chain 'F' and resid 113 through 145 removed outlier: 3.986A pdb=" N ALA F 117 " --> pdb=" O ASP F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 151 Processing helix chain 'G' and resid 4 through 35 Processing helix chain 'G' and resid 37 through 65 removed outlier: 3.504A pdb=" N ALA G 41 " --> pdb=" O TRP G 37 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU G 65 " --> pdb=" O ARG G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 110 Processing helix chain 'G' and resid 113 through 145 removed outlier: 4.024A pdb=" N ALA G 117 " --> pdb=" O ASP G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 151 Processing helix chain 'H' and resid 4 through 35 removed outlier: 3.511A pdb=" N LYS H 35 " --> pdb=" O LEU H 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 65 removed outlier: 3.510A pdb=" N LEU H 65 " --> pdb=" O ARG H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 110 Processing helix chain 'H' and resid 113 through 145 removed outlier: 4.017A pdb=" N ALA H 117 " --> pdb=" O ASP H 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 151 Processing helix chain 'I' and resid 4 through 35 removed outlier: 3.510A pdb=" N LYS I 35 " --> pdb=" O LEU I 31 " (cutoff:3.500A) Processing helix chain 'I' and resid 37 through 65 removed outlier: 3.506A pdb=" N ALA I 41 " --> pdb=" O TRP I 37 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU I 65 " --> pdb=" O ARG I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 82 through 110 Processing helix chain 'I' and resid 113 through 145 removed outlier: 4.034A pdb=" N ALA I 117 " --> pdb=" O ASP I 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 145 through 151 Processing helix chain 'J' and resid 4 through 36 removed outlier: 3.536A pdb=" N GLY J 36 " --> pdb=" O GLN J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 37 through 65 removed outlier: 3.518A pdb=" N ALA J 41 " --> pdb=" O TRP J 37 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU J 65 " --> pdb=" O ARG J 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 82 through 110 Processing helix chain 'J' and resid 113 through 145 removed outlier: 4.034A pdb=" N ALA J 117 " --> pdb=" O ASP J 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 145 through 151 Processing helix chain 'K' and resid 4 through 35 removed outlier: 3.516A pdb=" N LYS K 35 " --> pdb=" O LEU K 31 " (cutoff:3.500A) Processing helix chain 'K' and resid 37 through 65 removed outlier: 3.816A pdb=" N TYR K 43 " --> pdb=" O LYS K 39 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU K 65 " --> pdb=" O ARG K 61 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 110 Processing helix chain 'K' and resid 113 through 145 removed outlier: 3.996A pdb=" N ALA K 117 " --> pdb=" O ASP K 113 " (cutoff:3.500A) Processing helix chain 'K' and resid 145 through 151 Processing helix chain 'L' and resid 4 through 35 Processing helix chain 'L' and resid 37 through 65 removed outlier: 3.556A pdb=" N GLU L 56 " --> pdb=" O MET L 52 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU L 65 " --> pdb=" O ARG L 61 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 111 removed outlier: 3.570A pdb=" N LYS L 111 " --> pdb=" O VAL L 107 " (cutoff:3.500A) Processing helix chain 'L' and resid 113 through 145 removed outlier: 3.989A pdb=" N ALA L 117 " --> pdb=" O ASP L 113 " (cutoff:3.500A) Processing helix chain 'L' and resid 145 through 151 Processing helix chain 'M' and resid 4 through 35 removed outlier: 3.650A pdb=" N ILE M 8 " --> pdb=" O ASP M 4 " (cutoff:3.500A) Processing helix chain 'M' and resid 37 through 65 Processing helix chain 'M' and resid 82 through 111 removed outlier: 3.591A pdb=" N LYS M 111 " --> pdb=" O VAL M 107 " (cutoff:3.500A) Processing helix chain 'M' and resid 113 through 145 removed outlier: 3.881A pdb=" N ALA M 117 " --> pdb=" O ASP M 113 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASP M 126 " --> pdb=" O ALA M 122 " (cutoff:3.500A) Processing helix chain 'M' and resid 145 through 151 Processing helix chain 'N' and resid 4 through 36 removed outlier: 3.507A pdb=" N LYS N 35 " --> pdb=" O LEU N 31 " (cutoff:3.500A) Processing helix chain 'N' and resid 37 through 65 removed outlier: 3.519A pdb=" N LEU N 65 " --> pdb=" O ARG N 61 " (cutoff:3.500A) Processing helix chain 'N' and resid 82 through 110 Processing helix chain 'N' and resid 113 through 145 removed outlier: 3.987A pdb=" N ALA N 117 " --> pdb=" O ASP N 113 " (cutoff:3.500A) Processing helix chain 'N' and resid 145 through 151 Processing helix chain 'O' and resid 4 through 35 removed outlier: 3.596A pdb=" N ILE O 8 " --> pdb=" O ASP O 4 " (cutoff:3.500A) Processing helix chain 'O' and resid 37 through 65 Processing helix chain 'O' and resid 82 through 110 Processing helix chain 'O' and resid 113 through 145 removed outlier: 3.975A pdb=" N ALA O 117 " --> pdb=" O ASP O 113 " (cutoff:3.500A) Processing helix chain 'O' and resid 145 through 151 Processing helix chain 'P' and resid 4 through 36 Processing helix chain 'P' and resid 37 through 65 removed outlier: 3.827A pdb=" N TYR P 43 " --> pdb=" O LYS P 39 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU P 65 " --> pdb=" O ARG P 61 " (cutoff:3.500A) Processing helix chain 'P' and resid 82 through 110 Processing helix chain 'P' and resid 113 through 145 removed outlier: 4.011A pdb=" N ALA P 117 " --> pdb=" O ASP P 113 " (cutoff:3.500A) Processing helix chain 'P' and resid 145 through 151 Processing helix chain 'Q' and resid 4 through 35 Processing helix chain 'Q' and resid 37 through 65 removed outlier: 3.514A pdb=" N ALA Q 41 " --> pdb=" O TRP Q 37 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU Q 65 " --> pdb=" O ARG Q 61 " (cutoff:3.500A) Processing helix chain 'Q' and resid 82 through 110 Processing helix chain 'Q' and resid 113 through 145 removed outlier: 4.046A pdb=" N ALA Q 117 " --> pdb=" O ASP Q 113 " (cutoff:3.500A) Processing helix chain 'Q' and resid 145 through 151 Processing helix chain 'R' and resid 4 through 35 Processing helix chain 'R' and resid 37 through 65 removed outlier: 3.728A pdb=" N TYR R 43 " --> pdb=" O LYS R 39 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU R 65 " --> pdb=" O ARG R 61 " (cutoff:3.500A) Processing helix chain 'R' and resid 83 through 110 Processing helix chain 'R' and resid 113 through 145 removed outlier: 4.005A pdb=" N ALA R 117 " --> pdb=" O ASP R 113 " (cutoff:3.500A) Processing helix chain 'R' and resid 145 through 151 Processing helix chain 'S' and resid 4 through 35 removed outlier: 3.507A pdb=" N LYS S 35 " --> pdb=" O LEU S 31 " (cutoff:3.500A) Processing helix chain 'S' and resid 37 through 65 removed outlier: 3.693A pdb=" N TYR S 43 " --> pdb=" O LYS S 39 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU S 65 " --> pdb=" O ARG S 61 " (cutoff:3.500A) Processing helix chain 'S' and resid 83 through 110 Processing helix chain 'S' and resid 113 through 145 removed outlier: 3.980A pdb=" N ALA S 117 " --> pdb=" O ASP S 113 " (cutoff:3.500A) Processing helix chain 'S' and resid 145 through 151 Processing helix chain 'T' and resid 4 through 35 removed outlier: 3.503A pdb=" N LYS T 35 " --> pdb=" O LEU T 31 " (cutoff:3.500A) Processing helix chain 'T' and resid 37 through 65 removed outlier: 3.501A pdb=" N ALA T 41 " --> pdb=" O TRP T 37 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU T 65 " --> pdb=" O ARG T 61 " (cutoff:3.500A) Processing helix chain 'T' and resid 83 through 110 Processing helix chain 'T' and resid 113 through 145 removed outlier: 4.011A pdb=" N ALA T 117 " --> pdb=" O ASP T 113 " (cutoff:3.500A) Processing helix chain 'T' and resid 145 through 151 Processing helix chain 'U' and resid 4 through 35 removed outlier: 3.557A pdb=" N LYS U 35 " --> pdb=" O LEU U 31 " (cutoff:3.500A) Processing helix chain 'U' and resid 37 through 65 removed outlier: 3.826A pdb=" N TYR U 43 " --> pdb=" O LYS U 39 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU U 65 " --> pdb=" O ARG U 61 " (cutoff:3.500A) Processing helix chain 'U' and resid 82 through 110 Processing helix chain 'U' and resid 113 through 145 removed outlier: 4.018A pdb=" N ALA U 117 " --> pdb=" O ASP U 113 " (cutoff:3.500A) Processing helix chain 'U' and resid 145 through 151 Processing helix chain 'V' and resid 4 through 35 removed outlier: 3.644A pdb=" N ILE V 8 " --> pdb=" O ASP V 4 " (cutoff:3.500A) Processing helix chain 'V' and resid 37 through 65 Processing helix chain 'V' and resid 82 through 111 removed outlier: 3.601A pdb=" N LYS V 111 " --> pdb=" O VAL V 107 " (cutoff:3.500A) Processing helix chain 'V' and resid 113 through 145 removed outlier: 3.903A pdb=" N ALA V 117 " --> pdb=" O ASP V 113 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASP V 126 " --> pdb=" O ALA V 122 " (cutoff:3.500A) Processing helix chain 'V' and resid 145 through 151 Processing helix chain 'W' and resid 4 through 36 removed outlier: 3.545A pdb=" N GLY W 36 " --> pdb=" O GLN W 32 " (cutoff:3.500A) Processing helix chain 'W' and resid 37 through 65 removed outlier: 3.613A pdb=" N ALA W 41 " --> pdb=" O TRP W 37 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS W 42 " --> pdb=" O THR W 38 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N TYR W 43 " --> pdb=" O LYS W 39 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU W 65 " --> pdb=" O ARG W 61 " (cutoff:3.500A) Processing helix chain 'W' and resid 83 through 110 Processing helix chain 'W' and resid 113 through 145 removed outlier: 3.989A pdb=" N ALA W 117 " --> pdb=" O ASP W 113 " (cutoff:3.500A) Processing helix chain 'W' and resid 145 through 151 Processing helix chain 'X' and resid 4 through 35 removed outlier: 3.512A pdb=" N LYS X 35 " --> pdb=" O LEU X 31 " (cutoff:3.500A) Processing helix chain 'X' and resid 37 through 65 removed outlier: 3.712A pdb=" N TYR X 43 " --> pdb=" O LYS X 39 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU X 65 " --> pdb=" O ARG X 61 " (cutoff:3.500A) Processing helix chain 'X' and resid 83 through 110 Processing helix chain 'X' and resid 113 through 145 removed outlier: 4.003A pdb=" N ALA X 117 " --> pdb=" O ASP X 113 " (cutoff:3.500A) Processing helix chain 'X' and resid 145 through 151 2551 hydrogen bonds defined for protein. 7653 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.45 Time building geometry restraints manager: 2.84 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 3.000 nonbonded pdb=" OE1 GLU M 94 " pdb="FE FE M 202 " model vdw 1.953 3.000 nonbonded pdb=" OE2 GLU M 94 " pdb="FE FE M 202 " model vdw 2.025 3.000 nonbonded pdb=" OE1 GLU R 127 " pdb="FE FE R 202 " model vdw 2.054 3.000 nonbonded pdb=" OE2 GLU J 51 " pdb="FE FE J 202 " model vdw 2.056 3.000 ... (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: 1.210 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: 0.030 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 25.700 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.965 31998 Z= 0.618 Angle : 0.657 25.824 43354 Z= 0.323 Chirality : 0.036 0.301 4806 Planarity : 0.003 0.063 5596 Dihedral : 15.544 89.366 11862 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.00 % Allowed : 0.03 % Favored : 99.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.78 (0.13), residues: 3724 helix: 3.44 (0.08), residues: 2994 sheet: None (None), residues: 0 loop : -1.98 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 53 TYR 0.044 0.001 TYR T 71 PHE 0.048 0.003 PHE V 120 TRP 0.006 0.001 TRP H 37 HIS 0.004 0.001 HIS Q 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00520 / 0.23 (31968) covalent geometry : angle 0.65664 / 0.32 (43354) hydrogen bonds : bond 0.14135 / 9.63 ( 2551) hydrogen bonds : angle 4.61119 / 3.37 ( 7653) Misc. bond : bond 0.23895 / 14.99 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7448 Ramachandran restraints generated. 3724 Oldfield, 0 Emsley, 3724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 309 time to evaluate : 1.191 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: 0.2041 time to fit residues: 100.7818 Evaluate side-chains 263 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 263 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.7980 chunk 298 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... V 2 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.136113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.126302 restraints weight = 28659.701| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 0.65 r_work: 0.3169 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.466 31998 Z= 0.148 Angle : 0.530 16.877 43354 Z= 0.241 Chirality : 0.032 0.124 4806 Planarity : 0.003 0.067 5596 Dihedral : 6.969 85.463 4204 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Rotamer: Outliers : 0.03 % Allowed : 1.90 % Favored : 98.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.56 (0.13), residues: 3724 helix: 4.05 (0.08), residues: 3014 sheet: None (None), residues: 0 loop : -2.24 (0.21), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 45 TYR 0.022 0.001 TYR T 71 PHE 0.023 0.002 PHE N 26 TRP 0.008 0.001 TRP P 37 HIS 0.002 0.000 HIS L 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.15 (31968) covalent geometry : angle 0.53023 / 0.24 (43354) hydrogen bonds : bond 0.07755 / 5.30 ( 2551) hydrogen bonds : angle 3.41243 / 2.50 ( 7653) Misc. bond : bond 0.13447 / 9.99 ( 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 379 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 378 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASP cc_start: 0.8548 (t0) cc_final: 0.8297 (t70) REVERT: D 99 ASP cc_start: 0.8525 (t0) cc_final: 0.8293 (t70) REVERT: E 99 ASP cc_start: 0.8514 (t0) cc_final: 0.8284 (t70) REVERT: F 50 ASP cc_start: 0.8571 (m-30) cc_final: 0.8324 (m-30) REVERT: F 53 ARG cc_start: 0.7933 (mtt90) cc_final: 0.6998 (mtm110) REVERT: G 99 ASP cc_start: 0.8503 (t0) cc_final: 0.8282 (t70) REVERT: H 99 ASP cc_start: 0.8441 (t0) cc_final: 0.8221 (t70) REVERT: M 66 ASP cc_start: 0.8077 (t70) cc_final: 0.7822 (t0) REVERT: M 99 ASP cc_start: 0.8484 (t0) cc_final: 0.8245 (t70) REVERT: N 81 GLN cc_start: 0.8393 (mt0) cc_final: 0.8177 (mt0) REVERT: N 99 ASP cc_start: 0.8439 (t0) cc_final: 0.8189 (t70) REVERT: O 1 MET cc_start: 0.6811 (mtm) cc_final: 0.6401 (mtm) REVERT: O 66 ASP cc_start: 0.7848 (t70) cc_final: 0.7639 (t0) REVERT: P 1 MET cc_start: 0.7451 (mtm) cc_final: 0.7241 (mtm) REVERT: R 99 ASP cc_start: 0.8534 (t0) cc_final: 0.8309 (t70) REVERT: S 99 ASP cc_start: 0.8552 (t0) cc_final: 0.8326 (t70) REVERT: V 66 ASP cc_start: 0.7985 (t70) cc_final: 0.7646 (t0) REVERT: V 99 ASP cc_start: 0.8374 (t0) cc_final: 0.8166 (t70) REVERT: W 99 ASP cc_start: 0.8552 (t0) cc_final: 0.8326 (t70) outliers start: 1 outliers final: 0 residues processed: 378 average time/residue: 0.1958 time to fit residues: 118.0039 Evaluate side-chains 357 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 357 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 162 optimal weight: 0.7980 chunk 11 optimal weight: 9.9990 chunk 266 optimal weight: 9.9990 chunk 93 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 278 optimal weight: 5.9990 chunk 242 optimal weight: 9.9990 chunk 80 optimal weight: 5.9990 chunk 62 optimal weight: 9.9990 chunk 164 optimal weight: 7.9990 chunk 136 optimal weight: 7.9990 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 156 GLN W 156 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.114482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.104381 restraints weight = 28681.610| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 0.64 r_work: 0.2860 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.2713 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9066 moved from start: 0.0802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.440 31998 Z= 0.258 Angle : 0.657 20.298 43354 Z= 0.299 Chirality : 0.036 0.141 4806 Planarity : 0.004 0.079 5596 Dihedral : 7.107 89.194 4204 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 0.66 % Allowed : 3.95 % Favored : 95.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.97 (0.13), residues: 3724 helix: 3.60 (0.08), residues: 3037 sheet: None (None), residues: 0 loop : -2.43 (0.21), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 45 TYR 0.043 0.001 TYR T 71 PHE 0.026 0.002 PHE R 120 TRP 0.004 0.001 TRP S 37 HIS 0.007 0.001 HIS H 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00591 / 0.26 (31968) covalent geometry : angle 0.65680 / 0.30 (43354) hydrogen bonds : bond 0.12993 / 8.88 ( 2551) hydrogen bonds : angle 3.93331 / 2.88 ( 7653) Misc. bond : bond 0.11166 / 8.39 ( 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 364 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 342 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 99 ASP cc_start: 0.8629 (t0) cc_final: 0.8419 (t70) outliers start: 22 outliers final: 22 residues processed: 364 average time/residue: 0.1872 time to fit residues: 109.6088 Evaluate side-chains 336 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 314 time to evaluate : 1.127 ------------------------------------------------------------------------------- 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 55 optimal weight: 6.9990 chunk 325 optimal weight: 4.9990 chunk 157 optimal weight: 5.9990 chunk 175 optimal weight: 9.9990 chunk 21 optimal weight: 0.7980 chunk 264 optimal weight: 2.9990 chunk 278 optimal weight: 6.9990 chunk 188 optimal weight: 2.9990 chunk 272 optimal weight: 5.9990 chunk 336 optimal weight: 8.9990 chunk 39 optimal weight: 4.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.119008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.109031 restraints weight = 28377.721| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 0.64 r_work: 0.2935 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9003 moved from start: 0.0977 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= 0.201 Angle : 0.583 19.400 43354 Z= 0.267 Chirality : 0.033 0.135 4806 Planarity : 0.003 0.068 5596 Dihedral : 7.065 89.268 4204 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 0.54 % Allowed : 6.28 % Favored : 93.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.07 (0.13), residues: 3724 helix: 3.67 (0.08), residues: 3037 sheet: None (None), residues: 0 loop : -2.43 (0.21), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 45 TYR 0.049 0.001 TYR T 71 PHE 0.016 0.002 PHE N 120 TRP 0.003 0.001 TRP G 37 HIS 0.005 0.000 HIS H 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.20 (31968) covalent geometry : angle 0.58341 / 0.27 (43354) hydrogen bonds : bond 0.11090 / 7.58 ( 2551) hydrogen bonds : angle 3.68291 / 2.70 ( 7653) Misc. bond : bond 0.12125 / 8.79 ( 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 365 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 347 time to evaluate : 1.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ARG cc_start: 0.8627 (mtm-85) cc_final: 0.8427 (mtm180) REVERT: C 52 MET cc_start: 0.6843 (mtt) cc_final: 0.6531 (mtt) REVERT: E 73 ARG cc_start: 0.8706 (mtm-85) cc_final: 0.8433 (mtm180) REVERT: H 73 ARG cc_start: 0.8644 (mtm-85) cc_final: 0.8430 (mtm180) REVERT: J 73 ARG cc_start: 0.8434 (mtm-85) cc_final: 0.8184 (mtm180) REVERT: O 66 ASP cc_start: 0.8383 (t70) cc_final: 0.8028 (t0) REVERT: T 71 TYR cc_start: 0.8372 (m-80) cc_final: 0.7762 (m-80) REVERT: V 66 ASP cc_start: 0.8513 (t70) cc_final: 0.8164 (t0) outliers start: 18 outliers final: 18 residues processed: 363 average time/residue: 0.1866 time to fit residues: 108.3442 Evaluate side-chains 347 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 329 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C 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 M residue 79 VAL Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain R residue 26 PHE Chi-restraints excluded: chain R residue 79 VAL Chi-restraints excluded: chain S residue 79 VAL Chi-restraints excluded: chain T residue 79 VAL Chi-restraints excluded: chain V residue 79 VAL Chi-restraints excluded: chain W residue 79 VAL Chi-restraints excluded: chain X residue 79 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 251 optimal weight: 9.9990 chunk 243 optimal weight: 9.9990 chunk 233 optimal weight: 9.9990 chunk 143 optimal weight: 3.9990 chunk 357 optimal weight: 3.9990 chunk 190 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 chunk 54 optimal weight: 8.9990 chunk 197 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.113897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.103892 restraints weight = 28396.695| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 0.63 r_work: 0.2862 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9057 moved from start: 0.0947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.434 31998 Z= 0.245 Angle : 0.635 20.380 43354 Z= 0.292 Chirality : 0.035 0.139 4806 Planarity : 0.003 0.078 5596 Dihedral : 7.137 89.501 4204 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 0.81 % Allowed : 7.00 % Favored : 92.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.89 (0.13), residues: 3724 helix: 3.48 (0.08), residues: 3037 sheet: None (None), residues: 0 loop : -2.10 (0.23), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 45 TYR 0.042 0.001 TYR T 71 PHE 0.016 0.002 PHE W 120 TRP 0.003 0.001 TRP H 37 HIS 0.007 0.001 HIS H 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00553 / 0.24 (31968) covalent geometry : angle 0.63464 / 0.29 (43354) hydrogen bonds : bond 0.12750 / 8.72 ( 2551) hydrogen bonds : angle 3.86683 / 2.83 ( 7653) Misc. bond : bond 0.11531 / 8.43 ( 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 323 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 296 time to evaluate : 1.178 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 99 ASP cc_start: 0.8595 (t0) cc_final: 0.8380 (t70) outliers start: 27 outliers final: 27 residues processed: 321 average time/residue: 0.1950 time to fit residues: 99.6150 Evaluate side-chains 308 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 281 time to evaluate : 1.171 ------------------------------------------------------------------------------- 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 M residue 79 VAL Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain O 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 290 optimal weight: 5.9990 chunk 129 optimal weight: 6.9990 chunk 142 optimal weight: 4.9990 chunk 308 optimal weight: 2.9990 chunk 344 optimal weight: 3.9990 chunk 317 optimal weight: 10.0000 chunk 209 optimal weight: 4.9990 chunk 238 optimal weight: 0.9980 chunk 253 optimal weight: 2.9990 chunk 166 optimal weight: 3.9990 chunk 40 optimal weight: 10.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... X 156 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.121142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.111474 restraints weight = 27958.058| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 0.61 r_work: 0.2967 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8968 moved from start: 0.1141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.432 31998 Z= 0.191 Angle : 0.570 19.600 43354 Z= 0.260 Chirality : 0.033 0.136 4806 Planarity : 0.003 0.066 5596 Dihedral : 7.015 89.413 4204 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 0.81 % Allowed : 7.48 % Favored : 91.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.12 (0.13), residues: 3724 helix: 3.78 (0.08), residues: 3019 sheet: None (None), residues: 0 loop : -2.60 (0.20), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 45 TYR 0.055 0.001 TYR T 71 PHE 0.015 0.001 PHE N 26 TRP 0.003 0.001 TRP M 37 HIS 0.004 0.000 HIS H 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.19 (31968) covalent geometry : angle 0.56998 / 0.26 (43354) hydrogen bonds : bond 0.10630 / 7.27 ( 2551) hydrogen bonds : angle 3.60161 / 2.64 ( 7653) Misc. bond : bond 0.12668 / 8.94 ( 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 346 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 319 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 99 ASP cc_start: 0.8565 (t0) cc_final: 0.8346 (t70) REVERT: G 99 ASP cc_start: 0.8544 (t0) cc_final: 0.8321 (t70) REVERT: K 99 ASP cc_start: 0.8546 (t0) cc_final: 0.8321 (t70) REVERT: O 66 ASP cc_start: 0.8376 (t70) cc_final: 0.7968 (t0) REVERT: R 99 ASP cc_start: 0.8542 (t0) cc_final: 0.8309 (t70) REVERT: T 71 TYR cc_start: 0.8155 (m-80) cc_final: 0.7696 (m-80) REVERT: T 99 ASP cc_start: 0.8606 (t0) cc_final: 0.8379 (t70) REVERT: V 66 ASP cc_start: 0.8524 (t70) cc_final: 0.8132 (t0) outliers start: 27 outliers final: 26 residues processed: 343 average time/residue: 0.1874 time to fit residues: 104.0383 Evaluate side-chains 323 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 297 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain J residue 79 VAL Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain M residue 79 VAL Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain O 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 237 optimal weight: 0.9980 chunk 167 optimal weight: 9.9990 chunk 105 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 173 optimal weight: 0.7980 chunk 202 optimal weight: 6.9990 chunk 38 optimal weight: 9.9990 chunk 132 optimal weight: 7.9990 chunk 168 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 chunk 63 optimal weight: 8.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.120020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.110007 restraints weight = 28265.485| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 0.63 r_work: 0.2947 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8982 moved from start: 0.1154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.437 31998 Z= 0.196 Angle : 0.580 21.182 43354 Z= 0.262 Chirality : 0.033 0.130 4806 Planarity : 0.003 0.069 5596 Dihedral : 7.003 89.201 4204 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.09 % Allowed : 7.48 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.11 (0.13), residues: 3724 helix: 3.74 (0.08), residues: 3032 sheet: None (None), residues: 0 loop : -2.54 (0.21), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 45 TYR 0.047 0.001 TYR T 71 PHE 0.014 0.001 PHE N 26 TRP 0.002 0.001 TRP N 37 HIS 0.004 0.000 HIS H 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.20 (31968) covalent geometry : angle 0.58048 / 0.26 (43354) hydrogen bonds : bond 0.10842 / 7.41 ( 2551) hydrogen bonds : angle 3.61095 / 2.64 ( 7653) Misc. bond : bond 0.12900 / 9.20 ( 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 328 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 292 time to evaluate : 1.217 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 99 ASP cc_start: 0.8513 (t0) cc_final: 0.8292 (t70) REVERT: I 99 ASP cc_start: 0.8556 (t0) cc_final: 0.8333 (t70) REVERT: O 66 ASP cc_start: 0.8405 (t70) cc_final: 0.8162 (t0) REVERT: Q 53 ARG cc_start: 0.7887 (mtp-110) cc_final: 0.7617 (mtm110) REVERT: T 71 TYR cc_start: 0.8342 (m-80) cc_final: 0.7783 (m-80) REVERT: V 66 ASP cc_start: 0.8559 (t70) cc_final: 0.8163 (t0) REVERT: W 99 ASP cc_start: 0.8600 (t0) cc_final: 0.8384 (t70) outliers start: 36 outliers final: 35 residues processed: 325 average time/residue: 0.1916 time to fit residues: 99.7992 Evaluate side-chains 314 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 279 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain 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 I residue 83 VAL Chi-restraints excluded: chain J residue 79 VAL Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain M residue 79 VAL Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain O 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 U residue 83 VAL Chi-restraints excluded: chain V residue 79 VAL Chi-restraints excluded: chain W residue 79 VAL Chi-restraints excluded: chain X residue 79 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 173 optimal weight: 0.6980 chunk 149 optimal weight: 5.9990 chunk 245 optimal weight: 6.9990 chunk 330 optimal weight: 10.0000 chunk 94 optimal weight: 0.9980 chunk 169 optimal weight: 8.9990 chunk 302 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 318 optimal weight: 6.9990 chunk 214 optimal weight: 1.9990 chunk 306 optimal weight: 0.0470 overall best weight: 0.9482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.144701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.134895 restraints weight = 28322.130| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 0.65 r_work: 0.3280 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.523 31998 Z= 0.129 Angle : 0.519 17.131 43354 Z= 0.226 Chirality : 0.031 0.151 4806 Planarity : 0.002 0.055 5596 Dihedral : 6.977 88.514 4204 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Rotamer: Outliers : 0.51 % Allowed : 8.18 % Favored : 91.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.67 (0.13), residues: 3724 helix: 4.18 (0.08), residues: 3014 sheet: None (None), residues: 0 loop : -2.46 (0.21), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 45 TYR 0.031 0.001 TYR T 71 PHE 0.020 0.001 PHE N 26 TRP 0.007 0.001 TRP O 37 HIS 0.002 0.000 HIS Q 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.13 (31968) covalent geometry : angle 0.51906 / 0.23 (43354) hydrogen bonds : bond 0.06414 / 4.39 ( 2551) hydrogen bonds : angle 3.06948 / 2.25 ( 7653) Misc. bond : bond 0.14777 / 11.01 ( 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 372 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 355 time to evaluate : 1.665 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 99 ASP cc_start: 0.8454 (t0) cc_final: 0.8183 (t70) REVERT: F 53 ARG cc_start: 0.7657 (mtt90) cc_final: 0.6779 (mtm110) REVERT: G 99 ASP cc_start: 0.8486 (t0) cc_final: 0.8241 (t70) REVERT: H 99 ASP cc_start: 0.8399 (t0) cc_final: 0.8133 (t70) REVERT: I 73 ARG cc_start: 0.8079 (mtt90) cc_final: 0.7793 (ttm170) REVERT: I 99 ASP cc_start: 0.8489 (t0) cc_final: 0.8233 (t70) REVERT: J 99 ASP cc_start: 0.8464 (t0) cc_final: 0.8218 (t70) REVERT: K 99 ASP cc_start: 0.8530 (t0) cc_final: 0.8286 (t70) REVERT: N 132 ASP cc_start: 0.8923 (t70) cc_final: 0.8708 (t0) REVERT: O 99 ASP cc_start: 0.8449 (t0) cc_final: 0.8168 (t70) REVERT: Q 99 ASP cc_start: 0.8443 (t0) cc_final: 0.8209 (t70) REVERT: S 53 ARG cc_start: 0.7888 (mtt180) cc_final: 0.7047 (mtm110) REVERT: T 71 TYR cc_start: 0.8067 (m-80) cc_final: 0.7348 (m-80) REVERT: V 66 ASP cc_start: 0.8035 (t70) cc_final: 0.7792 (t0) REVERT: W 99 ASP cc_start: 0.8516 (t0) cc_final: 0.8273 (t70) REVERT: X 1 MET cc_start: 0.7532 (mtm) cc_final: 0.7328 (mtm) REVERT: X 53 ARG cc_start: 0.7786 (mtt180) cc_final: 0.7057 (mtm110) outliers start: 17 outliers final: 10 residues processed: 370 average time/residue: 0.1927 time to fit residues: 112.0528 Evaluate side-chains 339 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 329 time to evaluate : 1.100 ------------------------------------------------------------------------------- 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 G residue 79 VAL Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain Q residue 79 VAL Chi-restraints excluded: chain R residue 26 PHE Chi-restraints excluded: chain U residue 79 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 100 optimal weight: 4.9990 chunk 346 optimal weight: 1.9990 chunk 232 optimal weight: 6.9990 chunk 172 optimal weight: 0.9990 chunk 354 optimal weight: 9.9990 chunk 120 optimal weight: 10.0000 chunk 334 optimal weight: 5.9990 chunk 163 optimal weight: 0.7980 chunk 159 optimal weight: 2.9990 chunk 318 optimal weight: 2.9990 chunk 201 optimal weight: 5.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.131322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.121302 restraints weight = 28223.112| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 0.64 r_work: 0.3107 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.585 31998 Z= 0.160 Angle : 0.560 21.656 43354 Z= 0.245 Chirality : 0.032 0.173 4806 Planarity : 0.003 0.055 5596 Dihedral : 6.838 87.239 4204 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.45 % Allowed : 8.72 % Favored : 90.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.59 (0.13), residues: 3724 helix: 4.12 (0.08), residues: 3014 sheet: None (None), residues: 0 loop : -2.48 (0.21), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 45 TYR 0.036 0.001 TYR T 71 PHE 0.021 0.001 PHE R 26 TRP 0.004 0.001 TRP N 37 HIS 0.002 0.000 HIS M 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.16 (31968) covalent geometry : angle 0.56010 / 0.24 (43354) hydrogen bonds : bond 0.08730 / 5.96 ( 2551) hydrogen bonds : angle 3.31738 / 2.43 ( 7653) Misc. bond : bond 0.15384 / 11.73 ( 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 355 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 340 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 99 ASP cc_start: 0.8524 (t0) cc_final: 0.8295 (t70) REVERT: E 99 ASP cc_start: 0.8512 (t0) cc_final: 0.8289 (t70) REVERT: F 53 ARG cc_start: 0.7717 (mtt90) cc_final: 0.6871 (mtm110) REVERT: Q 99 ASP cc_start: 0.8516 (t0) cc_final: 0.8312 (t70) REVERT: S 99 ASP cc_start: 0.8600 (t0) cc_final: 0.8380 (t70) REVERT: T 71 TYR cc_start: 0.8295 (m-80) cc_final: 0.7908 (m-80) REVERT: T 99 ASP cc_start: 0.8623 (t0) cc_final: 0.8390 (t70) outliers start: 15 outliers final: 14 residues processed: 353 average time/residue: 0.1947 time to fit residues: 109.1991 Evaluate side-chains 340 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 326 time to evaluate : 0.910 ------------------------------------------------------------------------------- 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 79 VAL Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain Q residue 79 VAL Chi-restraints excluded: chain R residue 26 PHE Chi-restraints excluded: chain U residue 79 VAL Chi-restraints excluded: chain U residue 83 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 173 optimal weight: 9.9990 chunk 232 optimal weight: 3.9990 chunk 243 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 236 optimal weight: 9.9990 chunk 202 optimal weight: 8.9990 chunk 45 optimal weight: 10.0000 chunk 124 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 72 optimal weight: 8.9990 chunk 331 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.115194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.105058 restraints weight = 28300.232| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 0.63 r_work: 0.2883 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9034 moved from start: 0.1136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.696 31998 Z= 0.252 Angle : 0.702 24.418 43354 Z= 0.310 Chirality : 0.036 0.279 4806 Planarity : 0.003 0.078 5596 Dihedral : 6.964 89.667 4204 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.51 % Allowed : 8.78 % Favored : 90.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.15 (0.13), residues: 3724 helix: 3.71 (0.08), residues: 3019 sheet: None (None), residues: 0 loop : -2.10 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Q 53 TYR 0.051 0.001 TYR T 71 PHE 0.034 0.002 PHE R 26 TRP 0.005 0.001 TRP H 37 HIS 0.006 0.001 HIS H 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00586 / 0.25 (31968) covalent geometry : angle 0.70179 / 0.31 (43354) hydrogen bonds : bond 0.12441 / 8.50 ( 2551) hydrogen bonds : angle 3.75512 / 2.75 ( 7653) Misc. bond : bond 0.17670 / 13.66 ( 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 302 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 285 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: T 71 TYR cc_start: 0.8464 (m-80) cc_final: 0.8216 (m-80) outliers start: 17 outliers final: 16 residues processed: 300 average time/residue: 0.1966 time to fit residues: 93.3420 Evaluate side-chains 294 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 278 time to evaluate : 1.167 ------------------------------------------------------------------------------- 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 G residue 83 VAL Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 83 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 P residue 79 VAL Chi-restraints excluded: chain Q residue 79 VAL Chi-restraints excluded: chain R residue 26 PHE Chi-restraints excluded: chain U residue 79 VAL Chi-restraints excluded: chain U residue 83 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 338 optimal weight: 3.9990 chunk 160 optimal weight: 6.9990 chunk 84 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 82 optimal weight: 10.0000 chunk 225 optimal weight: 10.0000 chunk 323 optimal weight: 5.9990 chunk 146 optimal weight: 6.9990 chunk 178 optimal weight: 2.9990 chunk 354 optimal weight: 2.9990 chunk 246 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.122246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.112410 restraints weight = 28226.783| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 0.62 r_work: 0.2981 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8948 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.751 31998 Z= 0.189 Angle : 0.630 22.064 43354 Z= 0.276 Chirality : 0.033 0.169 4806 Planarity : 0.003 0.074 5596 Dihedral : 6.955 89.304 4204 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.42 % Allowed : 8.90 % Favored : 90.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.21 (0.13), residues: 3724 helix: 3.85 (0.08), residues: 3014 sheet: None (None), residues: 0 loop : -2.59 (0.21), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Q 53 TYR 0.042 0.001 TYR T 71 PHE 0.026 0.001 PHE R 26 TRP 0.003 0.001 TRP O 37 HIS 0.003 0.000 HIS L 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.19 (31968) covalent geometry : angle 0.63040 / 0.28 (43354) hydrogen bonds : bond 0.10324 / 7.06 ( 2551) hydrogen bonds : angle 3.57348 / 2.62 ( 7653) Misc. bond : bond 0.18162 / 14.24 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5440.48 seconds wall clock time: 94 minutes 15.37 seconds (5655.37 seconds total)